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  • Electronic Resource  (3,050)
  • Loose Leaf
  • 1990-1994  (3,050)
  • 1990  (3,050)
  • Analytical Chemistry and Spectroscopy  (1,434)
  • Organic Chemistry  (891)
  • Biochemistry and Biotechnology  (725)
Source
Material
  • Electronic Resource  (3,050)
  • Loose Leaf
Years
  • 1990-1994  (3,050)
Year
Keywords
  • 1
    Electronic Resource
    Electronic Resource
    The effect of mislabeled samples on the performance of the linear learning machine (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 47-50 
    Details
    ISSN: 0886-9383
    Keywords: Classification ; Pattern recognition ; Preprocessing ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Over the past 15 years the linear learning machine has been applied to a large number of chemical problems. The learning machine approach is conceptually simple and does not require knowledge about the statistical distribution of the data. However, there are problems associated with this approach. One problem which has not been investigated is the influence of mislabeled samples on the positioning of the hyperplane in feature space. If a few samples in a data set are incorrectly tagged prior to training (i.e. the samples are labeled as members of class 2 even though they are actually members of class 1), it is still possible using the linear learning machine to achieve a classification success rate of 100% for the training set. However, unfavorable results will be obtained for the prediction set. The magnitude of this effect and its potential implications regarding the proper use of the linear learning machine are discussed.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040106
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  • 2
    Electronic Resource
    Electronic Resource
    Enhancing the deconvolution of noisy chromatographic data by Jansson's method (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 51-59 
    Details
    ISSN: 0886-9383
    Keywords: Deconvolution ; Jansson's method ; Peak restoration ; Iterative deconvolution ; Peak resolution ; Non-linear deconvolution ; Super-resolution ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In previous papers Jansson's method was found to be successful at deconvolving severely overlapped gas chromatographic peaks. In the most recent paper the method was evaluated with respect to quantitative accuracy, peak area and retention time repeatability. The problems associated with deconvolving noisy data and some alternatives which can improve the ability of Jansson's method to deconvolve noisy data are discussed. These alternatives include presmoothing the data with a nine-point, third-order polynomial filter and data reblurring. This paper will test these methods on peaks with various degrees of resolution and signal-to-noise ratios.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040107
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  • 3
    Electronic Resource
    Electronic Resource
    A new approach to confirmation by infrared spectrometry (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 61-77 
    Details
    ISSN: 0886-9383
    Keywords: Infrared ; Spectroscopy ; Spectrometry ; Retrieval ; Confirmation ; Chemometrics ; Adequate peaks ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In the series of analytical techniques for identification of chemical substances, infrared spectrometry presents by far the highest information content. However, the information is most complicated too. It concerns a multitude of band positions, band intensities and band shapes, which, moreover, can be disturbed by matrix and other effects. The high redundancy, however, allows conclusions to be made by a qualitative, subjective procedure.IR is often used to prove the equality between a sample and a reference material, e.g. in quality control of a production process. In forensic control, the question to be answered is mostly not to prove equality, but whether or not the presence of a compound in a sample, e.g. a drug, can be proved. Moreover, testing has to be performed according to objective rules.To fulfil these requirements, a new retrieval algorithm, the ‘Adequate Peaks Search’, is presented. It concerns representing the reference spectra by sets of adequate peak positions and the sample spectrum by a set of all peak positions, whereafter the cross-sections of the sample set and the reference sets are determined. The concept ‘adequate peak’ is defined and criteria have been formulated to evaluate the results into a positive (presence of the analyte is proved) or negative (presence is not proved) conclusion.The detection limit when the Adequate Peaks Search (APS) method was applied was four to seven times lower than that attained by a number of experts.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040108
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  • 4
    Electronic Resource
    Electronic Resource
    Residual bilinearization. Part 1: Theory and algorithms (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 79-90 
    Details
    ISSN: 0886-9383
    Keywords: PLS ; Three-way matrices ; Calibration ; Residual bilinearization ; Background correction ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: When using hyphenated methods in analytical chemistry, the data obtained for each sample are given as a matrix. When a regression equation is set up between an unknown sample (a matrix) and a calibration set (a stack of matrices), the residual is a matrix R.The regression equation is usually solved by minimizing the sum of squares of R. If the sample contains some constituent not calibrated for, this approach is not valid. In this paper an algorithm is presented which partitions R into one matrix of low rank corresponding to the unknown constituents, and one random noise matrix to which the least squares restrictions are applied. Properties and possible applications of the algorithm are also discussed.In Part 2 of this work an example from HPLC with diode array detection is presented and the results are compared with generalized rank annihilation factor analysis (GRAFA).
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040109
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  • 5
    Electronic Resource
    Electronic Resource
    The problem of adequate sample size in pattern recognition studies: The multivariate normal case (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 91-96 
    Details
    ISSN: 0886-9383
    Keywords: Sample size ; Monte Carlo ; Multivariate, normal ; Q-Q plots ; Classification ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Because many pattern recognition techniques are predicated on the assumption of mutivariate normal data, Monte Carlo simulation studies were performed to determine the number of samples that are necessary to describe a multivariate normal population adequately. From these studies we have learned that hundreds of samples are required. These results suggest that parametric procedures should only be used to analyze very large data sets.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040110
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  • 6
    Electronic Resource
    Electronic Resource
    Comments on the NIPALS algorithm (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 97-100 
    Details
    ISSN: 0886-9383
    Keywords: Matrix decomposition ; NIPALS ; Principal component ; SIMCA ; PLS ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Non-linear Iterative Partial Least Squares (NIPALS) algorithm is used in principal component analysis to decompose a data matrix into score vectors and eigenvectors (loading vectors) plus a residual matrix. NIPALS starts with some guessed starting vector. The principal components obtained by NIPALS depends on the starting vector; the first principal component could not always be computed. Wold has suggested a starting vector for NIPALS, but we have found that even if this starting vector is used, the first principal component cannot be obtained in all cases. The reason why such a situation occurs is explained by the power method. A simple modification of the original NIPALS procedure to avoid getting smaller eigenvalues is presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040111
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  • 7
    Electronic Resource
    Electronic Resource
    From CA to CAS online, Hedda Schulz, VCH Publishers, Weinheim, Federal Republic of Germany, 1988. No. of pages: viii + 227. Price $39.95. ISBN 0-89573-815-5 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 101-101 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040112
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  • 8
    Electronic Resource
    Electronic Resource
    Call for papers (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 102-102 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040113
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  • 9
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990) 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040201
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  • 10
    Electronic Resource
    Electronic Resource
    Erratum (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 102-102 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040114
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  • 11
    Electronic Resource
    Electronic Resource
    Diary (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. i 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040202
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  • 12
    Electronic Resource
    Electronic Resource
    Recursive parameter estimation (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 103-121 
    Details
    ISSN: 0886-9383
    Keywords: Kalman filter ; Recursive digital filter ; Square-root filter ; Information filter ; Parameter estimation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of recursive filtering techniques for parameter estimation in a variety of areas is reviewed. In particular, the Kalman filter algorithm is described, along with several variations, including square-root, UDUT and information filters. The solution to parameter estimation problems is discussed for both linear and non-linear models. Applications described include calibration, curve resolution in spectroscopy, chromatography, electrochemistry, kinetic analysis and process monitoring.
    Additional Material: 5 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040203
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  • 13
    Electronic Resource
    Electronic Resource
    Diary (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. i 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040502
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  • 14
    Electronic Resource
    Electronic Resource
    The start and early history of chemometrics: Selected interviews. Part 1 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 337-354 
    Details
    ISSN: 0886-9383
    Keywords: Chemometrics ; Chemometrics Society ; History of chemometrics ; Pioneers of modern chemometrics ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This is a first foray into the historical start and early years of chemometrics from about 1972 onwards. We have gathered interviews with three originators (Kowalski, Wold and Massart) as well as with a selected group of six other well-known chemometricians who gradually became active in the 1970s (Christie, Clementi, Hopke, Martens, Brown and Deming). The interviews include amongst a host of subjective recollections a succinct record of the key historical literature as highlighted by the interviewees' own rankings of ‘earliest’ and ‘best’.A discussion of the most general commonalities in these interviews together with other historical material is presented in the second part of the paper.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040503
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  • 15
    Electronic Resource
    Electronic Resource
    U. K. usage of chemometrics and artificial intelligence in QSAR analysis (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 355-360 
    Details
    ISSN: 0886-9383
    Keywords: Pattern recognition ; U.K. chemometrics usage ; Quantitative structure-activity relationships ; Artificial intelligence ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A survey of members of the U.K. QSAR Discussion Group has been made to determine the extent of use and development of chemometric and artificial intelligence (AI) methods in the analysis of multivariate quantitative structure-activity relationship (QSAR) data in the U.K. Chemometric methods were found to be well established in both industrial and educational establishments and there was significant method development occurring. AI methods were not employed to any great extent and the general level of interest in these techniques was low compared to chemometric methods. A requirement for more education in multivariate statistical methods and regression methods was indicated. A need for a user-friendly, comprehensive, commercially available multivariate statistical package containing multivariate stability testing and regression diagnostic methods was identified.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040504
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  • 16
    Electronic Resource
    Electronic Resource
    Factor analysis of a simulated data matrix involving aqueous complex equilibria (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 361-377 
    Details
    ISSN: 0886-9383
    Keywords: Abstract factor analysis ; Exploratory data analysis ; Principal components ; Simulated equilibria ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract factor analyses were performed on databases consisting of simulated samples from aqueous equilbria. The program COMPLEX was used to generate equilibrium species in a system of three reactant metals and five reactant bases. Reactant concentrations and pH were drawn from random-normal distributions so that sample data vectors comprised a multivariate log-normal distribution of equilibrium concentrations. In addition, sample groups were created containing different distributions for pH and reactant concentrations.Equilibrium species were shown to contain variance contributed by change in pH among samples as well as change in reactant concentrations. Factor modelling revealed the qualitative relationships among the species and how the relationships change with pH. Factors also revealed those reactants containing variance in the data matrix. In some cases, reactant variance obscured relationships between pH and the equilibrium species.Since factor modelling of a simulated data matrix revealed the expected chemical equilibrium interactions, a potentially powerful tool exists for investigating the effects of outliers and error.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040505
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  • 17
    Electronic Resource
    Electronic Resource
    The start and early history of chemometrics: Selected interviews. Part 2 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 389-412 
    Details
    ISSN: 0886-9383
    Keywords: Chemometrics ; Chemometrics Society ; History of chemometrics ; Pioneers of modern chemometrics ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: This is a first foray into the historical start and early years of chemometrics from about 1972 onwards. We have gathered interviews with three originators (Kowalski, Wold and Massart) as well as with a selected group of six other well-known chemometricians who gradually became active in the 1970s (Christie, Clementi, Hopke, Martens, Brown and Deming). The interviews include amongst a host of subjective recollections a succinct record of the key historical literature as highlighted by the interviewees' own rankings of ‘earliest’ and ‘best’.A discussion of the most general commonalities in these interviews together with other historical material is presented in the second part of the paper.
    Additional Material: 6 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040604
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  • 18
    Electronic Resource
    Electronic Resource
    Stepwise canonical discriminant analysis of continuous digitalized signals: Application to chromatograms of wheat proteins (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 413-427 
    Details
    ISSN: 0886-9383
    Keywords: Discriminant analysis ; Size-exclusion chromatography ; Wheat proteins ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Continuous digitalized signals such as spectra, electrophoregrams or chromatograms generally have a large number of data points and contain redundant information. It is therefore troublesome performing discriminant analysis without any preliminary selection of variables. A procedure for the application of canonical discriminant analysis (CDA) on this kind of data is studied. CDA can be presented as a succession of two principal component analyses (PCAs). The first is performed directly on the raw data and gives PC scores. The second is applied on the gravity centres of each qualitative group assessed on the normalized PC scores. A stepwise procedure for selection of the relevant PC scores is presented. The method has been tested on an illustrative collection of 165 size-exclusion high-performance (SE-HPLC) chromatograms of proteins of wheat belonging to 55 genotypes and grown in three locations. The discrimination of the growing locations was performed using seven to nine PC scores and gave more than 86% accurate classifications of the samples both in the training sets and the verification sets. The genotypes were also rather well identified, with more than 85% of the samples correctly classified. The studied method gives a way of assessing relevant mathematical distances between digitalized signals according to qualitative knowledge of the samples.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040605
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  • 19
    Electronic Resource
    Electronic Resource
    Dependence between fusion temperatures and chemical components of a certain type of coal using classical, non-parametric and bootstrap techniques (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 429-439 
    Details
    ISSN: 0886-9383
    Keywords: Principal components ; Multiple and stepwise regression ; Non-parametric density and regression estimation ; Bootstrap inference ; Canonical correlation ; PLS regression ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A statistical study of the dependence between various critical fusion temperatures of a certain kind of coal and its chemical components is carried out. As well as using classical dependence techniques (multiple, stepwise and PLS regression, principal components, canonical correlation, etc.) together with the corresponding inference on the parameters of interest, non-parametric regression and bootstrap inference are also performed.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040606
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  • 20
    Electronic Resource
    Electronic Resource
    A genetic screen to identify variants of bovine pancreatic trypsin inhibitor with altered folding energetics (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 16-31 
    Details
    ISSN: 0887-3585
    Keywords: BPTI ; dithiothreitol ; DTT-sensitive mutants ; protein folding ; random mutagenesis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A genetic screening procedure has been developed to identify mutant forms of bovine pancreatic trypsin inhibitor (BPTI) that can fold to an active conformation but are inactivated more rapidly than the wild type protein. Small cultures of Escherichia coli containing plasmids with mutagenized BPTI genes were grown in microtiter plates, lysed, and treated with dithiothreitol (DTT). Under these conditions, unfolding and inactivation of wild-type protein has a half-time of about 10 hours. Variants of BPTI that are inactivated within 1 hour were identified by adding trypsin and a chromogenic substrate. Approximately 11,000 mutagenized clones were screened in this way and 75 clones that produce proteins that can fold but are inactivated by DTT were isolated. The genes coding for 68 “DTT-sensitive” mutant proteins were sequenced, and 25 different single amino acid substitutions at 15 of the 58 residues of the protein were identified. Most of the altered residues are largely buried in the core of the naive wild-type structure and are highly conserved among proteins homologous to BPTI. These results indicate that a large fraction of the sequence of the protein contributes to the kinetic stability of the active conformation, but it also appears that substitutions can be tolerated a most sites without completely preventing folding Because this genetics, further studies of the isolated mutants are expected to provide information about the roles of the altered residues in folding and unfolding.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070103
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  • 21
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070201
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  • 22
    Electronic Resource
    Electronic Resource
    Erratum (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 296-297 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070311
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  • 23
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070401
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  • 24
    Electronic Resource
    Electronic Resource
    Role of phosphorylation in conformational adaptability of bovine myelin basic protein (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 32-40 
    Details
    ISSN: 0887-3585
    Keywords: myelin basic protein ; phosphorylation ; protein conformation ; β-structure ; thrombin ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Controlled thrombic digestion of a preparation of components 2 + 3 isolated from the 18.5 kDa bovine myelin basic protein (MBP) yielded a polypeptide that was monophosphorylated on threonine 97 (component 3pT97). This is the first posttranslationally phosphorylated MBP isolated in pure form. We studied the effect of this single phosphate on the conformational adaptability of 18.5 kDa bovine MBP by comparing the circular dichroism (CD) spectrum of component 3pT97 with the spectra of highly purified nonphosphorylated components 1 and 2. The CD spectra of nonphosphorylated component 1 and component 2 [monodeamidated forms(s) of component1] were indistinguishable, while component 3pt97 exhibited a different spectrum. The singly phophorylated MBP component exhibited 13% more ordered conformations than that adopted by nonphosphorylated MBP in dilute aqueous solutions. This was estimated from the CD spectra, and apparently involved about 17 additional amino acid residues in β-structure(s).
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070104
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  • 25
    Electronic Resource
    Electronic Resource
    Crystallographic refinement of human serum retinol binding protein at 2Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 44-61 
    Details
    ISSN: 0887-3585
    Keywords: RBP ; RBP family ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human serum retinol binding protein (RBP) in complex with retinol has been crystallographically refined to an R-factor of 18.1% with 2Å resolution data. The protein topology results in an anti-parallel β-barrel that encapsulates the retinol ligand. A detailed description of the protein and the binding site is provided. Our structural work has helped to define a family of proteins, many of which are carrier proteins for smaller ligand molecules. We describe the structural basis for the conservation of sequence within the family.
    Additional Material: 15 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080108
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  • 26
    Electronic Resource
    Electronic Resource
    The three-dimensional structure of recombinant bovine chymosin at 2.3 Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 82-101 
    Details
    ISSN: 0887-3585
    Keywords: chymosin ; acid proteinase ; rennin ; X-ray structure ; structure comparison ; catalytic site ; crystal packing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The crystal structure of recombinant bovine chymosin (EC 3.4.23.4; renin), which was cloned and expressed in Escherichia coli, has been determined using X-ray data extending to 2.3 Å resolution. The crystals of the enzyme used in this study belong to the space group I222 with unit cell dimensions a = 72.7 Å, b = 80.3 Å, and c = 114.8 Å. The structure was solved by the molecular replacement method and was refined by a restrained least-squares procedure. The crystallographic R factor is 0.165 and the deviation of bond distances from ideality is 0.020 Å. The resulting model includes all 323 amino acid residues, as well as 297 water molecules. The enzyme has an irregular shape with approximate maximum dimensions of 40 × 50 × 65 Å. The secondary structure consists primarily of parallel and antiparallel β-strands with a few short α-helices. The enzyme can be subdivided into N- and C- terminal domains which are separated by a deep cleft containing the active aspartate residues Asp-34 and Asp-216. The amino acid residues and waters at the active site form an extensive hydrogen-bonded network which maintains the pseudo 2-fold symmetry of the entire structure. A comparison of recombinant chymosin with other acid proteinases reveals the high degree of structural similarity with other members of this family of proteins as well as the subtle differences which make chymosin unique. In particular, Tyr-77 of the flap region of chymosin does not hydrogen bond to Trp-42 but protrudes out in the P1 pocket forming hydrophobic interactions with Phe-119 and Leu-32. This may have important implications concerning the mechanism of substrate binding and substrate specificity.
    Additional Material: 11 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080110
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    Conformational flexibility of a scorpion toxin active on mammals and insects: A circular dichroism study (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 164-172 
    Details
    ISSN: 0887-3585
    Keywords: protein secondary structure ; sodium channel ; CD spectra analysis program ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Three scorpion toxins have been analyzed by circular dichroism in water and in 2,2,2-trifluoroethanol (TFE) solutions. These toxins were chosen because they are representative of three kinds of pharmacological activities: (1) toxin AaH IT2, an antiinsect toxin purified from the venom of Androctonus australis Hector, which is able to bind to insect nervous system preparation, (2) toxin Css II, from the venom of Centruroides suffusus suffusus, which is a β-type antimammal toxin capable of binding to mammal nervous system preparation, and (3) the toxin Ts VII from the venom of Tityus serrulatus, which is able to bind to both types of nervous systems. In order to minimize bias, CD data were analyzed by a predictive algorithm to assess secondary structure content. Among the three molecules, Ts VII presented the most unordered secondary structure in water, but it gained in ordered forms when solubilized in TFE. These results indicated that the Ts VII backbone is the most flexible, which might result in a more pronounced tendency for this toxin molecule to undergo conformational changes. This is consistent with the fact that it competes with both antiinsect and β-type antimammal toxins for the binding to the sodium channel.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080206
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    Electronic Resource
    Electronic Resource
    HERA - A program to draw schematic diagrams of protein secondary structures (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 203-212 
    Details
    ISSN: 0887-3585
    Keywords: hydrogen bonding diagram ; motifs ; helical wheel ; helical net ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A program is described which generates hydrogen bonding diagrams of protein structures and optionally helical wheels and helical nets. The program can also be used simply to calculate the connectivities of β-strands and to automatically extract simple structural motifs such as hairpins or Greek keys. The program greatly reduces the effort required to produce these diagrams and offers considerable flexibility in the information which can be represented. The usefulness of the program is illustrated by several examples including comparing homologous families, correlating protein structure with attributes of individual residues, and extracting all examples of the ψ-loop motif from the Brookhaven Data Bank.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080303
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    Electronic Resource
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    Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 251-257 
    Details
    ISSN: 0887-3585
    Keywords: peroxidase ; active site ; structure conservation ; hydrophobic cluster analysis ; sequence comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080307
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    Electronic Resource
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    Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 237-250 
    Details
    ISSN: 0887-3585
    Keywords: elongation factor ; energy minimization ; G-protein ; Guanine nucleotide binding ; protein structure ; protein synthesis ; structural homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative molecular modeling has been used to generate several possible structures for the G-domain of chloroplast elongation factor Tu (EF-Tuchl) based on the crystallographic data of the homologous E. coli protein. EF-Tuchl contains a 10 amino acid insertion not present in the E. coli protein and this region has been modeled based on its predicted secondary structure. The insertion appears to lie on the surface of the protein. Its orientation could not be determined unequivocally but several likely structures for the nucleotide binding domain of EF-Tuchl have been developed. The effects of the presence of water in the Mg2+ coordination sphere and of the protonation sate of the GDP ligand on the conformation of the guanine nucleotide binding site have been examined. Relative binding constants of several guanine nucleotide analogs for EF-Tuchl have been obtained. The interactions between EF-Tuchl and GDP predicted to be important by the models that have been developed are discussed in relation to the nucleotide binding properties of this factor and to the interactions proposed to be important in the binding of guanine nucleotides to related proteins.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080306
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    In memoriam (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080402
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    Hormone phage: An enrichment method for variant proteins with altered binding properties (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 309-314 
    Details
    ISSN: 0887-3585
    Keywords: hormone-receptor interactions ; epitope libraries ; binding selection ; fusion phage ; human growth hormone ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Human growth hormone (hGH), a 191 residue protein containing two disulfide bonds, was fused to the carboxyl-terminal domain of the gene III protein, a minor coat protein exposed at one end of the filamentous phage M13. The gene fusion was cloned into a plasmid containing origins of replication for Escherichia coli and filamentous phage and was packaged into phagemid particles upon infection by an M13KO7 helper phage. Transcription of the hGH-gene III fusion was controlled so that usually no more than one copy of the fusion protein was displayed along with the four copies of the wild-type gene III protein. The hGH-gene III fusion protein was properly folded, as judged by reactivity with six hGH monoclonal antibodies whose epitopes are sensitive to the folded conformation of hGH. Moreover, the hGH-gene III phagemid particles were enriched over 5000-fold from non-hGH phage, and 8-fold from a mutant hGH phagemid following a single hGH-specific elution step from hGH receptor-coated beads. The hGH phagemid should be useful for isolating new receptor binding mutants of hGH. More generally, this expression system may allow other large proteins with discontinuous binding epitopes to be displayed, and binding selections applied to their mutated gene III fusions on filamentous phage.
    Additional Material: 2 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080405
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    Distinct character in hydrophobicity of amino acid compositions of mitochondrial proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 173-178 
    Details
    ISSN: 0887-3585
    Keywords: mitochondria ; amino acid composition ; hydrophobicity ; composition space ; membrane protein ; transmembrane region ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt-proteins) were examined in the 20-dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt-proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G-C-rich base composition.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080207
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    Models of δ-hemolysin membrane channels and crystal structures (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 213-225 
    Details
    ISSN: 0887-3585
    Keywords: molecular modeling ; energy calculations ; δ-hemolysin ; melittin ; crystal packing ; raft ; bilayer ; membrane insertion ; channel formation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Molecular modeling and energy calculations have been used to study how δ-hemolysin and melittin helices may aggregate on membrane surfaces and insert through membranes to form channels. In these models adjacent antiparallel amphipathic helices form planar “raft” structures, in which one surface is hydrophobic and the other hydrophilic. Models of δ-hemolysin crystal structure were developed using these “rafts.” These models are based on the unit cell constants and the crystal symmetry obtained from the preliminary crystal data. Energy calculations favor channel models of δ-hemolysin with six or eight monomers per channel.
    Additional Material: 7 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080304
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    Changes in secondary structure follow the dissociation of human insulin hexamers: A circular dichroism study (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 280-286 
    Details
    ISSN: 0887-3585
    Keywords: circular dichroism ; secondary structure ; insulin ; insulin analogs ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Vacuum UV circular dichroism spectra measured down to 178 nm for hexameric 2-zinc human insulin, zinc-free human insulin, and the two engineered and biologically active monomeric mutants, [B/S9D] and [BS9D, T27E] human insulin, show significant differences. The secondary structure analysis of the 2-zinc human insulin (T6) in neutral solution was determined: 57% helix, 1% β-strand, 18% turn, and 24% random coil. This is very close to the corresponding crystal structure showing that the solution and solid structures are similar. The secondary structure of the monomer shows a 10-15% increase in antiparallel β-structure and a corresponding reduction in random coil structure. These structural changes are consistent with an independent analysis of the corresponding difference spectra. The advantage of secondary structure analyses of difference spectra is that the contribution of odd spectral features stemming mainly from side chain chromophores is minimized and the sensitivity of the analyses improved. Analysis of the CD spectra of T6 2-zinc, zinc-free human insulin and monomeric mutant insulin by singular value decomposition indicates that the secondary structure changes following the dissociation of hexamers into dimers and monomers are two-state processes.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080309
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    Design of biologically active, conformationally constrained GnRH antagonists (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 295-304 
    Details
    ISSN: 0887-3585
    Keywords: gonadotropin-releasing hormone ; molecular dynamics ; nuclear magnetic resonance ; antagonist design ; conformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The introduction of conformational constraints into a flexible peptide hormone can be exploited to develop models for the conformation required for receptor binding and activity. In this review, we illustrate this approach to analog design using our work on antagonists of gonadotropin-releasing hormone (GnRH). Design of a conformationally constrained, competitive antagonist of GnRH, cyclo[Δ3,4 Pro-D4ClPhe-DTrp-Ser-Tyr-DTrp-NMeLeu-Arg-Pro-βAla], led to the prediction of its bioactive conformation. Template forcing experiments show that this conformation is accessible to other active GnRH analogs. Two-dimensional NMR studies verified the predicted conformation in solution. The predicted binding conformation has recently been used to design two new analogs incorporating side chain-side chain linkages suggested by the conformational model: These analogs were synthesized and the one predicted to be most similar to the parent conformation had equivalent potency while the second, designed to refine the conformational hypothesis, was found to exhibit enhanced potency, thus confirming the original binding conformation hypothesis. These compounds and their derivatives now provide a new class of GnRH antagonists possessing both high biological potency and limited conformational flexibility, thus making them ideal for both biophysical and structure-activity studies.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080403
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    A helix-turn-strand structural motif common in α-β proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 334-340 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; structural comparison ; α-β barrels ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: By exhaustive structural comparisons, we have found that about one-third of the α-helix-turn-β-strand polypeptides in α-β barrel domains share a common structural motif. The chief characteristics of this motif are that first, the geometry of the turn between the α-helix and the β-strand is somewhat constrained, and second, the β-strand contains a hydrophobic patch that fits into a hydrophobic pocket on the α-helix. The geometry of the turn does not seem to be a major determinant of the α-β unit, because the turns vary in length from four to six residues. However, the motif does not occur when there are few constraints on the geometry of the turn-for instance, when the turns between the α-helix and the β-strands are very long. It also occurs much less frequently in flat-sheet α-β proteins, where the topology is much less regular and the amount of twist on the sheet varies considerably more than in the barrel proteins. The motif may be one of the basic building blocks from which α-β barrels are constructed.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080407
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    Fragment peptide library for classification and functional prediction of proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 341-351 
    Details
    ISSN: 0887-3585
    Keywords: conserved sequence ; diagnostic peptide ; superfamily classificaiton ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: From protein sequence comparison data found in the literature, a library was organized using peptide fragment sequences which are common to related proteins. Each of the fragments was then examined for its occurrence in all the protein superfamilies defined by the NBRF-PIR data base. We have selected those fragment peptides that appear exclusively in one or a few superfamilies, and thus made a library of fragment peptides that characterize specific superfamilies. Such characteristic peptides are, in general, five to seven residues long and contain unusually high proportions of glycine and cysteine. This collection is a useful resource for the classification and functional prediction of protein molecules.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080408
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    The structure of rubredoxin from Desulfovibrio desulfuricans strain 27774 at 1.5 Å resolution (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 352-364 
    Details
    ISSN: 0887-3585
    Keywords: crystallography ; refinement ; structure comparison ; molecular replacement ; precision ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of a small rubredoxin from the bacterium Desulfovibrio desulfuricans has been determined and refined at 1.5 Å resolution. The hairpin loop containing seven residues in other rubredoxins is missing in this 45 residue molecule, and once that fact was determined by amino acid sequencing studies, refinement progressed smoothly to an R value of 0.093 for all reflections from 5 to 1.5 Å resolution. Nearly all of the water molecules in the well-ordered triclinic unit cell have been added to the crystallographic model. As in the other refined rubredoxin models, the Fe-S4 complex is slightly distorted from ideal tetrahedral coordination.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080409
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    Refinement of the NMR structures for acyl carrier protein with scalar coupling data (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 377-385 
    Details
    ISSN: 0887-3585
    Keywords: structure deteremination ; two-dimensional NMR ; molecular mechanics ; molecular dynamics ; conformational equilibrium ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structure determination of small proteins using NMR data is most commonly pursued by combining NOE derived distance constraints with inherent constraints based on chemical bonding. Ideally, one would make use of a variety of experimental observation, not just distance constraints. Here, coupling constant constraints have been added to molecular mechanics and molecular dynamics protocols for structure determination in the form of a psuedoenergy function that is minimized in a search for an optimum molecular conformation. Application is made to refinement of a structure for a 77 amino acid protein involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP). 54 3JHNα coupling constants, 12 coupling constants for stereospecifically assigned side chain protons, and 450 NOE distance contraints were used to calculate the 3-D structure of ACP. A three-step protocol for a molecular dynamics calculation is described, in analogy to the protocol previously used in molecular mechanics calculations. The structures calculated with the molecular mechanics approach and the molecular dynamics apporach using a rigid model for the protein show similar molecular energies and similar agreement with experimental distance and coupling constant constraints. The molecular dynamics approach shows some advantage in overcoming local minimum problems, but only when a two-state averaging model for the protein was used, did molecular energies drop significantly.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080411
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    α-Helical coiled coils and bundles: How to design an α-helical protein (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 1-15 
    Details
    ISSN: 0887-3585
    Keywords: α-fibrous proteins ; 4-α-helix bundle ; membrane-spanning proteins ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070102
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  • 42
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    Molecular dynamics study of secondary structure motion in proteins: Application to myohemerythrin (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 265-279 
    Details
    ISSN: 0887-3585
    Keywords: potential of means force ; motions of helices ; correlated fluctuations ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The concept of secondary structure motions is examined in a molecular dynamics simulation of the protein myohemerythrin. We extracted from the simulation a corresponding trajectory of helices and demonstrated that the fluctuations of the protein are dominated by a rigid shift of these secondary structure elements. The relative motions of the helices are regular, with no clear periodicity. They are bounded by ∼2 for the center of mass motions and by 20° for the relative orientations. The potential of mean force for the interactions of the helices was calculated, and the correlations between the different extended motions were investigated. It shown that the one-dimensional mean force potentials are close to quadratic for most of the helices coordinates. The anharmonicity is reflected by changes in the direction of the normal modes as a function of the energy and by the existence of multiple free energy minima for the helices packing. The multiple conformations are associated with a single type of secondary structure coordinate: the angle that describes the relative orientation of the helices in a plane perpendicular to the line connecting their center of mass.
    Additional Material: 12 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070308
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    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990) 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040101
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    Diary (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. i 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040102
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  • 45
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    Mixture analysis using factor analysis. II: Self-modeling curve resolution (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 1-13 
    Details
    ISSN: 0886-9383
    Keywords: Factor analysis ; Self-modeling curve resolution ; Spectra isolation ; Target transformation factor analysis ; Iterative target transformation factor analysis ; Evolving factor analysis ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: One of the major applications of factor analysis in the chemical literature, self-modeling curve resolution (SMCR), is covered in this review, including a historical account of the methods derived from Lawton and Sylvestre's original method. Papers treating the theory or applications of SMCR are included. Qualitative and quantitative applications are described where appropriate.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040103
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  • 46
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    Resolution of multicomponent fluorescent mixtures by analysis of the excitation-emission-frequency array (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 15-28 
    Details
    ISSN: 0886-9383
    Keywords: Resolution of total luminescence spectra ; Phase-resolved fluorescence spectroscopy ; Generalized rank annihilation method ; Excitation-emission-frequency array ; Simultaneous diagonal decomposition ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Fluorescence lifetime provides a third independent dimension of information for the resolution of total luminescence spectra of multicomponent mixtures. The incorporation of this parameter into the excitation-emission matrix (EEM) by the phase modulation technique results in a three-dimensional excitation-emission-frequency array (EEFA). Multicomponent analysis based on the three-dimensional EEFA brings a qualitative change for the resolved spectra, i.e. individual spectra can be uniquely resolved, which is impossible with any two-dimensional analysis. In this paper we present a method for analyzing the EEFA. We show mathematically that with the three-dimensional analysis of the EEFA individual spectra and lifetimes can be obtained. Our algorithm is developed in mathematical detail and is demonstrated by its application to a two-component mixture.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040104
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    Tensorial resolution: A direct trilinear decomposition (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 29-45 
    Details
    ISSN: 0886-9383
    Keywords: Tensor ; Superdiagonalization ; GRAM ; Three-way ; Multilinear ; Trilinear ; PARAFAC ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Modern instrumentation in chemistry routinely generates two-dimensional (second-order) arrays of data. Considering that most analyses need to compare several samples, the analyst ends up with a three-dimensional (third-order) array which is difficult to visualize or interpret with the conventional statistical tools.Some of these data arrays follow the so-called trilinear model, \documentclass{article}\pagestyle{empty}\begin{document}$$ {\rm R}_{ijk} = \sum\limits_{r = 1}^N {{\rm X}_{ir} {\rm Y}_{jr} {\rm Z}_{kr} + {\rm Error}_{ijk} } $$\end{document} These trilinear arrays of data are known to have unique factor analysis decompositions which correspond to the true physical factors that form the data, i.e. given the array ∝, a unique solution can be found in many cases for each order X, Y and Z. This is in contrast to the well-known second-order bilinear data factor analysis, where the abstract solutions obtained are not unique and at best cannot be easily compared with the underlying physical factors owing to a rotational ambiguity.Trilinear decompositions have had the disadvantage, however, that a non-linear optimization with many parameters is necessary to reach a least-squares solution. This paper will introduce a method for reducing the problem to a rectangular generalized eigenvalue-eigenvector equation where the eigenvectors are the contravariant form (pseudo-inverse) of the actual factors. It is shown that the method works well when the factors are linearly independent in at least two orders (e.g. Xir and Yjr are full rank matrices).Finally, it is shown how trilinear decompositions relate to multicomponent calibration, curve resolution and chemical analysis.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/cem.1180040105
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    A review of information theory in analytical chemometrics (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 195-216 
    Details
    ISSN: 0886-9383
    Keywords: Entropy ; Decrease of uncertainty ; Information gain ; Relevance coefficients ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Information theory makes it possible to judge and evaluate methods and results in chemical analysis. The obtained information can be expressed in different ways. One way is to define information as the decrease of uncertainity after analysis. Conditional probabilities are therefore considered when evaluating the information provided by qualitative analyses. However, the use of other information measures, such as the information gain, is often preferable. In multicomponent analysis the translation of information from signals to the amounts of the analytes has been investigated along with the relevance of individual components. Information theory can also be applied to find the optimum experimental conditions. The evaluation of the properties of analytical methods by information theory has been proposed.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040303
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    Cross-validation, influential observations and selection of variables in chemometric studies of wines by principal components analysisPaper presented at the EUCHEM Conference on ‘Chemometrics in Organic and Bio-organic Chemistry’, Trieste, Italy, 19-26 June 1988. (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 217-240 
    Details
    ISSN: 0886-9383
    Keywords: Principal component ; Cross-validation ; Selection of variables ; Residual ; Influential observation ; Procrustes analysis ; Chemometrics ; Wine analysis ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Cross-validatory estimation of the bilinear model based on principal components is reviewed and Krzanowski's modification of Wold's procedure is described. Two different types of residuals useful for checking model adequacy are defined and indices measuring the influence of each observed unit on the estimates of the parameters are discussed. A method for the selection of variables derived from Procrustes analysis is described. Results arising from the study of two sets of enological data are given.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040304
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  • 50
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    Dedicated principal properties for peptide QSARs: Theory and applications (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 241-253 
    Details
    ISSN: 0886-9383
    Keywords: Peptide QSAR ; Dedicated principal properties ; Principal component analysis ; Partial least squares projections to latent structures ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Dedicated principal properties (DPPs) are presented. The DPP approach is an iterative process based on PLS wherein principal properties are calibrated on QSARs with improved predictive capabilities as a consequence. The DPP approach is illustrated by two examples. In the first example the z-scales developed for structural description in peptide QSARs are optimized according to the DPP approach. In the second example DDPs based on simulated pentapeptide-like sequences are calculated and evaluated.A comparison is made of the predictive power of peptide QSAR models based on structural description of the peptides with (a) 29 physico-chemical variables with (b) three principal properties (z-scales) and (c) three sets of DPPs. The results show that models based on all 29 variables give better predictions than models based on principal properties. Modelling based on DPPs improves the predictive power to the same level as models based on all 29 variables.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040305
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    A similarity measure for chemical data: Applications to cluster analysis (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 255-266 
    Details
    ISSN: 0886-9383
    Keywords: Similarity measure ; Cluster analysis ; Riemannian space ; Metric tensor ; Curvature ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The results of unsupervised pattern recognition methods are critically dependent on the measure of similarity used for clustering objects. There is little a priori information available on the relative utility of various similarity measures. We introduce here an alternative similarity measure based on the metric tensor measure (MTM). Two standard clustering strategies are tested with the proposed similarity measure: hierarchical clustering and the K-median method. As data we use the ARCH obsidian data, a data set on Hungarian coal, and trace element data on Hungarian paprika. Differences from the Mahalanobis distance measure are described for intraclass relations.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040306
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    Announcement (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 267-268 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040307
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    Algorithms for chemists, Jure Zupan, John Wiley and Sons, Ltd., Chichester, 1989. Price: £39.50, US$75.90, ISBN 0 47192173 4 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 269-269 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040308
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990) 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040401
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    Diary (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. i 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040402
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  • 56
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    Data analysis in the shot noise limit. Part III: Adaptive data smoothing filters (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 271-289 
    Details
    ISSN: 0886-9383
    Keywords: Smoothing ; Digital filter ; Shot noise ; Signal processing ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Digital filter smoothing methods for shot-noise-limited data are addressed in this study. The preferred method is based on a Gaussian filter in which the width of the Gaussian filter function is varied depending on the estimate of the second derivative of the raw data. This filter is developed from the standpoint of maximum likelihood parameter estimation of the probability density function which describes shot-noise-limited data. The smoothing filter is tested and compared with the conventional sequential regression filter. This adaptive Gaussian smoothing filter works better than both the sequential regression and the adaptive Gaussian filter derived for normal noise. For data containing both high- and low-frequency components, the limiting step in the adaptive filter is an estimation of the smoothing interval. Methods for determining an optimum smoothing interval are discussed. With the optimized smoothing interval, the adaptive Gaussian filter works well for data sets with a wide range of varying frequency components. In particular, synthetic data typical of atomic emission spectra are used to test this smoothing filter.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040403
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    The use of a cross-correlation technique to enhance Jansson's deconvolution procedure (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 291-298 
    Details
    ISSN: 0886-9383
    Keywords: Deconvolution ; Jansson's method ; Peak restoration ; Iterative deconvolution ; Peak resolution ; Chromatographic deconvolution ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The use of a cross-correlation prefiltering technique to enhance the ability of Jansson's iterative deconvolution procedure to deconvolve extremely noisy chromatographic data is investigated. Test cases include peaks whose resolutions are as low as 0.35 and whose signal-to-noise ratios are as low as 1:1. Evaluation criteria include RMS error, relative peak error and peak area repeatability. For comparison purposes, relative peak area errors and peak area variances are also evaluated for noisy but well resolved peaks that have only been prefiltered with the cross-correlation filter. Jansson's method in conjunction with cross-correlation prefiltering is shown not only to resolve overlapped peaks but in some cases to improve their signal-to-noise ratios. The study also establishes some limits to the capabilities of Jansson's method will regard to adverse data conditions.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040404
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    The Free-Wilson paradigm redux: Significance of the Free-Wilson coefficients, insignificance of coefficient ‘uncertainities’ and statistical sins (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 299-321 
    Details
    ISSN: 0886-9383
    Keywords: Quantitative structure-activity relationships (QSARs) ; Free-Wilson ; Fujita-Ban Stepwise principal components regression analysis (SPCRA) ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The Free-Wilson paradigm is an established and powerful tool for quantitatively relating activity with chemical structure. Current implementations of the paradigm, however, are flawed both conceptually and in execution. As part of an attempt to more fully realize the promise of the paradigm, it was necessary to examine these limitations in detail.This report introduces a robust, theory-founded Free-Wilson implementation: stepwise principal components regression analysis (SPCRA). SPCRA is computationally superior to previous implementations but does not in itself correct their conceptual flaws.The development of SPCRA did, however, facilitate derivation of a simple and chemically significant interpretation of the Free-Wilson structure-activity model. A number of statistical aspects of this model commonly misused in previous applications are discussed at length. These discussions provide critical background for the development of an alternative implementation of the Free-Wilson paradigm.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/cem.1180040405
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    Target factor analysis: UV spectrophotometry for the simultaneous determination of six amino acids (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 323-330 
    Details
    ISSN: 0886-9383
    Keywords: Target factor analysis ; Spectrophotometry ; Amino acids ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: The UV spectra of mixture solutions consisting of tyrosine, tryptophane, phenylalanine, cystine, histidine and 3,4-dihydroxyl phenylalanine have been measured. The numbers, identities and concentrations of the amino acids in the mixtures have been determined successfully using target factor analysis. The effects of the wavelength range and the selected sampling interval on the results are discussed. Twenty-five synthetic mixture samples have been analysed successfully. The average recoveries are 98.9 for Tyr, 96.5 for Trp, 105.6 for Phe, 98.1 for Cys, 98.9 for His and 106.4 for Di-phe. The results obtained are in good agreement with those obtained by the Kalman filter method.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040406
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    Announcement (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 335-335 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040408
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    Comments on the power method (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 331-334 
    Details
    ISSN: 0886-9383
    Keywords: Power method ; NIPALS algorithm ; Singular value decomposition ; Experimental design ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: In a recent short communication, Miyashita et al. have commented on the weakness of the NIPALS algorithm (equivalently the power method) for calculating the eigenvalues out of order. They offer a diagnostic to ascertain when this may have occurred and suggested a modification to the NIPALS algorithm to avoid this situation. Further comments regarding the use of the power method and Miyashita's presentation of its weakness are warranted. The general inadequacies of methods for decomposing a matrix with degenerate eigenvalues and their relationship to the orthogonal design of experiments are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040407
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990) 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040501
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  • 63
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    An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 41-51 
    Details
    ISSN: 0887-3585
    Keywords: DNA binding proteins ; maximum likelihood ; CRP ; finite mixtures ; transcription regulation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Statistical methodology for the identification and characterization of protein binding sites in a set of unaligned DNA fragments is presented. Each sequence must contain at least one common site. No alignment of the sites is required. Instead, the uncertainty in the location of the sites is handled by employing the missing information principle to develop an “expectation maximization” (EM) algorithm. This approach allows for the simultaneous identification of the sites and characterization of the binding motifs. The reliability of the algorithm increases with the number of fragments, but the computations increase only linearly. The method is illustrated with an example, using known cyclic adenosine monophophate receptor protein (CRP) binding sites. The final motif is utilized in a search for undiscovered CRP binding sites.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070105
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    Understanding structural relationships proteins of unsolved three-dimensional structure (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 99-111 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070202
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    Protein secondary structure and circular dichroism: A practical guide (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 205-214 
    Details
    ISSN: 0887-3585
    Keywords: protein secondary structures ; circular dichroism ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070302
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    Modelling of the human intercellular adhesion molecule-1, the human rhinovirus major group receptor (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 227-233 
    Details
    ISSN: 0887-3585
    Keywords: rhinovirus receptor ; ICAM-1 ; structure prediction ; immunoglobulin superfamily ; docking receptor to virus ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A model has been built of the amino-terminal domain of the intercellular adhesion molecule-1 (ICAM-1), the receptor for most human rhinovirus serotypes. The model was based on sequence and presumed structural homology to immunoglobulin constant domains. It fits well into the putative receptors attachment site, the canyon, on the human rhinovirus-14 (HRV14) surface in a manner consistent with most of the mutational data for ICMA-1 (Staunton, D. E., Dustin, M. L., Erickson, H. P., Springer, T. A. Cell, in press, 1989) and HRV14 (Colonno, R. J., Condra, J. H., Mizutani, S., Callahan, P. L., Davies, M. E., Murcko, M. A. Proc. Natl. Acad. Sci. U.S.A. 85: 5449-5453, 1988).
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070304
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    Structure determination and refinment of Bacillus stearothermophilus lactate dehydrogenase (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 74-92 
    Details
    ISSN: 0887-3585
    Keywords: thermostability ; bacterial lactate dehydrogenase ; allosteric regulations ; crystallography ; molecular replacement ; coenzyme binding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Structures have been determined of Bacillus stearothermophilus “apo” and holo lactate dehydrogenase. The holo-enzyme had been co-crystallized with the activator fructose 1,6-biosphosphate. The “apo” lactate dehydrogenase structure was solved by use of the known apo-M4 dogfish lactate dehydrogenase molecule as a starting model. Phases were refined and extended from 4 Å resolution by means of the noncrystallographic molecular 222 symmetry. The R-factor was reduced to 28.7%, using 2.8 Å resolution data, in a restrained least-squares refnement in which the molecula rsymmetry was imposed as a constraint. A low occupancy of coenzyme was found in each of the four subunits of the “apo” enzyme.Further refinement proceeded with the isomorphous holo-enzyume from Bacillus Stearothermophilus. After removing the noncrystallographic constraints, the R-factor dropped from 30.3% to a final value of 26.0% with a 0.019 Å and 1.7° r.m.s. deviation from idealized bond length and angles, respectively.Two sulfate ions per subunit were included in the final model of the “apo” -from-one at the substrate binding site and one close to the molecular P -axis near the location of the fructose 1,6-bisphosphate activator. The final model of the holo-enzyme incorporated two sulfate ions per subunit, one at the substrate binding site and another close to the R-axis. One nicotinamide adenine dinucleotide coenzyme molecule per subunit and two fructose 1,6-bisphosphate molecules per tetramer were also included. The phosphate positions of fructose 1,6-bisphosphate are close to the sulfate ion near the P-axis in the “apo” model.This structure represents the first reported refined model of an allosteric activated lactate dehydrogenase. The structure of the activated holo-enzyme showed far greater similarity to the ternary complex of dogfish M4 lactate dehydrogenase with incotinamide adenine dinucleotide and oxamate than to apo-M4 dogfish lactate dehydrogenase. The conformations of nicotinamide adenine dinucleotide and fructose, 1,6-bisphosphate were also analyzed.
    Additional Material: 15 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070108
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    Substrate recognition by the EcoRI endonuclease (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 185-197 
    Details
    ISSN: 0887-3585
    Keywords: restriction enzyme ; DNA-protein interactions ; DNA recognition ; enzyme-substrate interaction ; active site ; site-directed mutagenesis ; protein structure-function ; DNA double-strand breaks ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The EcoRI restriction endonuclease is one of the most widely used tools for recombinant DNA manipulations. Because the EcoRI enzyme has been extremely well characterized biochemically and its structure is known at 3 Å resolution as an enzyme-DNA complex, EcoRI also serves as an important model of DNA-protein interactions. To facilitate a genetic analysis of the EcoRI enzyme, we devised an in vivo DNA scission assay based on our finding that DNA double-strand breaks induce the Escherichia coli SOS response and thereby increase β-galactosidase expression from SOS::lacZ gene fusions. By site-directed mutagenesis, 50 of 60 possible point mutations were generated at three amino acids (E144, R145, and R200) implicated in substrate recognition by the crystal structure. Although several of these mutant enzymes retain partial endonuclease activity, none are altered in substrate specificity in vivo or in vitro. These findings argue that, in addition to the hydrogen bond interactions revealed by the crystal structure, the EcoRI enzyme must make additional contacts to recognize its substrate.
    Additional Material: 5 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070207
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    Model for the interaction of amphiphilic helices with troponin C and calmodulin (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 234-248 
    Details
    ISSN: 0887-3585
    Keywords: computer modelling ; Ca2+-binding proteins ; hydrophobic binding interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Crystals of troponin are stabilized by an intermolecular interaction that involves the packing of helix A from the N-terminal domain of one molecule onto the exposed hydrophobic cleft of the C-terminal domain of a symmetry related molecules. Analysis of this molecular recognition interaction in troponin C suggests a possible mode for the binding of amphiphilic helical molecules to troponin C and to calmodulin. From the template provided by this troponin C packing, it has been possible to build a model of the contact region of mastoporan as it might be bound to the two Ca2+ binding proteins. A possible binding mode of melittin to calmodulin is also proposed. Although some of the characteristics of binding are similar for the two amphiphilic peptides, the increased length of melittin requires a significant bend in the calmodulin central helix similar to that suggested recently for the myosin light chain kinase calmodulin binding peptide (Persechini and Kretsinger: Journal of Cardiovascular Pharmacology 12:501-512, 1988). Not only are the hydrophobic interactions important in this model, but there are several favorable electrostatic interactions that are predicted as a result of the molecular modeling. The regions of troponin-C and calmodulin to which amphiphilic helices bind are similar to the regions to which the neuroleptic drugs such as trifluoperazine have been predicted to bind (Strynadka and James: Proteins 3:1-17, 1988).
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070305
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    The design of idealized α/β-barrels: Analysis of β-sheet closure requirements (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 249-256 
    Details
    ISSN: 0887-3585
    Keywords: β-barrels ; β-strand ; scaffold design ; molecular modeling ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The 8-old parallel α/β-barrel topology is encountered in proteins that display an impressive variety of functions, suggesting that this topology may be a rather nonspecific and stable folding motif. Consequently, this motif can be considered as an interesting framework to design novel proteins. It has been shown that the shape of the β-sheet portion of the barrel can be approximated by a hyperboloid. This geometric object may therefore be used as a scaffold to construct an idealized eight-standard β-barrel. To facilitate the de novo design of such structures, a collection of modelling tools has been developed allowing secondary structure elements to be mapped onto the scaffold surface and rotation and translation operations to be performed about user defined axes while evaluating their contribution to the conformational energy of the system. These tools have been applied in a systematic study assessing the φ, ψ requirements to design symmetric eight standard β barrels with optimal hydrogen bonding between adjacent β-strands. It is observed that: (a) the β-sheet structure can be closed without introducing irregular stagger between β-strands and (b) the region of φ, ψ dihedral angle space compatible with the formation of regular symmetric eight standard β-barrels coincides with the φ, ψ region corresponding to average β-strands in known protein structures, suggesting that barrel closure does not impose gross constraints on β-strand geometry.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070306
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    The characterization of recombinant mouse glandular kallikreins from E. coli (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 280-290 
    Details
    ISSN: 0887-3585
    Keywords: proteases ; protein turnover ; post-translational processing ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A system has been developed or the expression in E. coli of 12 of the 14 expressed mouse submandibular gland kallikreins as cassettes subcloned directly from cDNA. Using the epidermal growth factor binding protein (mGK-9) and the γ-subunit of nerve growth factor (nGK)-3, as test cases, mature processed forms, obtained as functionally active proteins, as well as various precursor forms, were isolated. The expression system described allows rapid isolation of kallikrein protein from corresponding cDNA with yields of approximately 1.0 mg of purified protein from 10 g of initial cell paste. This expression system will facilitate structure/function studies of the mouse glandular kallikrein gene family and help elucidate the regions of the mature proteins responsible for the diverse catalytic behavior and growth factors interactions observed in this family of proteins.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070309
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  • 72
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    Functionally acceptable substitutions in two α-helical regions of λ repressor (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 306-316 
    Details
    ISSN: 0887-3585
    Keywords: neutral mutations ; random mutagenesis ; protein structure ; protein folding ; protein families ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A method of targeted random mutagenesis has been used in investigate the informational content of 25 residue positions in two α-helical regions of the N-terminal domain of λ repressor. Examination of the functionally allowed sequences indicates that there is a wide range in tolerance to amino acid substitution at these position. At position that are buried in the structure, there are severe limitations on the number and type of residues allowed. At most surface positions, many different residues and residue types are tolerated. However, at several surface positions there is a string preference for hydrophilic amino acids, and at one surface position proline is absolutely conserved. The results reveal the high level of degeneracy in the information that specifies a particular protein fold.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070403
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    Crystal structure of subtilisin BPN′ variants containing disulfide bonds and cavities: Concerted structural rearrangements induced by mutagenesis (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 343-357 
    Details
    ISSN: 0887-3585
    Keywords: engineered disulfide groups ; X-ray structure ; hydrophobic cavities ; water structure, altered ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The X-ray structure of four genetically engineered disulfide variants of subtilisin have been analyzed to determine the energetic and structural constraints involved in inserting disulfide bonds into proteins. Each of the engineered disulfides exhibited atypical sets of dihedral angles compared with known structures of natural disulfide bridges in proteins and affected its local structural environment to a different extent. The disulfides located in buried regions, Cys26-Cys232 and Cys29-Cys87 and Cys22-Cys87, which are located on the surface of the molecule. An analysis of the concerted changes in secondary structure units such as α-helices and β-sheets indicated systematic long-range effects. The observed changes in the mutants were largely distributed asymmetrically around the inserted disulfides, reflecting different degrees of inherent flexibility of neighboring secondary structure types. The disulfide substitution in each variant molecule created some invaginations or cavities, causing a reorganization of the surrounding water structure. These changes are described, as well as the changes in side chain positions of groups that border the cavities.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070406
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    The building of protein structures form α-carbon coordinates (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 366-377 
    Details
    ISSN: 0887-3585
    Keywords: computer modeling ; protein ; structure ; α-carbons ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A procedure for the construction of complete protein structures from only αcarbon coordinates is described. This involves building the backbone by sequential addition of Pro, Gly, or Ala residues. This main chain structure is then refined using molecular dynamics. Side chains are constructed by sequential addition of atoms with intermediate molecular dynamics refinement. For α lytic protease (a structure that is mostly β sheet) a backbone root mean square deviation (RMSD) of 0.19 Å and an overall RMSD of 1.24 Å from the crystallographic coordinates are attained. For troponin C (67% β-helix), where the coordinates are available only for the α-carbons, a backbone RMSD of 0.41 Å and an overall RMSD of 1.68 Å are attained (fits kindly provided by Dr. Michael James and Natalie Strynadka). For flavodoxin a backbone RMSD of 0.49 Å and an overall RMSD of 1.64 Å were attained.
    Additional Material: 1 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070408
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    Quantitative organization of the known protein x-ray structures. I. Methods and short-length-scale results (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 378-402 
    Details
    ISSN: 0887-3585
    Keywords: conformational distance ; conformational comparison ; generalized bond matrix representation ; structure space ; evolution ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We address herein the problem of delineating the relationships between the known protein structures. In order to study this problem, methods have been developed to represent arbitrarily sized fragments of biopolymer backbone, and to compare distributions of such fragments. These methods are applied to a classification of 123 structures representing the entire set of known x-ray structures. The resulting data are analyzed (on the four-Cα length scale) to determine both the large-scale organization of the set of known structures (i.e., the relationships between large groups of structures, each comprised of proteins that are structurally related) and its local structure (i.e., the quantitative degree of similarity between any two specific structures). It is shown that the set of structures from a continuum of structural types, ranging from allhelical to all-sheet/barrel proteins. It is further demonstrated that the density of protein structures is not uniform across this continuum, but rather that structures cluster in certain regions, separated by regions of lower population. The properties of the various regions of the structural space are determined. The existence is demonstrated of strong quantitative correlations between the contents of different types of four-Cα fragments within protein structures, which imply significant constraints on the types of architecture that can occur in proteins. Analysis of the distribution of structures demonstrates some hitherto unsuspected similarities and suggests that, in some circumstances, neither structural similarity no sequence homology may be necessary conditions for evolutionary relationship between proteins. It is also suggested that these unsuspected similarities may imply similar folding mechanisms for structures of apparently different global architecture. Cases are also noted in which apparently similar structures may fold by different mechanisms. The connection between structure and dynamic properties is discussed, and a possible role of dynamics in the evolution of protein structures is suggested. The sensitivity of the methods presented herein to anomalies of structure refinement is demonstrated. It is suggested that present results provide a frame-work for analyzing experimental results on structural similarity obtained using vibrational circular dichroism spectra, which are sensitive to local backbone structure.
    Additional Material: 10 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340070409
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    Prediction of homologous protein structures based on conformational searches and energetics (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 30-43 
    Details
    ISSN: 0887-3585
    Keywords: molecular mechanics ; solvation energy ; trypsin ; energy minimization ; side chains ; protein crystallography ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A “knowledge-based” method of predicting the unknown structure of a protein from a homologous known structure using energetics to determine a sidechain conformation is proposed. The method consists of exchangin the residues in the known structure for the sequence of the unknown protein. Then a conformational search with molecular mechanics energy minimization is done on the exchanged residues. The lowest energy conformer is the one picked to be the predicted structure. In the structure of bovine trypsin, the importance of including a solvation energy term in the search is demonstrated for solvent accessible residues, while molecular mechanics alone is enough to correctly predict the conformation of internal residues. The correctness of the model is assessed by a volume error overlap of the predicted structure compared to the crystal structure. Finally, the structure of rat trypsin is predicted from the crystal structure of bovine trypsin. The sequences of these two proteins are 74% identical and all of the significant changes between them are on external residues. Thus, the inclusion of solvation energy in the conformational search is necessary to accurately predict the structure of the exchanged residues.
    Additional Material: 13 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080107
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    Revised 2.3 Å structure of porcine pepsin: Evidence for a flexible subdomain (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 62-81 
    Details
    ISSN: 0887-3585
    Keywords: pepsin ; aspartic proteinases ; subdomains ; structure comparison ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A revised three-dimensional crystal structure of ethanol-inhibited porcine pepsin refined to an R-factor of 0.171 at 2.3 Å resolution is presented and compared to the refined structures of the fungal aspartic proteinases: penicillopepsin, rhizopuspepsin, and endothiapepsin. Pepsin is composed of two nearly equal N and C domains related by an intra dyad. The overall polypeptide fold and active site structures are homologous for pepsin and the fungal enzymes. The weak inhibition of pepsin by ethanol can be explained by the presence of one or more ethanol molecules, in the vicinity of the active site carboxylates, which slightly alter the hydrogen-bonding network and which may compete with substrate binding in the active site. Structural superposition analysis showed that the N domains aligned better than the C-domains for pepsin and the fungal aspartic proteinases: 107-140 Cα pairs aligned to 0.72-0.85 Å rms for the N domains; 64-95 Cα pairs aligned to 0.78-1.03 Å rms for the C domains. The major structural difference between pepsin and the fungal enzymes concerns a newly described subdomain whose conformation varies markedly among these enzyme structures. The subdomain in pepsin comprises nearly 100 residues and is composed of two contiguous segments within the C domain (residues 192-212 and 223-299). The subdomain is connected, or “hinged,” to a mixed β-sheet that forms one of the structurally invariant, active site ψ-loops. Relative subdomain displacements as large as a 21.0° rotation and a 5.9 Å translation were observed among the different enzymes. There is some suggestion in pepsin that the subdomain may be flexible and perhaps plays a structural role in mediating substrate binding, determining the substrate specificity, or in the activation of the zymogen.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080109
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    Acid helix-turn activator motif (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 156-163 
    Details
    ISSN: 0887-3585
    Keywords: transcription activation ; secondary structure ; machine learning ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA-binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein-protein transcription activation interaction.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080205
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    Automated docking of substrates to proteins by simulated annealing (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 195-202 
    Details
    ISSN: 0887-3585
    Keywords: simulated annealing ; computer-aided drug design ; substrate docking ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080302
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  • 80
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    Bundles of amphipathic transmembrane α-helices as a structural motif for ion-conducting channel proteins: Studies on sodium channels and acetylcholine receptors (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 226-236 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; ionic pores ; neural membranes ; protein design ; energy minimization ; molecular dynamics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Channel proteins are transmembrane symmetric (or pseudosymmetric) oligomers organized around a central ionic pore. We present here a molecular model of the pore forming structures of two channel proteins with different primary structures and oligomeric size: the voltage-sensitive sodium channel and the nicotinic cholinergic receptor. We report low-energy arrangements of α-helical bundles calculated by semiempiricial potential energy functions and optimization routines and further refined using molecular dynamics. The ion-conducting pore is considered to be a symmetric or pseudosymmetric homooligomer of 3-5 amphipathic α-helices arranged such that the polar residues line a central hydrophilic pathway and the apolar residues face the hydrophobic bilayer interior. The channel lining exposes either charged (Asp, Glu, Arg, Lys) or polar-neutral (Ser, Thr) residues. A bundle of four parallel helices constrained to C4 symmetry, the helix axis aligned with the symmetry axis, and the helices constrained to idealized dihedral angles, produces a structure with a pore of the size inferred for the sodium channel protein (area ∼ 16 Å2). Similarly, a pentameric array optimized with constraints to maintain C5 symmetry and backbone torsions characteristic of α-helices adopts a structure that appears well suited to form the lining of the nicotinic cholinergic receptor (pore area ∼ 46 Å2). Thus, bundles of amphipathic α-helices satisfy the structural, energetic, and dynamic requirements to be the molecular structural motif underlying the function of ionic channels.
    Additional Material: 8 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080305
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    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080401
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  • 82
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    Preliminary crystallographic analysis of class 3 rat liver aldehyde dehydrogenase (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 305-308 
    Details
    ISSN: 0887-3585
    Keywords: aldehyde dehydrogenase ; crystals ; X-ray analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: NAD-linked aldehyde dehydrogenases (A1DH) (EC 1.2.1.3) catalyze the irreversible oxidation of a wide variety of aldehydes to their respective carboxylic acids. Crystals of a class 3 A1DH (from an Escherichia coli expression system) suitable for X-ray analysis have been obtained. These crystals, which can be grown to a size of 0.8 × 0.3 × 0.2 mm, diffract to 2.5 Å resolution. Analysis of the diffraction pattern indicates that the crystals belong to the monoclinic space group P21, with cell parameters a = 65.11 Å, b = 170.67 Å, c = 47.15 Å, and β = 110.5°. Assuming one dimer per asymmetric unit, the value Vm is calculated to be 2.45 and the solvent content of the crystal is estimated to be 50%. A self-rotation function study produced significant rotation peaks (58% of the origin) on the K = 180 section at ψ = 90° and φ = 71° and 341°, indicating that the pseudo-dimer axis is (or is very nearly) perpendicular to the b-axis.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080404
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    Plastic adaptation toward mutations in proteins: Structural comparison of thymidylate synthases (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 315-333 
    Details
    ISSN: 0887-3585
    Keywords: thymidylate synthase ; plasticity ; crystal structure ; B factor ; mutation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The structure of thymidylate synthase (TS) from Escherichia coli was solved from cubic crystals with a = 133 Å grown under reducing conditions at pH 7.0, and refined to R = 22% at 2.1 Å resolution. The structure is compared with that from Lactobacillus casei solved to R = 21% at 2.3 Å resolution. The structures are compared using a difference distance matrix, which identifies a common core of residues that retains the same relationship to one another in both species. After subtraction of the effects of a 50 amino acid insert present in Lactobacillus casei, differences in position of atoms correlate with temperature factors and with distance from the nearest substituted residue. The dependence of structural difference on thermal factor is parameterized and reflects both errors in coordinates that correlate with thermal factor, and the increased width of the energy well in which atoms of high thermal factor lie. The dependence of structural difference on distance from the nearest substitution also depends on thermal factors and shows an exponential dependence with half maximal effect at 3.0 Å from the substitution. This represents the plastic accommodation of the protein which is parameterized in terms of thermal B factor and distance from a mutational change.
    Additional Material: 16 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080406
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    Announcement (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. i 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080102
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    Energetics of the structure and chain tilting of antiparallel β-barrels in proteins (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 14-22 
    Details
    ISSN: 0887-3585
    Keywords: computation ; conformational energy ; interactions in proteins ; protein folding ; twisted β-sheets ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The preferred structural pattern of antiparallel β-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of β-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel β-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted β-barrel is favored energetically, in agreement with anti-parallel β-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of β-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel β-barrels of globular proteins. The computations indicate that a structure with Val…Gly pairs can be accommodated in a β-barrel with no distortion.
    Additional Material: 4 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080105
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    Conformational and helicoidal analysis of the molecular dynamics of proteins: “Curves,” dials and windows for a 50 psec dynamic trajectory of BPTIEditors note: The authors submitted an entire data set, and agreed to publish in this article only the first panel in each of Figures 9 through 12. The entire data set in these figures is available from David Beveridge or Richard Lavery upon request. (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 179-193 
    Details
    ISSN: 0887-3585
    Keywords: protein conformation ; helicoidal parameters ; molecular dynamics ; bovine pancreatic trypsin inhibitor ; simulation ; protein-protein interactions ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method “Curves,” developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46-60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels (“dials”) for each torsional parameter and “windows” on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2° structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein-protein interactions.
    Additional Material: 15 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080208
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    Normal mode analysis of human lysozyme: Study of the relative motion of the two domains and characterization of the harmonic motion (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 258-279 
    Details
    ISSN: 0887-3585
    Keywords: topology of atom packing ; hinge bending motion ; accessible surface area ; elastic deformation ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A normal mode analysis of human lysozyme has been carried out at room temperature. Human lysozyme is an enzyme constituted of two domains separated by an active site cleft, the motion of which is thought to be relevant for biological function. This motion has been described as a hinge bending motion. McCammon et al.1 have determined the characteristics of the hinge bending motion but they assumed a prior knowledge of the hinge axis. In this work we propose a method which is free from this assumption and determines the hinge axis and root mean square (rms) rotation angle which give the best agreement with the pattern of changes in all the distances between nonhydrogen atoms in the two domains, obtained by the normal mode analysis. The hinge axis we found is notably different from the one previously determined and goes, roughly, through the Cα 55 and Cα 76, i.e., it is located at the base of the β-sheet of the second domain. The rms value for the rotation angle is also twice as large as the previous one: 3.37°. It is shown that this hinge bending motion provides a fairly good approximation of the dynamics of human lysozyme and that the normal mode with the lowest frequency has a dominating contribution to this hinge bending motion.A study of the accessible surface area of the residues within the cleft reveals that the motion does not result in a better exposure to the solvent of these residues.A characterization of the thermally excited state (under the hypothesis of the harmonicity of the potential energy surface) has been done using the concept of topology of atom packing. Under this hypothesis the thermal fluctuations result only in a small change of the topology of atom packing, leading therefore to nearly elastic deformations of the protein.
    Additional Material: 12 Ill.
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    URL: http://dx.doi.org/10.1002/prot.340080308
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    The effect of solvent viscosity on the rate-determining step of fatty acid synthetase (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 8 (1990), S. 287-293 
    Details
    ISSN: 0887-3585
    Keywords: fatty acid synthetase ; overall activity ; viscogens ; diffusion limited intramolecular motion ; rate-determining step ; microviscosity ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The overall activity of animal fatty acid synthetase at the saturation level of substrate concentration decreased when the solvent viscosity, η, of the reaction mixture was increased with viscogens such as glycerol, sucrose, and polyethylene glycol. The activity of the enzyme changed roughly proportional to η-p, where p = 1.0 for glycerol, p = 0.66 for sucrose, and p 〈 0.6 for polyethylene glycol with different molecular sizes. The thioesterase activity, which catalyzes the final partial reaction in the multifunctional enzyme, was not affected by 5-fold increase of solvent viscosity with sucrose. These results suggested that the rate-determining step of the enzyme other than the thioesterase reaction involves a microscopic transport step, the rate of which is influenced by the solvent viscosity. The microscopic transport step may be related to the transfer of the reaction intermediate from one active site to another or to the motion of a larger part of the enzyme requisite for the catalytic reaction. In the solution containing glycerol, the rate-determining motion was primarily diffusion limited since the inverse of the initial rate was proportional to η, i.e., p = 1. Since the substrate concentration was at a saturation level in this experiment, the viscosity-dependent step cannot be the encounter between the enzyme and substrates, but must be intramolecular in origin, most probably the reaction catalyzed by β-ketoacyl synthetase. In solutions containing other viscogens, however, p was less than 1.0, indicating a significant involvement of chemical steps in the rate-determining step as well. Bovine serum albumin, when used as a proteinic viscogen, also decreased the initial rate. In the living cells therefore, the rate-determining intramolecular motion of fatty acid synthetase could be affected by the presence of high concentrations of cytoplasmic proteins.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340080310
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  • 89
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    Electronic Resource
    Latent features with maximal correlation between two equal sets of variables (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 187-189 
    Details
    ISSN: 0886-9383
    Keywords: Analysis of correlation ; Common latent features ; Trace elements in human tissues ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: If in two data tables X and Y objects are characterized by the same variables (measured at different occasions), then looking for common latent features should be more appropriate than choosing latent features in X and Y separately (e.g. as in canonical correlation or PLS). The procedure to be proposed here is a slight modification of the method of linear characteristics (according to De Groot and Li) by disclaiming the assumption of equal inner-block covariance matrices. In order to find weights defining a latent feature with maximal correlation between X and Y, a system of non-linear equations has to be solved. The procedure is applied to the investigation of heavy metal concentrations in different human tissues.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040209
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  • 90
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    PARVUS: An extendable package of programs for data exploration, classification and correlation, M. Forina, R. Leardi, C. Armanino and S. Lanteri, Elsevier, Amsterdam, 1988, Price: US $645 ISBN 0-444-43012-1 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 191-193 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040210
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  • 91
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    Electronic Resource
    Introduction to multivariate data analysis, Bruce R. Kowalski, University of Washington Instructional Media Services, Seattle, WA, 1989. Price: $195 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 194-194 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040211
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  • 92
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990) 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040301
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  • 93
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    Electronic Resource
    Diary (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. i 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040302
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  • 94
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    Multivariate calibration, H. Martens and T. Naes, Wiley, New York, 1989. ISBN 0 471 90979 3. Price: £75.00, US$138.00. No. of pages: 504 (1990)
    New York, NY : Wiley-Blackwell
    Journal of Chemometrics 4 (1990), S. 441-441 
    Details
    ISSN: 0886-9383
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cem.1180040607
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  • 95
    Electronic Resource
    Electronic Resource
    Functional interaction among catalytic residues in subtilisin BPN′ (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 335-342 
    Details
    ISSN: 0887-3585
    Keywords: serine protease ; catalytic triad ; oxyanion binding site ; site-directed mutagenesis ; protease inhibitor ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Variant of the serine protease, subtilisin BPN′, in which the catalytic triad residues (Ser-221, His-64, and Asp-32) are replaced singly or in combination by alanine retain activities with the substrate N-succinyl-L-Ala-L-Ala-L-Pro-L-Phe-p-nitroanilide (sAAPF-pna) that are at at least 103 to 104 above the non-enzymatic rate [Carter, P., Wells, J.A. Nature (London) 322:564-568, 1988]. A possible source of the residual activity was the hydrogen bond with the Nδ2 of Asn-155 that helps to stabilize the oxyanion generated in the tetrahedral transition state during amide bond hydrolysis by the wild-type enzyme. Replacing Asn-155 by Gly (N155G) lowers the turnover number (kcat) for sAAPF-pna by 150-fold with virtually no change in the Michaelis constant (KM). However, upon combining the N155G and S221A mutations to give N155G:S221A, kcat is actually 5-fold greater than for the S221A enzyme. Thus, the catalytic role of Asn-155 is dependent upon the presence of Ser-221. The residual activity of the N155G:S221A enzyme (∼104-fold above the uncatalyzed rate) is not an artifact because it can be completely inhibited by the third domain of the turkey ovomucoid inhibitor (OMTKY3), which forms a strong 1:1 complex with the active site. the mutations N155G and S221A individually weaken the interaction between subtilisin and OMTKY3 by 1.8 and 2.0 kcal/mol, respectively, and in combination by 2.1 kcal/mol. This is consistent with disruption of stabilizing interactions around the reactive site carbonyl of the OMTKY3 inhibitor. These data suggest that Ser-221 functions together with Asn-155 to accelerate amide bond hydrolysis and that other transition state stabilizing interactions account for the residual rate enhancement of 103- to 104-fold. More generally, these studies illustrate the limitations of using site-directed mutagenesis to probe the energetic importance of a single catalytic group whose function is dependent upon the interaction with others.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070405
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  • 96
    Electronic Resource
    Electronic Resource
    Masthead (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990) 
    Details
    ISSN: 0887-3585
    Keywords: Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070301
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  • 97
    Electronic Resource
    Electronic Resource
    Solution structure of a zinc finger domain of yeast ADR1 (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 215-226 
    Details
    ISSN: 0887-3585
    Keywords: zinc finger ; DNA-binding motif ; two-dimensional NMR ; synthetic peptides ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: The “zinc finger” is a 30-residue repeating motif that has been identified in a variety of eukaryotic transcription factors. Each domain is capable of binding a Zn2+ ion through invariant Cys and His residues. We have determined the three-dimensional structure of a synthetic peptide that corresponds to one of the two zinc finger domains in the yeast transcription factor ADR1, using two-dimensional nuclear magnetic resonance spectroscopy. The Zn2+ -bound structure of the peptide consists of a loop containing the two Cys residues, a “fingertip,” a 12- to 13-residue α-helix containing the two His residues, and a C-terminal tail. A majority of the interrresidue contacts observed invlove the seven conserved residues of the prototypic zinc finger (i.e., four zinc ligands and the three hydrophobic residues), indicating that these residues are largely responsible for the three-dimensional structure of the domain and that all the zinc finger domains of the TFIIIA class will have similar structures, with the highest concentration of such residues on the external face of the α-helix.
    Additional Material: 9 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070303
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  • 98
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    Electronic Resource
    Identification of protein folds: Matching hydrophobicity patterns of sequence sets with solvent accessibility patterns of known structures (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 257-264 
    Details
    ISSN: 0887-3585
    Keywords: protein families ; structure prediction ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Hydrophobic side chains often are buried in the interior of a protein, and evolutionarily related proteins usually maintain the hydrophobic character of buried position. In this paper we shown that a pattern of hydrophobicity values derived from a set of related protein sequences is well correlated with the linear pattern of side-chain solvent accessibility values, calculated from a known protein structure representative of the sequences. In several cases, information from aligned sequences can be used to select the correct tertiary fold from a large database of protein structures.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070307
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  • 99
    Electronic Resource
    Electronic Resource
    ALMA, an editor for large sequence alignments (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 291-295 
    Details
    ISSN: 0887-3585
    Keywords: full screen editor ; consensus calculation ; secondary structure ; automatic alignment ; alignment merging ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A dedicated sequence editor ALMA, was developed for aligning many sequences of proteins or RNA molecules or longer DNA fragments. Like previously published editors, ALMA is menu directed, screen oriented, and offers similarity and consensus display. ALMA has the additional features of collective movement of sequences, acceptance of input from many sources including structure files and databases, secondary structure display, and easy merging of alignments. In order to maintain sequence integrity and save disk space, gaps and sequences are stored separately. Automatic recovery of a session is possible. Finally, The program allows interaction between manual and automatic alignment.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070310
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  • 100
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    Electronic Resource
    Comparative modeling methods: Application to the family of the mammalian serine proteases (1990)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 7 (1990), S. 317-334 
    Details
    ISSN: 0887-3585
    Keywords: protein structure ; computer modeling ; structure prediction ; sequence homology ; structure homology ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Comparative modeling methods are described that can be used to construct a three-dimensional model structure of a new protein from knowledge of its sequence and of the experimental structure and sequences of other members of its homology family. The methods are illustrated with the mammalian serine protease family, for which seven experimental structures have been reported in the literature, and the sequence for over 35 different protein members of the family are available. The strategy for modeling these proteins is presented, and criteria are developed for determining and assigning the reliability of the modeled structure. Criteria are described that are specially designed to help detect cases in which it is likely that the local structure diverges significantly from the usual conformation of the family.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340070404
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