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  • 1995-1999  (14)
  • 1900-1904
  • Biochemistry and Biotechnology  (11)
  • Tyr(P)-containing peptides  (3)
  • 1
    Electronic Resource
    Electronic Resource
    Reaction path and free energy calculations of the transition between alternate conformations of HIV-1 proteaseThe content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products, or organization imply endorsement by the U.S. Government. (1998)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 32 (1998), S. 7-16 
    Details
    ISSN: 0887-3585
    Keywords: conformational change ; free energy calculations ; HIV protease ; molecular dynamics simulations ; protein structure ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: Two different structures of ligand-free HIV protease have been determined by X-ray crystallography. These structures differ in the position of two 12 residue, β-hairpin regions (or “flaps”) which cap the active site. The movements of the flaps must be involved in the binding of substrates since, in either conformation, the flaps block the binding site. One of these structures is similar to structures of the ligand-bound enzyme; however, the importance of both structures to enzyme function is unclear. This transformation takes place on a time scale too long for conventional molecular dynamics simulations, so the process was studied by first identifying a reaction path between the two structures and then calculating the free energy along this path using umbrella sampling. For the ligand-free enzyme, it is found that the two structures are nearly equally stable, with the ligand-bound-type structure being less stable, consistent with X-ray crystallography data. The more stable open structure does not have a lower potential energy, but is stabilized by entropy. The transition occurs through a collapse and reformation of the β-sheet structure of the conformationally flexible, glycine-rich flap ends. Additionally, some problems in studying conformational changes in proteins through the use of a single reaction path are addressed. Proteins 32:7-16, 1998. © 1998 Wiley-Liss, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 2
    Electronic Resource
    Electronic Resource
    Synthesis of phosphopeptides by the multipin method: Evaluation of coupling methods for the incorporation of Fmoc-Tyr(PO3Bzl,H)-OH, Fmoc-Ser(PO3Bzl,H)-OH and Fmoc-Thr(PO3Bzl,H)-OH (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 91-97 
    Details
    ISSN: 1573-3904
    Keywords: Multipin multiple peptide synthesis ; phosphopeptides ; Tyr(P)-containing peptides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The efficiency of various coupling methods for the incorporation of the three monobenzyl phosphorodiesterprotected derivatives, Fmoc-Tyr(PO3Bzl,H)-OH, Fmoc-Ser(PO3Bzl,H)-OH and Fmoc-Thr(PO3Bzl,H)-OH, was examined through the test synthesis of Ala-Ser-Gln-Gly-Xxx(PO3H2)-Leu-Glu-Asp-Pro-Ala-NH2 (Xxx=Tyr, Ser, Thr) using the Multipin method of multiple peptide synthesis. The coupling methods examined were (1) PyBrop/DIEA; (2) BOP/HOBt/NMM; (3) BOP/HOBt/DIEA; (4) HBTU/HOBt/DIEA; (5) HATU/HOAt/DIEA; (6) HATU/DIEA; (7) DIC/HOBt; (8) DIC/HOBt/DIEA; (9)DIC/HOAt; (10) DIC/HOAt/DIEA. While all four DIC-based coupling procedures resulted in incomplete incorporation, both the HBTU/HOBt/DIEA and HATU/HOAt/DIEA coupling procedures provided most efficient incorporation of the three Fmoc-Xxx (PO3Bzl,H)-OH derivatives. In the subsequent synthesis of the α-helical Tyr(P)-peptide, Glu-Thr-Gly-The-Lys-Ala-Glu-Leu-Leu-Ala-Lys-Tyr(PO3H2)-Glu-Ala-Thr-His-Lys-NH2, analysis of the crude peptide by electrospray MS confirmed that several residue deletions had occurred but that complete incorporation of the Tyr(P)-residue had been accomplished using HBTU/HOBt/DIEA coupling of Fmoc-Tyr(PO3Bzl,H)-OH.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02443622
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  • 3
    Electronic Resource
    Electronic Resource
    Synthesis of phosphopeptides by the Multipinast method: Evaluation of coupling methods for the incorporation of Fmoc- Tyr(PO3Bzl,H)-OH, Fmoc- Ser(PO3Bzl,H)-OH and Fmoc- Thr(PO3Bzl,H)-OH (1999)
    Springer
    International journal of peptide research and therapeutics 6 (1999), S. 91-97 
    Details
    ISSN: 1573-3904
    Keywords: Multipin multiple peptide synthesis ; phosphopeptides ; Tyr(P)-containing peptides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract astMultipin is a trademark of Chiron Technologies Pty. Ltd., Clayton, Victoria, Australia. The efficiency of various coupling methods for the incorporation of the three monobenzyl phosphorodiester-protected derivatives, Fmoc- Tyr(PO3Bzl,H)-OH, Fmoc-Ser(PO3Bzl,H)-OH and Fmoc-Thr(PO3Bzl,H)-OH, was examined through the test synthesis of Ala-Ser-Gln-Gly-Xxx(PO3H2)-Leu- Glu-Asp-Pro-Ala-NH2 (Xxx = Tyr, Ser, Thr) using the Multipin method of multiple peptide synthesis. The coupling methods examined were (1) PyBrop/DIEA; (2) BOP/HOBt/NMM; (3) BOP/HOBt/DIEA; (4) HBTU/HOBt/DIEA; (5) HATU/HOAt/DIEA; (6) HATU/DIEA; (7) DIC/HOBt; (8) DIC/HOBt/DIEA; (9) DIC/HOAt; (10) DIC/HOAt/DIEA. While all four DIC-based coupling procedures resulted in incomplete incorporation, both the HBTU/HOBt/DIEA and HATU/HOAt/DIEA coupling procedures provided most efficient incorporation of the three Fmoc- Xxx(PO3Bzl,H)-OH derivatives. In the subsequent synthesis of the α-helical Tyr(P)-peptide, Glu-Thr-Gly-The-Lys- Ala-Glu-Leu-Leu-Ala-Lys-Tyr(PO3H2)-Glu-Ala-Thr- His-Lys-NH2, analysis of the crude peptide by electrospray MS confirmed that several residue deletions had occurred but that complete incorporation of the Tyr(P)-residue had been accomplished using HBTU/HOBt/DIEA coupling of Fmoc- Tyr(PO3Bzl,H)-OH.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1008823924135
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  • 4
    Electronic Resource
    Electronic Resource
    Synthesis of Tyr(P)-containing peptides via ‘on-line’ phosphorylation of the tyrosine residue on the solid phase (1996)
    Springer
    International journal of peptide research and therapeutics 3 (1996), S. 127-132 
    Details
    ISSN: 1573-3904
    Keywords: Di-t-butylN,N-diethylphosphoramidite ; Fmoc/solid-phase synthesis ; ‘On-line’ phosphorylation ; Phosphopeptide synthesis ; Tyr(P)-containing peptides
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A novel method for the efficient synthesis of Tyr(P)-containing peptides is described by the ‘phosphite-triester’ phosphorylation of the tyrosine residue after its incorporation into the peptide chain. In this approach, the peptide resin is assembled by Fmoc solid-phase peptide synthesis (PyBOP® couplings) with the tyrosine residue incorporated as Fmoc-Tyr-OH. The N-terminal tyrosine peptide resin is then phosphorylated with di-t-butylN,N-diethylphosphoramidite/1H-tetrazole and the intermediate di-t-butyl phosphite triester is oxidised by treatment withm-chloroperoxybenzoic acid. Peptide synthesis is then continued under usual conditions and the peptide resin is deprotected by acidolytic treatment. The improved efficiency of the ‘on-line’ phosphorylation approach is demonstrated through the syntheses of IVPNY(P)VEE and the Fcγ receptor peptide, EAENTITY(P)SLLKHPEAL, in both good yield and purity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00132975
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  • 5
    Electronic Resource
    Electronic Resource
    Effect of surfactant and particle size reduction on hydrolysis of deinking sludge and nonrecyclable newsprint (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 45 (1995), S. 239-244 
    Details
    ISSN: 0006-3592
    Keywords: cellulase ; newsprint ; deinking sludge ; surfactant ; hydrolysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Disposal of sludge from deinking mills represents a significant proportion of operating costs. Bioconversion of the cellulosic fraction of deinking sludge (DIS) to ethanol greatly reduces disposal costs while producing an environmentally friendly fuel. In this study, the cellulosic fraction of newsprint and deinking sludge was hydrolysed to produce fermentable sugars. For newsprint, a particle size of 1 to 1.5 mm provided optimal reaction rates in batch reactors over practical hydrolysis times, and reducing sugar concentrations as high as 35 g/L could be achieved using a fed-batch reactor configuration. For both newsprint and DIS, the hydrolysis rate increased nonlinearly with enzyme loading. Tween-80 only marginally improved sugar production but was able to release sugars from cellulosic substrates in the absence of lytic enzymes, in an amount proportional to the surfactant concentration and the substrate particle size. DIS was relatively recalcitrant to enzymatic hydrolysis, possibly due in part to inhibition by hydrophobic constituents. © 1995 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bit.260450308
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  • 6
    Electronic Resource
    Electronic Resource
    Simultaneous saccharification and extractive fermentation of cellulosic substrates (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 49 (1996), S. 504-511 
    Details
    ISSN: 0006-3592
    Keywords: cellulose ; cellulase ; simultaneous saccharification and extractive fermentation ; ethanol ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Alcohol fermentation has traditionally been carried out in aqueous environments because of the ready solubility of reactant (sugar) and product (ethanol). However, extraction of the product ethanol into a nonmiscible phase can result in kinetic benefits due to reduced inhibition of the fermentation reactions. In this study, we report the development of a novel simultaneous saccharification and extractive fermentation (SSEF) process. Ethanol productivity was increased by up to 65% over conventional (nonextractive) fed-batch simultaneous saccharification systems when calculated on the basis of aqueous phase volume. The amount of water required for SSEF reactions was dramatically reduced from that required for conventional SSF. In batch SSEF reactors with 2.5% aqueous phase, 50% conversion of 25% (aqueous phase concentration) Solka Floc could be achieved in 48 h using 2 FPU/g cellulase. © 1996 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Mathematical model for characterization of bacterial migration through sand cores (1997)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 53 (1997), S. 487-496 
    Details
    ISSN: 0006-3592
    Keywords: bacterial chemotaxis ; Escherichia coli ; random motility ; mathematical model ; sand core ; porous media ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: The migration of chemotactic bacteria in liquid media has previously been characterized in terms of two fundamental transport coefficients - the random motility coefficient and the chemotactic sensitivity coefficient. For modeling migration in porous media, we have shown that these coefficients which appear in macroscopic balance equations can be replaced by effective values that reflect the impact of the porous media on the swimming behavior of individual bacteria. Explicit relationships between values of the coefficients in porous and liquid media were derived. This type of quantitative analysis of bacterial migration is necessary for predicting bacterial population distributions in subsurface environments for applications such as in situ bioremediation in which bacteria respond chemotactically to the pollutants that they degrade.We analyzed bacterial penetration times through sand columns from two different experimental studies reported in the literature within the context of our mathematical model to evaluate the effective transport coefficients. Our results indicated that the presence of the porous medium reduced the random motility of the bacterial population by a factor comparable to the theoretical prediction. We were unable to determine the effect of the porous medium on the chemotactic sensitivity coefficient because no chemotactic response was observed in the experimental studies. However, the mathematical model was instrumental in developing a plausible explanation for why no chemotactic response was observed. The chemical gradients may have been too shallow over most of the sand core to elicit a measurable response. © 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 53: 487-496, 1997.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Patents in combi-space: Patent challenges in combinatorial chemistry (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 61 (1998), S. 69-75 
    Details
    ISSN: 0006-3592
    Keywords: combinatorial chemistry ; library ; array ; patent ; utility ; description requirement ; piracy ; algorithm ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Patent protection of inventions relating to combinatorial chemistry is attended by special challenges. The “breakthrough” nature of the field together with the always complex and often arcane chemical manipulations, apparatus, and strategies which suffuse this field make it difficult to describe the inventions adequately. It can be a challenge to communicate effectively with official authorities charged with patent examination. Extraordinary effort is called for in clarifying such inventions such that their patentability can be appreciated. The utility of some types of inventions in this field may be open to question; clear statements of at least one acceptable utility - even if only a minor utility - is beneficial. Because a principal product of many aspects of combinatorial chemistry is information, e.g., the identification of a lead compound, offshore “piracy” is a risk. Domestic claim tie-ins may improve the ability to abate such piracy. © 1998 John Wiley & Sons, Inc. Biotechnol Bioeng (Comb Chem) 61:69-75, 1998.
    Additional Material: 1 Tab.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Microbial removal of alkanes from dilute gaseous waste streams: Mathematical modeling of advanced bioreactor systems (1998)
    Chichester : Wiley-Blackwell
    Journal of Chemical Technology AND Biotechnology 72 (1998), S. 93-98 
    Details
    ISSN: 0268-2575
    Keywords: VOC ; biodegradation ; alkanes ; trickle-bed ; mass transfer ; kinetics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Process Engineering, Biotechnology, Nutrition Technology
    Notes: Many industries generate volatile organic compounds (VOCs) in dilute streams which must be removed before being released into the environment. Mathematical models for biological filters which can remediate waste streams are useful both as predictive tools and as a means to better understand the fundamental processes involved. Optimization of the system also necessitates a better understanding of the mechanisms by which biofilters work and can be approached through modeling and maximizing appropriate conditions for removal. In a trickle-bed bioreactor, VOCs (n-pentane and isobutane) were passed over a biofilm-coated packing which degraded the VOCs. Bacterial growth was controlled via liquid nutrient-limited media trickled through the reactor. Results from this trickle-bed system were analyzed by applying a simple mathematical model to accurately describe the processes which are believed to play important roles. The model was based on a two-step process: mass transfer in which the VOCs diffuse into the liquid biofilm, and kinetics by which VOCs are degraded by the biofilm. Modeling results revealed that both kinetic and mass transfer resistances were significant under typical operating conditions.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Development of separation systems for polynuclear aromatic hydrocarbon environmental contaminants using micellar electrokinetic chromatography with molecular micelles and free zone electrophoresis (1998)
    Weinheim : Wiley-Blackwell
    Electrophoresis 19 (1998), S. 2090-2094 
    Details
    ISSN: 0173-0835
    Keywords: Capillary electrophoresis ; Polynuclear aromatic hydrocarbons ; Laser-induced fluorescence ; Molecular micelles ; Environmental analysis ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Of four systems available from the literature, based on cyclodextrins, dioctyl-sulfosuccinate, bile salts, and molecular micelles consisting of oligomers of undecylenic acid, the most successful separation system in our hands is based on the molecular micelles, oligomers of sodium undecylenic acid (OSUA). We have employed organic additives of acetonitrile, acetone, and tetrahydrofuran in achieving separations of polyaromatic hydrocarbons (PNAs) using molecular micelles. Generally, successful separations are achieved with 20-40% composition as the organic additive in an 8 mM borate buffer. We separated 16 PNAs with 20% tetrahydrofuran in a system of 8 mM borate and 0.125 g/ 10 mL (ca. 6.25 mM) of OSUA. Typical extracts of environmental samples contain additional analytes besides the typical 16 target compounds. Among these are the nitrogen-containing aromatics that can act as cations under conditions of low pH and additional compounds that can act as anions under basic conditions in free-zone electrophoresis. These additional classes of analytes are separated by capillary zone electrophoresis/laser-induced fluorescence detection using a frequency-doubled laser operated at 257 nm.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/elps.1150191208
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