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  • 1
    Electronic Resource
    Electronic Resource
    Amide III frequencies for Ala-X peptides depend on the X amino acid sizeThe opinions or assertions contained herein are the private ones of the authors and are not to be construed as official or reflecting the views of the U.S. Department of Defense or the Uniformed Services University of the Health Sciences. (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 593-597 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Raman spectra of series of aqueous solutions of peptides containing two amino acids, glycine-X, alanine-X, and serine-X, where X is an uncharged amino acid, show that the amide III band shifts systematically to lower frequencies as the side chain of the X amino acid becomes larger. The range of this shift is about 20cm-1, starting at 1275cm-1 for alanine-glycine and moving to 1251 cm-1 for alanine-tryptophan, with a correlation coefficient of 0.93 with the mass of the X amino acid side chain for 10 peptides. The amide I frequencies remain constant as the X amino acid is changed. This shift may result from a change in the average conformational preference of the peptide, a change in vibrational coupling of the amide III modes with the X amino acid side chain, a change in molecular force constants, or a combination of these. These results present a test for computational methods.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300511
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  • 2
    Electronic Resource
    Electronic Resource
    Conformational preference functions for predicting helices in membrane proteins (1993)
    New York : Wiley-Blackwell
    Biopolymers 33 (1993), S. 255-273 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A suite of FORTRAN programs, PREF, is described for calculating preference functions from the data base of known protein structures and for comparing smoothed profiles of sequence-dependent preferences in proteins of unknown structure. Amino acid preferences for a secondary structure are considered as functions of a sequence environment. Sequence environment of amino acid residue in a protein is defined as an average over some physical, chemical, or statistical property of its primary structure neighbors. The frequency distribution of sequence environments in the data base of soluble protein structures is approximately normal for each amino acid type of known secondary conformation. An analytical expression for the dependence of preferences on sequence environment is obtained after each frequency distribution is replaced by corresponding Gaussian function. The preference for the α-helical conformation increases for each amino acid type with the increase of sequence environment of buried solvent-accessible surface areas. We show that a set of preference functions based on buried surface area is useful for predicting folding motifs in α-class proteins and in integral membrane proteins. The prediction accuracy for helical residues is 79% for 5 integral membrane proteins and 74% for 11 α-class soluble proteins. Most residues found in transmembrane segments of membrane proteins with known α-helical structure are predicted to be indeed in the helical conformation because of very high middle helix preferences. Both extramembrane and transmembrane helices in the photosynthetic reaction center M and L subunits are correctly predicted. We point out in the discussion that our method of conformational preference functions can identify what physical properties of the amino acids are important in the formation of particular secondary structure elements. © 1993 John Wiley & Sons, Inc.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360330208
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  • 3
    Electronic Resource
    Electronic Resource
    Relation between calculated amide frequencies and solution structure in Ala-X peptidesThe opinions or assertions contained herein are the private ones of the authors and are not to be construed as official or reflecting the views of the U.S. Department of Defense or the Uniformed Services University of the Health Sciences. (1990)
    New York : Wiley-Blackwell
    Biopolymers 30 (1990), S. 599-608 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Computational techniques have been used to aid interpretation of observed systematic shifts in the amide III frequencies of Ala-X peptides. Optimized structures and frequencies have been calculated for Ala-X peptides using GAUSSIAN86/88 with the 4-31G basis, MOPAC, and normal mode methods based on empirical force fields. We observe the following: (1) Frequencies calculated using scaled GAUSSIAN86 force constants correlate well with the experimental results. (2) Structures of the Ala-X peptides optimized by GAUSSIAN show a clear trend toward lower values of the dihedral angle φ as the X side chain becomes larger, while structures optimized here using semiempirical and empirical force fields do not show trends. (3) Computational changes in peptide conformations from β-sheet to α-helix produce large changes in both amide I and amide III frequencies that are inconsistent with the experimental results. (4) Computational changes in the dihedral angle φ of Ala-Ala produce a change in the amide III frequency consistent with the experimental results. (5) The experimental frequency shifts cannot be attributed directly to the effects of changing mass.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360300512
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  • 4
    Electronic Resource
    Electronic Resource
    Effects of hydration on scale factors for ab initio force constants. IV. trans and cis N-methylacetamideThe opinions or assertions contained herein are the private ones of the authors, and are not to be construed as official or reflecting the views of the U.S. Department of Defense or The Uniformed Services University of the Health Sciences. (1992)
    New York : Wiley-Blackwell
    Biopolymers 32 (1992), S. 829-847 
    Details
    ISSN: 0006-3525
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Scaled quantum mechanical force fields have been calculated using the 4-31G basis for trans and cis conformers of both isolated and water-solvated N-methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between the trans and cis conformers. This is also true of a single set of scale factors for trans and cis NMA in water. The total standard deviation between measured and calculated frequencies for trans NMA in both isolated and solvated states is 6 cm-1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA · nH2O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water-solvated or otherwise hydrogen-bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen-bonded to water, using frequencies measured from water-solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen-bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be generally transferable.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bip.360320711
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