Conformations polypeptides

The reverse turn as a polypeptide conformation in globular proteins. Proc. Natl. Acad. Sci. USA 70 538-542, 1973. 

Kleier, D. A., and W. N. Lipscomb. 1977. Molecular Orbital Study of Polypeptides. Conformational and Electronic Structure of Polyglycine. Int. J. Quantum Chem. Quantum Biol. Symp. 4, 73-86. 

Lewis, P. N., F. A. Momany, and H. A. Scheraga. 1973a. Energy Parameters For Polypeptides Conformational Energy Analysis Of The N-Acetyl N -Methyl Amides of The Twenty Naturally Occurring Amino Acids. Isr. J. Chem. 11, 121-152. 

Two moles of MgATP bind to the reduced Fe-protein containing the [4Fe-4S] cluster in the 1+ oxidation state as [Fe4S4]+. During this step, Fe-protein polypeptide conformation changes take place, altering the electronic properties of the [4Fe lS] cluster. 

Hill, E., Tsernoglou, D., Webb, L., Banaszak, L. Polypeptide conformation of cytoplasmic malate dehydrogenase from an electron density map at 3.0 A resolution. J. Mol. Biol. 72, 577-591 (1972). 

In one case, a small peptide with enzyme-like capability has been claimed. On the basis of model building and conformation studies, the peptide Glu-Phe-Ala-Ala-Glu-Glu-Phe-Ala-Ser-Phe was synthesized in the hope that the carboxyl groups in the center of the model would act like the carboxyl groups in lysozyme 17). The kinetic data in this article come from assays of cell wall lysis of M. lysodeikticus, chitin hydrolysis, and dextran hydrolysis. All of these assays are turbidimetric. Although details of the assay procedures were not given, the final equilibrium positions are apparently different for the reaction catalyzed by lysozyme and the reaction catalyzed by the decapeptide. Similar peptide models for proteases were made on the basis of empirical rules for predicting polypeptide conformations. These materials had no amidase activity and esterase activity only slightly better than that of histidine 59, 60). 

Chapter B outlines a typical statistical-mechanical formulation of polypeptide conformations in terms of these three parameters and describes its use for the evaluation of s and tr from observed helix-coil transition curves. Then the reported values of AH and a for selected polypeptide-solvent pairs are given and their implications are briefly discussed from a molecular standpoint. Here AH denotes the transition enthalpy derived from s by a thermodynamic relation. 

Wada 109, 110) pioneered studies of polypeptide conformation by the dielectric method. He found 110) a linear dependence of (ft2)1 2 on Mw for a series of PBLG samples (ranging from 7 x 104 to 18 x 104 in Mw) in EDC at 25° C and obtained 3.5 D for gh, where D stands for debye units. He computed (ft2) by the use of an approximate equation derived by himself 109) for rigid-rod molecules, which for very dilute solutions may be written... 

Table 1.2 Torsion angles for regular polypeptide conformations...

It is worthwhile to begin the discussion by first stating the conventions adopted for the description of polypeptide conformation. These conventions (Edsall et ah, 1966) were discussed at the 1965 Gordon Conference on Proteins some additional nomenclature was suggested at a workshop on protein conformation in Madras in January 1967. The whole subject is, at present, under consideration by the IUPAC-IUB Commission on Biochemical Nomenclature. 

Computations of polypeptide conformation must be based on accurate values of bond distances and bond angles. From a survey of the literature, it appears that, whereas these parameters may vary from compound to compound, there is a general consensus of accepted values these are listed in Tables 5-11. 

While early calculations of polypeptide conformation were carried out with very simplifying assumptions about the internal energies, it seems preferable to present here the present status of the attempts to obtain as reliable a set of energy functions as possible. In later sections we will present results obtained both with the simplified and with the more complete expressions for the energy. 

Jahn, T.R., and Radford, S.E. "Folding versus aggregation polypeptide conformation on competing pathways". Arch. Biochem. Biophys. 469, 100-117 (2008). 

In the sections to follow we show that hydrogen bonds are the primary type of bonds that stabilize helical and extended polypeptide conformations. 

Pauling L, Corey RB. The polypeptide conformation in hemoglobin and other globular proteins, Proc Natl Acad Sci. 1951 37 282. 

Scheiner S, Kar T (2007) Underlying source of the relation between polypeptide conformation and strength of NH--0 hydrogen bonds. J Mol Struct 844-845 166-172... 

A. Anderson, M. Carson, and J. Hermans, Ann. N.Y. Acad. Sci., 482,51 (1986). Molecular Dynamics Simulation Study of Polypeptide Conformational Equilibria A Progress Report. 

H. Meirovitch, M. Vasquez and H. A. Scheraga, Biopolymers, 26, 651 (1987). Stability of Polypeptide Conformational States as Determined by Computer Simulation of the Free Energy. 

H. A. Scheraga, Harvey Lectures, 63, 99 (1969). Calculation of Polypeptide Conformation. 

Y. Paterson, S. M. Rumsey, E. Benedetti, G. Nemethy, and H. A. Scheraga, J. Am. Chem. Soc., 103, 2947 (1981). Sensitivity of Polypeptide Conformation to Geometry. Theoretical Conformational Analysis of Oligomers of a-Aminoisobutyric Acid. 

W. Braun, C. Bosch, L. R. Brown. N. Go, and K. Wiithrich, Biochim. Biophys. Acta, 667, 377 (1981). Combined Use of Proton-Proton Overhauser Enhancements and a Distance Geometry Algorithm for Determination of Polypeptide Conformations. 

A. DiNola, H. J. C. Berendsen, and O. Edholm, Macromolecules, 17, 2044 (1984). Free Energy Determination of Polypeptide Conformations Generated by Molecular Dynamics. 

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