Study of hydrogen bonds in amino acids and peptides.
09 Jan 2009-International Journal of Protein Research (Int J Protein Res)-Vol. 3, Iss: 4, pp 209-231
TL;DR: An analysis of the various parameters associated with N-H… O type of hydrogen bonds has been made using data from reported crystal structures of amino acids and simple peptides, indicating that the group NH has a very strong tendency to point towards the acceptor oxygen atom.
Abstract: An analysis of the various parameters associated with N-H… O type of hydrogen bonds has been made using data from reported crystal structures of amino acids and simple peptides. The different parameters at the donor and the acceptor ends have been suitably defined and evaluated. In some cases the analysis is done depending upon the chargedness or other characteristics of the donor and acceptor groups. Histograms giving the distribution of these parameters have been drawn and possible conclusions arrived at:
1. The distribution shows a maximum between 2.8 A and 2.9 A for the charged donor group and 2.9 A and 3.0 A for the uncharged donor group and is probably not dependent upon the charge on the acceptor group.
2. The angle between the directions CO and O. N tends to lie between two cones about C O with semi-vertical angles 40 and 70°. The orientation of the directions O. N and O. H with respect to the lone pair orbital directions on the acceptor oxygen atoms are analysed in detail using spherical polar coordinates. The analysis indicates that the group NH has a very strong tendency to point towards the acceptor oxygen atom. A general feature has been found in that the direction N-H tends to be closer to an orbital if the oxygen is an acceptor of two hydrogen bonds, while the direction tends to lie in between the orbitals when the acceptor oxygen is the receipient of only one hydrogen bond. The possible explanation of this on the basis of lone pair interaction is briefly discussed.
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References
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TL;DR: This chapter considers the parameters that are required for an adequate description of a polypeptide chain and the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out.
Abstract: Publisher Summary This chapter deals with the recent developments regarding the description and nature of the conformation of proteins and polypeptides with special reference to the stereochemical aspects of the problem. This chapter considers the parameters that are required for an adequate description of a polypeptide chain. This chapter focuses the attention on what may be called “internal parameters”—that is, those which can be defined in terms of the relationships among atoms or units that form the building blocks of the polypeptide chains. This chapter also provides an account of the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference, so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out. This chapter observes conformations in amino acids, peptides, polypeptides, and proteins.
2,802 citations
TL;DR: The theory is compared with all the available crystallographic data on simple (di- and tri-) peptides, cyclic peptide, polypeptide and protein structures, and the observed data fully support the conclusions from theory.
696 citations
TL;DR: The discovery of two helical configurations of the polypeptide chain that satisfy the conditions for diffraction of x-rays in the equatorial direction are reported.
Abstract: During recent years we have been gathering information about interatomic distances, bond angles, and other properties of simple substances related to proteins, and have been attempting to formulate configurations of the polypeptide chain that are compatible with this information and that might constitute a structural feature of proteins. We have reported the discovery of two helical configurations that satisfy these conditions. (1,2) In the following paragraphs we discuss the atomic positions for these configurations, and their form factors for diffraction of x-rays in the equatorial direction.
364 citations
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