Conformation of amino-acid residues

Pullman, B., and A. Pullman. 1974. Molecular Orbital Calculations on the Conformation of Amino Acid Residues of Proteins. Adv. Protein Chem. 28, 347-526. 

Molecular Orbital Calculations on the Conformation of Amino Acid Residues of Proteins... 

Pullman B, Pullman A (1974) Molecular orbital calculations on the conformation of amino acid residues of proteins. Adv Protein Chem 28 347 - 526... 

B. Pullman I would like to make a comment about nomenclature which may avoid some misunderstandings. For the majority of people dealing with the conformation of amino acid residues of proteins, and in particularly those interested in theoretical computations, the term dipeptide (tripeptide etc.) refer to neutral species of the type... 

The use of nuclear Overhauser effects has been proposed as a useful tool in determining the conformations of amino acid residues in oligopeptides (Leach et al, 1977). NOE effects can be useful in determining the backbone angles in peptides because the Overhauser effect between an a-proton and the amide proton of the following residue depends on the dihedral angle ij/. Calibration curves have been calculated giving the % NOE as a function l/. In some cases NOE data can be used to determine side chain... 

The spatial macrostructure of the native protein (the equilibrium location of the polypeptide main chain backbone and bulky side groups) is strictly determined. Individual protein molecules having the same sequence of amino acid residues do not differ in their three-dimensional structure, which is the equilibrium one and averaged in time. The activation energy of conformational transitions may be as high as several hundreds of kilojoules per mole. Therefore, the extended fluctuations which are associated with the unfolding of the native macro structure and transitions between conformations occur rather rarely. 

All proteins begin their existence on a ribosome as a linear sequence of amino acid residues (Chapter 27). This polypeptide must fold during and following synthesis to take up its native conformation. We have seen that a native protein conformation is only marginally stable. Modest changes in the protein s environment can bring about structural changes that can affect function. We now explore the transition that occurs between the folded and unfolded states. 

As with the majority of transmembrane proteins, the hydrophobic membrane-spanning region consists mainly of amino acid residues with hydrophobic side-chains that are folded in an a-helical conformation (see Topic B3). As each amino acid residue adds 0.15 nm to the length of an a-helix, a helix of 25 residues would have a length of 3.75 nm, just enough to span the hydrophobic core of the bilayer. The hydrophobic side-chains of the residues in the helix protrude outwards from the helix axis to interact via hydrophobic bonds with... 

In medicinal chemistry we can use isolated, well-defined artificial peptides made from a few amino acid residues only, and which have a specific microstructure, to investigate the biological function of a selected peptide segment of a large protein (see also Chapter 1.2). It is, therefore, an important challenge in bioorganic chemistry to stabilize specific conformations of amino acids and small peptides to fix defined three-dimensional structures [2, 3]. 

In this chapter selected examples from our group are discussed to show how metal coordination to ligand-modified amino acids or peptides can be used for induction or fixing of defined conformations in amino acid residues or di- and tripeptides. In this context Ramachandrarfs method for conformational analysis of peptide or protein structures will be introduced. 

For compact proteins with molecular masses of greater than 10,000 and saturation of native structure by intramolecular hydrogen bonds of about 0.75 0.10 mole of bonds per mole of amino acid residues, the asymptotic values of enthalpy and entropy of the conformational transition, calculated per amino acid residue, amount to A%H(TX) = (6.25 0.2) kJ mol-1 and A 5(7 x) = (17.6 0.6) J K-1 mol-1. For some noncompact proteins (e.g., histones) or small globular proteins with molecular masses... 

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