Theory of protein secondary structure and algorithm of its prediction
BiopolymersPublished 1 January 1983
Oleg B. Ptitsyn, Alexei V. Finkelstein
Citations238
SJR quartileQ2
SJR score0.55
SNIP0.57
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long‐range interactions between different regions, incorporating all these interactions in a single Ising‐like model.
Abstract
Abstract A molecular theory of protein secondary structure is presented that takes account of both local interactions inside each chain region and long‐range interactions between different regions, incorporating all these interactions in a single Ising‐like model. Local interactions are evaluated from the stereochemical theory describing the relative stabilities of α‐ and β‐structures for different residues in synthetic polypeptides, while long‐range effects are approximated by the interaction of each chain region with the averaged hydrophobic template. Based on this theory, an algorithm of protein secondary structure prediction is proposed and examples are given of “blind” predictions made before the x‐ray structural data became available.
Keywords
Materials ScienceBiochemistry, Genetics and Molecular Biology
Biochimica et Biophysica Acta (BBA) - Protein StructureComparison of the predicted and observed secondary structure of T4 phage lysozyme
5,357 Citations1975Brian W. Matthews
Although empirical predictions based on larger numbers of known protein structure tend to be more accurate than those based on a limited sample, the improvement in accuracy is not dramatic, suggesting that the accuracy of current empirical predictive methods will not be substantially increased simply by the inclusion of more data from additional protein structure determinations.
Advances in protein chemistryThe Anatomy and Taxonomy of Protein Structure
3,389 Citations1981Jane S. Richardson
This chapter investigates the anatomy and taxonomy of protein structures, based on the results of three-dimensional X-ray crystallography of globular proteins.
BiochemistryConformational parameters for amino acids in helical, β-sheet, and random coil regions calculated from proteins
2,176 Citations1974Peter Y. Chou, Gerald D. Fasman
The helix, s Applequist, 1963) in which the Zimm-Bragg parameters u and s are defined respectively as the cooperativity factor for helix initiation, and the equi- librium constant for converting a coil residue to a helical helix.
The Journal of Chemical PhysicsTheory of the Phase Transition between Helix and Random Coil in Polypeptide Chains
1,788 Citations1959B Zimm, J. K. Bragg
NatureStructural patterns in globular proteins
1,282 Citations1976Michael Levitt, Cyrus Chothia
A simple diagrammatic representation has been used to show the arrangement of α helices and β sheets in 31 globular proteins, which are classified into four clearly separated classes.
Biophysical JournalUse of Helical Wheels to Represent the Structures of Proteins and to Identify Segments with Helical Potential
1,182 Citations1967M. Schiffer, Allen B. Edmundson
The three-dimensional structures of alpha-helices can be represented by two-dimensional projections which the authors call helical wheels, and these wheels can be used to divide sequences into segments with either helical or nonhelical potential.
NatureHydrophobic bonding and accessible surface area in proteins
887 Citations1974Cyrus Chothia
The hydrophobic bond is the term used by Kauzmann to describe the gain in free energy on the transfer of non-polar residues from an aqueous environment to the interior of proteins.
Journal of Molecular BiologyAlgorithms for prediction of α-helical and β-structural regions in globular proteins
466 Citations1974Vanessa Lim
Algorithms are suggested for identifying α-helical and β-structural regions in native globular proteins with accuracy of ~80 and ~85% respectively for 25 proteins, the three-dimensional structures of which have been determined by X-ray diffraction crystallography.
Journal of Molecular BiologyStructural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure
351 Citations1974Vanessa Lim
An a priori theory is developed which permits the identification, in good agreement with experiment, of α-helical and β-structural regions in globular proteins from their primary structure.
Quarterly Reviews of BiophysicsSimilarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?
194 Citations1980Oleg B. Ptitsyn, Alexei V. Finkelstein
The three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded in 1960 and the decoding of the subsequent proteins, lysozyme, ribonuclease, chymotrypsin and other serine proteases redoubled the feeling of amazement and even of some confusion.
NatureComparison of predicted and experimentally determined secondary structure of adenyl kinase
174 Citations1974Georg E. Schulz, C. D. Barry +11 more
The aim of this paper is to demonstrate directly the current standing of prediction schemes for the prediction of secondary structures in globular proteins from amino acid sequences, and to suggest new approaches to structure elucidation.
Journal of Molecular BiologyTyrosyl-tRNA synthetase forms a mononucleotide-binding fold
152 Citations1982Talapady N. Bhat, D. M. Blow +2 more
The crystal structure of Tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been re-interpreted using a new density-modification technique and reveals two new α-helices in the α β domain, and some changes in chain connections.
Journal of Molecular BiologyX-ray crystallographic analysis of a progesterone-binding protein. The C2221 crystal form of oxidized uteroglobin at 2.2 Å resolution
83 Citations1980Jean‐Paul Mornon, F. Fridlansky +2 more
Oxidized uteroglobin, in the C 222 1 crystal form, has been analyzed by X-ray diffraction and the observed structure is in agreement with one of the amino acid sequence determinations previously described.
Journal of Molecular BiologyA theory of protein molecule self-organization
74 Citations1976Alexei V. Finkelstein, Oleg B. Ptitsyn
A conclusion has been drawn that λ-helices can initiate self-organization of the tertiary structure serving as blocks for its assembling while the irregular local structures cannot initiate protein folding.
BiopolymersPotentiometric titration of poly‐<scp>L</scp>‐lysine: the coil‐to‐β transition
60 Citations1971Dennis Pederson, Don A. Gabriel +1 more
MacromoleculesHelix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. I. Properties of Copolymers and Approximate Theories
51 Citations1971P. H. Von Dreele, Douglas Poland +1 more
BiopolymersTheory of protein molecule self‐organization. II. A comparison of calculated thermodynamic parameters of local secondary structures with experiments
48 Citations1977Alexei V. Finkelstein, Oleg B. Ptitsyn +1 more
A direct correlation is demonstrated between theoretical parameters of residue incorporation into α‐helical termini and β‐bends in an unfolded polypeptide chain and the occurrence of residues in corresponding positions of the globular protein secondary structures.
BiopolymersThe β conformation of polypeptides of valine, isoleucine, and threonine in solution and solid‐state: Optical and infrared studies
46 Citations1975Shigeo Kubota, Gerald D. Fasman
The optical properties of these valyl and isoleucyl polypeptides were quite different from those of previously reported synthetic homopolypeptide in the β structure, and could be explained by the presence of a “single extended β chain” without either intra‐ or interchain association.
Pure and Applied ChemistryThermodynamic parameters of helix-coil transitions in polypeptide chains
42 Citations1972Oleg B. Ptitsyn
New possibilities of more detailed thermodynamic analysis of helix-coil transition parameters, particularly with respect to their splitting into energy and entropy terms are outlined.
BiopolymersTheory of protein molecule self‐organization. I. Thermodynamic parameters of local secondary structures in the unfolded protein chain
38 Citations1977Alexei V. Finkelstein, Oleg B. Ptitsyn
The results of a stereochemical analysis of local interactions in unfolded protein chains (sterical repulsions, hydrogen, and hydrophobic bonds, etc.) by means of space‐filling modeles are presented.
BiopolymersTheory of protein molecule self‐organization. III. A calculating method for the probabilities of the secondary structure formation in an unfolded polypeptide chain
27 Citations1977Alexei V. Finkelstein
A mathematical model is developed adequately describing an unfolded polypeptide chain without long‐range interactions in which fluctuating hydrogen‐bonded α‐helices, β‐bends, fragments of helices 310, and other local structures are formed.
International Journal of Quantum ChemistryMechanism of protein folding
24 Citations1979Oleg B. Ptitsyn, Alexei V. Finkelstein
MacromoleculesHelix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 17. Threonine Parameters from Random Poly(hydroxylbutylglutamine-co-L-threonine)
19 Citations1978Michael H. Hecht, B. O. Zweifel +1 more
Principles of Protein Folding
14 Citations2013Ali Bandehagh, Pouya Motie Noparvar +1 more
The main objective of this review is to unveil the fact; despite there are many factors controlling protein folding, mainspring is amino acids sequence which itself rises from chemo-physical laws.
MacromoleculesHelix-coil stability constants for the naturally occurring amino acids in water. 19. Isoleucine parameters from random poly[(hydroxypropyl)glutamine-co-L-isoleucine]
14 Citations1981R. A. Fredrickson, Mu‐Chieh Chang +2 more
MacromoleculesHelix-Coil Stability Constants for the Naturally Occurring Amino Acids in Water. 18. Tryptophan Parameters from Random Poly[(hydroxypropyl)glutamine-co-L-tryptophan]
14 Citations1980Julianna Nagy, Stephen Powers +2 more