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Volumn 7, Issue 1, 1997, Pages 60-71

Protein structure: What is it possible to predict now?

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

EID: 0031052179     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80008-5     Document Type: Article
Times cited : (72)

References (113)
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    • s′ is the energy dispersion for subsequence s′ computed by a no-gap threading of s′ onto a control set of protein folds: the higher the z-score, the more probable is the alignment, and the more probable is that the native fold of the investigated sequence is similar to the given target fold.
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    • of special interest. The paper presents a description of the database containing a comprehensive classification of protein folds, superfamilies, families, etc.
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    • of outstanding interest. A critical analysis of the authors' blind protein-fold recognitions is presented which stresses that a successful fold recognition depends on the accurate definition of those parts of the fold that are, or are not, likely to be conserved in protein evolution.
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    • of special interest. The paper presents a general approach to the prediction of 3D folds of protein chains from their amino-acid sequences. It is based on the use of the SCMF theory for long-range interactions, on the use of 1D statistical mechanics for short-range interactions, and on the fact that there are only a relatively small set of 'potentially stable' folding patterns. This makes it possible to examine the whole variety of potentially stable folds and to find the thermodynamically stable structure. The paper contains a detailed presentation of a SCMF theory as applied to protein chains and (as an Appendix) the computer algorithms of 1D statistical mechanics.
    • Finkelstein AV, Reva BA. Search for the most stable folds of protein chains. I. Application of a self-consistent molecular field theory to a problem of protein three-dimensional structure prediction. of special interest Protein Eng. 9:1996;387-397 The paper presents a general approach to the prediction of 3D folds of protein chains from their amino-acid sequences. It is based on the use of the SCMF theory for long-range interactions, on the use of 1D statistical mechanics for short-range interactions, and on the fact that there are only a relatively small set of 'potentially stable' folding patterns. This makes it possible to examine the whole variety of potentially stable folds and to find the thermodynamically stable structure. The paper contains a detailed presentation of a SCMF theory as applied to protein chains and (as an Appendix) the computer algorithms of 1D statistical mechanics.
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    • Search for the most stable folds of protein chains. II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory
    • of special interest. In this paper, a general SCMF approach is applied to single out the most stable fold for the chains of different β-sandwich proteins. The choice is made from the library of 96 different idealized β-sandwich-folding patterns. The native pattern is found out of 1-3, or sometimes out of 6, patterns having the lowest free energy for this chain (however, the results are much worse for the chains that have very long loops in their native folds). Computing a detailed chain fold within its native folding pattern, one obtains a rather close (although not perfect) similarity of calculated and observed structures.
    • Reva BA, Finkelstein AV. Search for the most stable folds of protein chains. II. Computation of stable architectures of β-proteins using a self-consistent molecular field theory. of special interest Protein Eng. 9:1996;397-411 In this paper, a general SCMF approach is applied to single out the most stable fold for the chains of different β-sandwich proteins. The choice is made from the library of 96 different idealized β-sandwich-folding patterns. The native pattern is found out of 1-3, or sometimes out of 6, patterns having the lowest free energy for this chain (however, the results are much worse for the chains that have very long loops in their native folds). Computing a detailed chain fold within its native folding pattern, one obtains a rather close (although not perfect) similarity of calculated and observed structures.
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    • Reva, B.A.1    Finkelstein, A.V.2
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    • Outline structures for the extracellular domains of the fibroblast growth factor receptors
    • of special interest. The work presented is based on the 'key residues' that are identified in the known 3D structure as those primarily responsible for the structure of the central core of the protein through their packing, hydrogen-bonding or unusual conformations.
    • Bateman A, Chothia C. Outline structures for the extracellular domains of the fibroblast growth factor receptors. of special interest Nat Struct Biol. 2:1995;1068-1074 The work presented is based on the 'key residues' that are identified in the known 3D structure as those primarily responsible for the structure of the central core of the protein through their packing, hydrogen-bonding or unusual conformations.
    • (1995) Nat Struct Biol , vol.2 , pp. 1068-1074
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    • Assigning amino acid sequences to 3-dimensional protein folds
    • of outstanding interest. This is a review of the different approaches to fold recognition. The main steps are singled out: creation of a library of 'target' folds; representation of folds; alignment of the probe sequence to the target fold using the sequence-to-fold compatibility function; assessment of significance of compatibility. Various techniques used at each step are compared and the main technical problems to be solved are outlined.
    • Fisher D, Rice D, Bowie JU, Eisenberg D. Assigning amino acid sequences to 3-dimensional protein folds. of outstanding interest FASEB J. 10:1996;126-136 This is a review of the different approaches to fold recognition. The main steps are singled out: creation of a library of 'target' folds; representation of folds; alignment of the probe sequence to the target fold using the sequence-to-fold compatibility function; assessment of significance of compatibility. Various techniques used at each step are compared and the main technical problems to be solved are outlined.
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    • Potential energy functions for threading
    • of special interest. of outstanding interest. A very clearly written review of the different potential functions used for recognition of tertiary folds. The review concerns both the most simplified residue-energy functions and the sophisticated full-atom ones. The authors stress that although the pairwise interaction potentials mostly encode the residue-solvation preferences, the threading methods based on pairwise interactions work better than the profile-based (i.e. solvation) methods because accessibility is not well conserved in similar folds. Together with [87], the review underlines a parallel between experimental protein folding to a molten-globule state and fold prediction using simplified energy functions. The review ends with the phrase "In experimental folding, attaining correct sidechain packing appears to be rate-limiting step. Let's hope this is not the case for prediction". I am afraid that I believe this hope is weak.
    • of special interest Jones DT, Thornton J. Potential energy functions for threading. of outstanding interest Curr Opin Struct Biol. 6:1996;210-216 A very clearly written review of the different potential functions used for recognition of tertiary folds. The review concerns both the most simplified residue-energy functions and the sophisticated full-atom ones. The authors stress that although the pairwise interaction potentials mostly encode the residue-solvation preferences, the threading methods based on pairwise interactions work better than the profile-based (i.e. solvation) methods because accessibility is not well conserved in similar folds. Together with [87], the review underlines a parallel between experimental protein folding to a molten-globule state and fold prediction using simplified energy functions. The review ends with the phrase "In experimental folding, attaining correct sidechain packing appears to be rate-limiting step. Let's hope this is not the case for prediction". I am afraid that I believe this hope is weak.
    • (1996) Curr Opin Struct Biol , vol.6 , pp. 210-216
    • Jones, D.T.1    Thornton, J.2
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    • Prediction of protein structure by evaluation of sequence-structure fitness. Aligning sequences to contact profiles derived from three-dimensional structures.
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    • Detection of protein 3D - 1D compatibility characterised by the evaluation of side-chain packing and electrostatic interactions
    • of special interest. The central point of this interesting but rather complicated paper is an attempt to take into account the sidechain packing in protein-fold recognition, that is, to take into account not only the interresidue distance but also the orientation of sidechains.
    • Matsuo Y, Nakamura H, Nishikava K. Detection of protein 3D - 1D compatibility characterised by the evaluation of side-chain packing and electrostatic interactions. of special interest J Biochem (Tokyo). 118:1995;137-148 The central point of this interesting but rather complicated paper is an attempt to take into account the sidechain packing in protein-fold recognition, that is, to take into account not only the interresidue distance but also the orientation of sidechains.
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    • of special interest. See annotation [65].
    • Matsuo Y, Nishikava K. Assessment of protein fold recognition method that takes into account four physicochemical properties: side-chain packing, solvation, hydrogen-bonding and local conformations. of special interest Proteins. 23:1995;370-375 See annotation [65].
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    • Matsuo, Y.1    Nishikava, K.2
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    • Successful protein fold recognition by optimal sequence threading validated by rigorous blind test
    • of special interest. This paper, together with [64], analyzes the results of the authors' blind protein-structure recognitions.
    • Jones DT, Miller L, Thornton JM. Successful protein fold recognition by optimal sequence threading validated by rigorous blind test. of special interest Proteins. 23:1995;387-397 This paper, together with [64], analyzes the results of the authors' blind protein-structure recognitions.
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    • Jones, D.T.1    Miller, L.2    Thornton, J.M.3
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    • Inverse protein folding by the residue pair preference method: Estimating the correctness of alignments of structurally compatible sequences
    • of special interest. The method described in this paper combines environmental profiles with the pair-preference based profile; the latter is adjusted in the course of iterative computations. Testing shows that this method gives a 50% (on average) correct alignment when the rmsd between the native folds of target and probe chains is less than 2.
    • Wilmanns M, Eisenberg D. Inverse protein folding by the residue pair preference method: estimating the correctness of alignments of structurally compatible sequences. of special interest Protein Eng. 8:1995;627-639 The method described in this paper combines environmental profiles with the pair-preference based profile; the latter is adjusted in the course of iterative computations. Testing shows that this method gives a 50% (on average) correct alignment when the rmsd between the native folds of target and probe chains is less than 2.
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    • Evaluation of threading alignments
    • of special interest This paper describes a modification of the original 'fingerprint' approach to modelling [47]. The amino-acid environment of each point of the target fold is updated in the course of threading. The authors stress that the choice of gap insertion/deletion penalties is crucial for the quality of threading, and that this problem is yet unsolved. It is shown that sequence alignments are less accurate than threading alignments for distantly related proteins that have a sequence identity of 30% or less
    • Jaroszewski L, Godzik A. Evaluation of threading alignments. of special interest Protein Eng. 1997; This paper describes a modification of the original 'fingerprint' approach to modelling [47]. The amino-acid environment of each point of the target fold is updated in the course of threading. The authors stress that the choice of gap insertion/deletion penalties is crucial for the quality of threading, and that this problem is yet unsolved. It is shown that sequence alignments are less accurate than threading alignments for distantly related proteins that have a sequence identity of 30% or less.
    • (1997) Protein Eng
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    • Empirical protein energy maps
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    • Why do protein architectures have a Boltzmann-like statistics?
    • of special interest. A theoretical investigation of the typical statistics of the stable folds of random heteropolymers is performed to explain the basis of a Boltzmann-like form of the statistics of globular proteins. It is shown that the statistics resemble more the correlation functions observed in liquids or solids, in other words, they reflect the energy of interactions within a given element (which dominates when the internal interactions are strong), plus the interaction of this element with the environment. The 'temperature' in these statistics is the freezing temperature of the heteropolymers. The origin of these statistics is simply that the more stable is the element, the more sequences can provide stability to the folds with the element, and, as a result, the more often this element is observed in a random or quasirandom soup of sequences.
    • Finkelstein AV, Badretdinov AY, Gutin AM. Why do protein architectures have a Boltzmann-like statistics? of special interest Proteins. 23:1995;142-150 A theoretical investigation of the typical statistics of the stable folds of random heteropolymers is performed to explain the basis of a Boltzmann-like form of the statistics of globular proteins. It is shown that the statistics resemble more the correlation functions observed in liquids or solids, in other words, they reflect the energy of interactions within a given element (which dominates when the internal interactions are strong), plus the interaction of this element with the environment. The 'temperature' in these statistics is the freezing temperature of the heteropolymers. The origin of these statistics is simply that the more stable is the element, the more sequences can provide stability to the folds with the element, and, as a result, the more often this element is observed in a random or quasirandom soup of sequences.
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    • Statistical potentials extracted from protein structures: How accurate they are?
    • of special interest. The results of this paper suggest that current statistical potentials may have a limited value: an exact lattice-model test has shown that these potentials often rank in order the true relative strengths of interresidue interactions correctly, but (at least for the investigated chains composed of two sorts of residues: in such chains the many-body effects are most visible [69,110]) they do not correctly reflect the true underlying energies.
    • Thomas PD, Dill KA. Statistical potentials extracted from protein structures: how accurate they are? of special interest J Mol Biol. 257:1995;457-469 The results of this paper suggest that current statistical potentials may have a limited value: an exact lattice-model test has shown that these potentials often rank in order the true relative strengths of interresidue interactions correctly, but (at least for the investigated chains composed of two sorts of residues: in such chains the many-body effects are most visible [69,110]) they do not correctly reflect the true underlying energies.
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    • Are database-derived potentials valid for the scoring both forward and inverted protein folding?
    • of special interest. The paper shows a way to correct the database-derived potentials for the many-body effects and stresses the necessity of this correction.
    • Rooman M, Wodak S. Are database-derived potentials valid for the scoring both forward and inverted protein folding? of special interest Protein Eng. 8:1995;849-858 The paper shows a way to correct the database-derived potentials for the many-body effects and stresses the necessity of this correction.
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    • Rooman, M.1    Wodak, S.2
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    • Are proteins ideal mixtures of amino acids? Analysis of energy parameter set
    • of outstanding interest. This paper presents a very useful comparative analysis of various popular sets of mean-force two-body potentials that are based on protein structures. The authors show that the difference between these sets can be traced to the difference in a reference state used to define the zero energy. After a correction for this difference, various sets of potentials correlate at the level of 50-80%, although before the correction the correlation was much worse. In addition, the authors point to a good correlation of potentials derived from big and small proteins, and to an unexplained bad correlation between the potentials derived from crystallographic protein structures and those derived from NMR structure.
    • Godzik A, Kolinski A, Skolnick J. Are proteins ideal mixtures of amino acids? Analysis of energy parameter set. of outstanding interest Protein Sci. 4:1995;2107-2117 This paper presents a very useful comparative analysis of various popular sets of mean-force two-body potentials that are based on protein structures. The authors show that the difference between these sets can be traced to the difference in a reference state used to define the zero energy. After a correction for this difference, various sets of potentials correlate at the level of 50-80%, although before the correction the correlation was much worse. In addition, the authors point to a good correlation of potentials derived from big and small proteins, and to an unexplained bad correlation between the potentials derived from crystallographic protein structures and those derived from NMR structure.
    • (1995) Protein Sci , vol.4 , pp. 2107-2117
    • Godzik, A.1    Kolinski, A.2    Skolnick, J.3
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    • Structure-derived potentials and protein simulations
    • of special interest. A critical review of knowledge-based mean-force potentials. The review stresses that a correct determination of a 'reference state' (e.g. 'residues dissolved in water' or 'residues dissolved in a random mixture of amino acids') is critically important for successful application of the potential functions.
    • Jernigan R, Bahar I. Structure-derived potentials and protein simulations. of special interest Curr Opin Struct Biol. 6:1996;195-209 A critical review of knowledge-based mean-force potentials. The review stresses that a correct determination of a 'reference state' (e.g. 'residues dissolved in water' or 'residues dissolved in a random mixture of amino acids') is critically important for successful application of the potential functions.
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    • Self-consistently optimised statistical mechanical energy functions for sequence structure alignment
    • of outstanding interest. This paper describes an optimization of energy functions and their application to the discrimination of correctly folded protein chains from the misfolded ones. The main idea of the optimization [22] is that the optimal energy functions can be obtained by maximising the ratio of the stability gap, between the average energy of the correct fold and the mean energy of the full ensemble of misfolded structures, to the standard deviation of energies of the misfolded structures.
    • Koretke KK, Luthey-Schulten ZA, Wolynes PG. Self-consistently optimised statistical mechanical energy functions for sequence structure alignment. of outstanding interest Protein Sci. 5:1996;1043-1059 This paper describes an optimization of energy functions and their application to the discrimination of correctly folded protein chains from the misfolded ones. The main idea of the optimization [22] is that the optimal energy functions can be obtained by maximising the ratio of the stability gap, between the average energy of the correct fold and the mean energy of the full ensemble of misfolded structures, to the standard deviation of energies of the misfolded structures.
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    • A self-consistent mean-field approach to simultaneous gap closure and side-chain positioning in homology modelling
    • of outstanding interest. This paper describes a new approach which simultaneously calculates loop conformation and sidechain positioning in homology modelling. It uses a database of possible loop conformations, a rotamer sidechain library, and an iterative refinement based on the SCMF theory.
    • Koehl P, Delarue M. A self-consistent mean-field approach to simultaneous gap closure and side-chain positioning in homology modelling. of outstanding interest Nat Struct Biol. 2:1995;163-170 This paper describes a new approach which simultaneously calculates loop conformation and sidechain positioning in homology modelling. It uses a database of possible loop conformations, a rotamer sidechain library, and an iterative refinement based on the SCMF theory.
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    • Evaluation of threading specificity and accuracy
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    • Bryant SH. Evaluation of threading specificity and accuracy. of special interest Proteins. 26:1996;172-185 A threading experiment using globins shows that a sequence can recognize, as a cognate, the fold of its remote homologue only when the native fold of this sequence and the fold of the homologue have at least 60% of super-imposible analogous residue sites. Not all the pairs of globins satisfy this condition. Threading alignment is even more sensitive to structure similarity (the alignment places the majority of residues correctly only when a deviation of superimposed-residue sites is less than 2 Å).
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    • TOPITS: Threading one-dimensional predictions into three-dimensional structure
    • of special interest. AAA Press, Menlo Park, The paper describes a simplified threading approach based the on alignments of predicted (using PHD [31]) secondary structures and predicted residue accessibilities with those observed in proteins of known 3D structure
    • Rost B. TOPITS: threading one-dimensional predictions into three-dimensional structure. of special interest ISMB-95: Proceedings of the 3rd Internatal Conference on Intelligent Systems for Molecular Biology. 1995;314-320 AAA Press, Menlo Park, The paper describes a simplified threading approach based the on alignments of predicted (using PHD [31]) secondary structures and predicted residue accessibilities with those observed in proteins of known 3D structure.
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* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.