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Chen H, Chen X, Chen X, Lin S, Cheng J, You L, Xiong C, Cai X, Wang S. New perspectives on fabrication of peptide-based nanomaterials in food industry: A review. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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2
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Naassaoui I, Aschi A. Evaluation of Properties and Structural Transitions of Poly-L-lysine: Effects of pH and Temperature. J MACROMOL SCI B 2019. [DOI: 10.1080/00222348.2019.1638593] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Imen Naassaoui
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR99ES16, Laboratoire Physique de la Matière Molle et de la Modélisation Électromagnétique, Tunis, Tunisia
| | - Adel Aschi
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR99ES16, Laboratoire Physique de la Matière Molle et de la Modélisation Électromagnétique, Tunis, Tunisia
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3
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Balasco N, Smaldone G, Vigorita M, Del Vecchio P, Graziano G, Ruggiero A, Vitagliano L. The characterization of Thermotoga maritima Arginine Binding Protein variants demonstrates that minimal local strains have an important impact on protein stability. Sci Rep 2019; 9:6617. [PMID: 31036855 PMCID: PMC6488590 DOI: 10.1038/s41598-019-43157-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
The Ramachandran plot is a versatile and valuable tool that provides fundamental information for protein structure determination, prediction, and validation. The structural/thermodynamic effects produced by forcing a residue to adopt a conformation predicted to be forbidden were here explored using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model. Specifically, we mutated TmArgBP Gly52 that assumes a conformation believed to be strictly disallowed for non-Gly residues. Surprisingly, the crystallographic characterization of Gly52Ala TmArgBP indicates that the structural context forces the residue to adopt a non-canonical conformation never observed in any of the high-medium resolution PDB structures. Interestingly, the inspection of this high resolution structure demonstrates that only minor alterations occur. Nevertheless, experiments indicate that Gly52 replacements in TmArgBP produce destabilizations comparable to those observed upon protein truncation or dissection in domains. Notably, we show that force-fields commonly used in computational biology do not reproduce this non-canonical state. Using TmArgBP as model system we here demonstrate that the structural context may force residues to adopt conformations believed to be strictly forbidden and that barely detectable alterations produce major destabilizations. Present findings highlight the role of subtle strains in governing protein stability. A full understanding of these phenomena is essential for an exhaustive comprehension of the factors regulating protein structures.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, Italy
| | | | - Marilisa Vigorita
- Department of Science and Technology, University of Sannio, via Port'Arsa 11, Benevento, Italy
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia, Napoli, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Port'Arsa 11, Benevento, Italy
| | - Alessia Ruggiero
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, Napoli, Italy.
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4
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Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? J Comput Aided Mol Des 2018; 33:133-203. [DOI: 10.1007/s10822-018-0111-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 10/27/2022]
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5
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Sung SS. Peptide folding driven by Van der Waals interactions. Protein Sci 2015; 24:1383-8. [PMID: 26013298 DOI: 10.1002/pro.2710] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Revised: 05/08/2015] [Accepted: 05/13/2015] [Indexed: 11/09/2022]
Abstract
Contrary to the widespread view that hydrogen bonding and its entropy effect play a dominant role in protein folding, folding into helical and hairpin-like structures is observed in molecular dynamics (MD) simulations without hydrogen bonding in the peptide-solvent system. In the widely used point charge model, hydrogen bonding is calculated as part of the interaction between atomic partial charges. It is removed from these simulations by setting atomic charges of the peptide and water to zero. Because of the structural difference between the peptide and water, van der Waals (VDW) interactions favor peptide intramolecular interactions and are a major contributing factor to the structural compactness. These compact structures are amino acid sequence dependent and closely resemble standard secondary structures, as a consequence of VDW interactions and covalent bonding constraints. Hydrogen bonding is a short range interaction and it locks the approximate structure into the specific secondary structure when it is included in the simulation. In contrast to standard molecular simulations where the total energy is dominated by charge-charge interactions, these simulation results will give us a new view of the folding mechanism.
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Affiliation(s)
- Shen-Shu Sung
- Department of Pharmacology, College of Medicine, Penn State University, Hershey, Pennsylvania, 17033
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7
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8
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Conformational Analysis of Polypeptides and Proteins for the Study of Protein Folding, Molecular Recognition, and Molecular Design. Isr J Chem 2013. [DOI: 10.1002/ijch.198600023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Knof S, Engel J. Conformational Stability, Partial Specific Volumes and Spectroscopic Properties of Poly-L-Proline, Poly-L-Hydroxyproline and Some of Its O-Acyl-Derivatives in Various Solvent Systems. Isr J Chem 2013. [DOI: 10.1002/ijch.197400016] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Affiliation(s)
- A. E. Woodward
- a Department of Chemistry , The City College of the City University of New York , New York , New York 10031
| | - H. Stefanou
- a Department of Chemistry , The City College of the City University of New York , New York , New York 10031
- b Pennwalt Corp. , King of Prussia , Pa
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11
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Tonelli AE. Approximate treatment of the conformational characteristics of a cyclic nonapeptide, cyclolinopeptide a. Proc Natl Acad Sci U S A 2010; 68:1203-7. [PMID: 16591929 PMCID: PMC389154 DOI: 10.1073/pnas.68.6.1203] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Possible conformations for a cyclic nonapeptide that are consistent with conformation-dependent information obtained from an NMR investigation of the peptide in solution are presented. These several conformations are deduced from the myriad of possible conformations by eliminating from consideration all cyclic species having one or more residues in a conformation that does not correspond to the vicinal coupling constants observed by NMR between the amide and alpha-protons. A Karplus-like relation connecting the dihedral angle [unk]' and the vicinal coupling J(Nalpha) between N-H and C(alpha)-H(alpha) is used to test this correspondence. A further reduction in the number of cyclic conformations under consideration is made possible by rejecting the conformations that have a high intramolecular conformational energy. The intramolecular conformational energy of the cyclic nonapeptide is estimated by summing the independent residue energies. These have been calculated by others with approximate potential functions to account for the intrinsic torsional potentials and the nonbonded steric (6-12 potential) and electrostatic (monopole-monopole) interactions solely dependent upon one or both of the residue rotations, [unk] and Psi, about the N-C(alpha) and C(alpha)-C bonds, respectively.
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Affiliation(s)
- A E Tonelli
- Bell Telephone Laboratories, Incorporated, Murray Hill, New Jersey 07974
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12
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13
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Balasubramanian R, Ramakrishnan C. STEREOCHEMICAL CRITERIA FOR POLYPEPTIDE AND PROTEIN CHAIN CONFORMATIONS. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1972.tb03404.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Ramachandran GN. Molecular forces in protein structure and crystallography. INTERNATIONAL JOURNAL OF PROTEIN RESEARCH 2009; 1:5-17. [PMID: 5406489 DOI: 10.1111/j.1399-3011.1969.tb01622.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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15
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Ramakrishnan C, Sarathy KP. Stereochemical studies on cyclic peptides. IV. Conformational analysis of cyclopentapeptides. INTERNATIONAL JOURNAL OF PROTEIN RESEARCH 2009; 1:63-71. [PMID: 5406490 DOI: 10.1111/j.1399-3011.1969.tb01626.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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16
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Liquori AM. The role of van der Waals interactions on the conformational stability of helical macromolecules. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/polc.5070120117] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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18
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Pizzi A, Eaton N. The Structure of Cellulose by Conformational Analysis. 1. Cellobiose and Methyl-β-cellobioside. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/00222338408055675] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- A. Pizzi
- a National Timber Research Institute Council for Scientific and Industrial Research , Pretoria, Republic of South Africa
| | - N. Eaton
- a National Timber Research Institute Council for Scientific and Industrial Research , Pretoria, Republic of South Africa
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20
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Affiliation(s)
- H. Stef Anou
- a Department of Chemistry , The City College of the City University of New York , New York , New York
| | - A. E. Woodward
- a Department of Chemistry , The City College of the City University of New York , New York , New York
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21
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Farmer BL, Lando JB. Isotactic poly(p-fluorostyrene): Conformation and molecular packing analysis. J MACROMOL SCI B 2006. [DOI: 10.1080/00222347408215161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- B. L. Farmer
- a Department of Macromolecular Science , Case Western Reserve University , Cleveland, Ohio
- b National Bureau of Standards , Washington, D.C
| | - J. B. Lando
- a Department of Macromolecular Science , Case Western Reserve University , Cleveland, Ohio
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22
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Fillaux F, De Lozé C. Spectroscopic study of monosubstituted amides. II. Rotation isomers in amides substituted by aliphatic side-chain models. Biopolymers 2004. [DOI: 10.1002/bip.1972.360111007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Némethy G, Ramachandran GN, Seheraga HA. A proposal of standard conventions and nomenclature for the description of polypeptide conformations. Biopolymers 2004. [DOI: 10.1002/bip.1966.360040113] [Citation(s) in RCA: 135] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Wedemeyer WJ, Baker D. Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins 2003; 53:262-72. [PMID: 14517977 DOI: 10.1002/prot.10525] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Angular potentials play an important role in the refinement of protein structures through angle-dependent restraints (e.g., those determined by cross-correlated relaxations, residual dipolar couplings, and hydrogen bonds). Analytic derivatives of such angular potentials with respect to the dihedral angles of proteins would be useful for optimizing such restraints and other types of angular potentials (i.e., such as we are now introducing into protein structure prediction) but have not been described. In this article, analytic derivatives are calculated for four types of angular potentials and integrated with the efficient recursive derivative calculation methods of Gō and coworkers. The formulas are implemented in publicly available software and illustrated by refining a low-resolution protein structure with idealized vector-angle, dipolar-coupling, and hydrogen-bond restraints. The method is now being used routinely to optimize hydrogen-bonding potentials in ROSETTA.
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25
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26
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27
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Hurley JH, Mason DA, Matthews BW. Flexible-geometry conformational energy maps for the amino acid residue preceding a proline. Biopolymers 1992; 32:1443-6. [PMID: 1457725 DOI: 10.1002/bip.360321104] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Previously calculated conformational energy maps suggest that the alpha-helical conformation for the residue preceding a proline is disfavored relative to the extended conformation by more than 7 kcal/mol. In known protein structures this conformation is observed, however, to occur for about 9% of all prolines. In addition, introduction or removal of prolines at theoretically unfavorable positions in proteins and peptides can have modest effects on stability and structure. To investigate the discrepancy between calculation and experiment, we have determined how the conformation of the proline affects the calculated energy. We have also explored the effect of bond length and bond angle relaxation on the conformational energy map. The conformational energy of the preceding residue is found to be unaffected by the conformation of the proline, but the effect of allowing covalent bond relaxation is dramatic. If bond lengths and angles, and dihedral angles within the pyrrolidine ring, are allowed to relax, a calculated energy difference between the alpha and beta conformations of 1.1 kcal/mol is obtained, in reasonable agreement with experiment. The detailed shape of the calculated energy surface is also in excellent agreement with the observed conformational distributions in known protein structures.
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Affiliation(s)
- J H Hurley
- Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, Oregon
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29
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On the resolution of dihydroxydiphenylmethanes on achiral crystalline cellulose II. Correlation of experimental and calculated results. Chem Phys 1992. [DOI: 10.1016/0301-0104(92)87145-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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30
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DeSantis P, Palleschi A, Savino M, Scipioni A. Theoretical prediction of the gel electrophoretic retardation changes due to point mutations in a tract of SV40 DNA. Biophys Chem 1992; 42:147-52. [PMID: 1314680 DOI: 10.1016/0301-4622(92)85004-n] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The changes of gel electrophoretic retardation due to single base substitutions in a 173 bp fragment of Sv40 DNA were predicted by using a theoretical model based on conformational energy calculations. As described in previous papers, this model allows successful prediction of the gel electrophoretic retardation of synthetic as well as natural DNAs reported in literature. The experimental retardations related to 195 point-mutated DNAs were reproduced with a standard deviation of 0.05 comparable with the experimental one of 0.04. This result, which represents a very critical test for the proposed model, indicates that DNA superstructures can be satisfactorily predicted on the simple physical basis of the integration of the nearest-neighbour perturbations in the dinucleotide steps. Thus, cooperative effects appear, in the majority of cases investigated, to play a second order role.
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Affiliation(s)
- P DeSantis
- Dipartimento di Chimica, Università di Roma La Sapienza, Italy
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31
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Abstract
The prediction of the secondary and tertiary structure of globular and membrane proteins is reviewed. Prospects are encouraging for future developments, but present algorithms require cautious interpretation.
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32
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Abstract
Distortions from the uniform idealized B-DNA structure are investigated in terms of differential interactions between adjacent nucleotide pairs on the basis of conformational energy calculations. A theoretical model of DNA curvature is proposed based on the evaluation of the curvature vector defined in the complex plane and the corresponding variance. The model appears to contain the basic physical features for translating the deterministic fluctuations of DNA sequences in superstructure elements. It allows the quantitative reproduction of all the available gel electrophoresis experiments on both periodical polynucleotides and tracts of DNAs as well as the theoretical prediction of the sequence dependent DNA writhing in good agreement with the experimental data. The general pattern of agreement between the theoretical and experimental data and the biological significance of the results obtained allow an extensive application of the model for the screening of DNA regions which are possible candidates for protein recognition.
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Affiliation(s)
- P De Santis
- Dipartimento di Chimica, Università di Roma La Sapienza, Italy
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33
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Abstract
In this report we describe a general survey of all helices found in 57 of the known protein crystal structures, together with a detailed analysis of 48 alpha-helices found in 16 of the structures that are determined to high resolution. The survey of all helices reveals a total of 291 alpha-helices, 71 3(10)-helices and no examples of pi-helices. The conformations of the observed helices are significantly different from the "ideal" linear structures. The mean phi, psi angles for the alpha- and 3(10)-helices found in proteins are, respectively, (-62 degrees, -41 degrees) and (-71 degrees, -18 degrees). A computer program, HBEND, is used to characterize and to quantify the different types of helix distortion. alpha-Helices are classified as regular or irregular, linear, curved or kinked. Of the 48 alpha-helices analysed, only 15% are considered to be linear; 17% are kinked, and 58% are curved. The curvature of helices is caused by differences in the peptide hydrogen bonding on opposite faces of the helix, reflecting carbonyl-solvent/side-chain interactions for the exposed residues, and packing constraints for residues involved in the hydrophobic core. Kinked helices arise either as a result of included proline residues, or because of conflicting requirements for the optimal packing of the helix side-chains. In alpha-helices where there are kinks caused by proline residues, we show that the angle of kink is relatively constant (approximately 26 degrees), and that there is minimal disruption of the helix hydrogen bonding. The proline residues responsible for the kinks are highly conserved, suggesting that these distortions may be structurally/functionally important.
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Affiliation(s)
- D J Barlow
- Department of Crystallography, Birkbeck College London, U.K
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34
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Paul PK, Ramakrishnan C. Studies on hydrogen bonds. Part V--Hydrogen bonding in energy minimization studies of peptides. J Biomol Struct Dyn 1985; 2:879-98. [PMID: 3916936 DOI: 10.1080/07391102.1985.10507607] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An energy term, representing the N-H...O type of hydrogen bond, which is a function of the hydrogen bond length (R) and angle (theta) has been introduced in an energy minimization program, taking into consideration its interpolation with the non-bonded energy for borderline values of R and theta. The details of the mathematical formulation of the derivatives of the hydrogen bond function as applicable to the energy minimization have been given. The minimization technique has been applied to hydrogen bonded two and three linked peptide units (gamma-turns and beta-turns), and having Gly, Ala and Pro side chains. Some of the conformational highlights of the resulting minimum energy conformations are a) the occurrence of the expected 4----1 hydrogen bond in all of the burn-turn tripeptide sequences and b) the presence of an additional 3----1 hydrogen bond in some of the type I and II tripeptides with the hydrogen bonding scheme in such type I beta-turns occurring in a bifurcated form. These and other conformational features have been discussed in the light of experimental evidence and theoretical predictions of other workers.
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Affiliation(s)
- P K Paul
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore
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35
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Scheraga HA. Protein structure and function, from a colloidal to a molecular view. ACTA ACUST UNITED AC 1984. [DOI: 10.1007/bf02913964] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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36
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Kolaskar AS, Ramabrahmam V. Side chain characteristic main chain conformations of amino acid residues. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1982; 19:1-9. [PMID: 7118379 DOI: 10.1111/j.1399-3011.1982.tb03016.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Main chain conformation characteristics of the respective side chains of the 20 naturally occurring amino acid residues were obtained by the analysis of (phi, psi)-data from the crystal structures of 38 different globular proteins. The following observations are of interest: (i) For amino acids other than Glu, Thr and aliphatic amino acids, at least one main chain conformation is stabilised solely by side chain atoms. Such conformations are listed. (ii) In globular proteins, the main chain conformations which are significantly destabilised by side chain atom interactions are observed. The stabilising force for those conformations seems to come from main chain atom interactions. (iii) A set of conformations for which the main chain and side chain interactions are almost equal but in opposite directions, is listed and these conformations will be taken by residues mainly due to the effect of surroundings. The results can be used to study the folding of polypeptide chains and they also provide an insight into the role of the respective side chains on main chin conformations of amino acid residues.
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37
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de Santis P, Morosetti S, Palleschi A, Savino M. Conformational analysis of double-stranded B-type DNA structures. Biopolymers 1981; 20:1727-39. [PMID: 7260337 DOI: 10.1002/bip.1981.360200812] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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38
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Subba Rao G, Tyagi R, Mishra R. Calculation of the minimum energy conformation of biomolecules using a global optimization technique II. Conformation of N-acetylglycine N-methyl amide, a model dipeptide unit. J Theor Biol 1981. [DOI: 10.1016/0022-5193(81)90319-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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39
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Ohasaku M, Imamura A. CNDO/2 calculations of the relative stability of poly (l-proline I) and poly (l-proline II). Int J Biol Macromol 1980. [DOI: 10.1016/0141-8130(80)90016-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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41
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Knappenberg M, Brison J, Dirkx J, Hallenga K, Deschrijver P, van Binst G. Conformational studies on somatostatin. II. The C-terminal hexapeptide fragment. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 580:266-76. [PMID: 518902 DOI: 10.1016/0005-2795(79)90139-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The results of a conformational study on the C terminal hexapeptide of Somatostatin are presented. Semi-empirical energy calculations and high resolution NMR methods have been used to obtain information on the conformational properties of SRIF9-14 in [2H6]dimethylsulfoxide and 2H2O. It is concluded from the energy calculations that the peptide has an averaged conformation in which semi extended and folded structures are important. Only some of the folded conformations can explain the chemical shift differences between the amino acid residues Thr10 and Thr12 as a ring current shift by the Phe11 aromatic ring on Thr10. The nonequivalence is more pronounced in dimethyl-sulfoxide (0.23--0.15 ppm) where it decreases with increasing temperature towards the temperature independent value in 2H2O (0.03 ppm). This suggests that the folded conformations are somewhat predominant in dimethylsulfoxide solutions. In 2H2O the semi extended and folded structures are statistically equally important and the peptide is more flexible. A comparison with a study on the smaller fragments SRIF10-12 and SRIF10-13 which have similar conformational properties, demonstrates the usefulness of the fragment approach in conformational studies of peptides.
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42
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Saenger W, Suck D, Knappenberg M, Dirkx J. Theoretical drug design: 6-azauridine-5'-phosphate--its X-ray crystal structure, potential energy maps, and mechanism of inhibition of orotidine-5'-phosphate decarboxylase. Biopolymers 1979; 18:2015-36. [PMID: 497352 DOI: 10.1002/bip.1979.360180814] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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43
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Hallenga K, van Binst G, Knappenberg M, Brison J, Michel A, Dirkx J. The conformational properties of some fragments of the peptide hormone somatostatin. BIOCHIMICA ET BIOPHYSICA ACTA 1979; 577:82-101. [PMID: 427218 DOI: 10.1016/0005-2795(79)90010-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The conformational properties of some somatostatin fragments have been studied using high resolution NMR and semi-empirical calculations. The fragments are Thr10-Phe11, Phe11-Thr12, Thr10-Phe11-Thr12 and Thr10-Phe11-Thr12-Ser13. The results of high resolution 1H and 13C NMR using dimethylsulfoxide and 2H2O as solvents, combined with a new method for determining dihedral angles phi and psi from 13C and 1H spin lattice relaxation times are presented. A marked inequivalence of the two Thr10,12 residues is attributed to a shielding of the the Thr10 side chain by the Phe11 aromatic ring. The calculations show the existence of extended and folded low energy conformations in the tri and tetrapeptide. Only the folded structures give the observed shielding of Thr10. A temperature study of the tri and the tetrapeptide indicates that the folded structures are energetically the most favorable conformations at room temperature in dimethylsulfoxide. Increasing temperature reduces the nonequivalence of the Thr residues towards the differences that are observed in 2H2O. A detailed comparison of 3JalphaNH coupling constants and relaxation time measurements with the calculated conformations gives in general good agreement between both approaches. It is concluded that in these linear peptides, although several quite different low energy conformations exist, some of them are predominant. The continuity of both NMR parameters and calculated low energy conformations, when going from the smaller to the larger peptides, demonstrates the existence of structural properties far from the "random conformation".
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Dirkx J, Knappenberg M, Dufour P. A program for generation and selection of possible conformations of cyclic molecules. COMPUTER PROGRAMS IN BIOMEDICINE 1979; 9:63-8. [PMID: 759089 DOI: 10.1016/0010-468x(79)90018-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An algorithm has been developped for the computer generation of the possible conformations of non-planar cyclic molecules. This algorithm has been used successfully to select the known conformations of the ribose ring, of substituted cyclohexane and of disulfide bridged peptides. Its use may be extended to open molecules when the end-to-end distance is known or imposed.
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Zimmerman SS, Scheraga HA. Influence of local interactions on protein structure. III. Conformational energy studies ofN-acety-N?-methylamides of Gly-X and X-Gly dipeptides. Biopolymers 1978. [DOI: 10.1002/bip.1978.360170805] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mitra AK. Backbone torsional potential functions for rotations about N--Calpha and Calpha--C bonds in dipeptide model systems in relation to nuclear magnetic resonance and infra red spectral data. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1978; 11:166-78. [PMID: 640776 DOI: 10.1111/j.1399-3011.1978.tb02836.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
In principle, it is possible to predict theoretically the three-dimensional structure of a protein from its amino acid sequence. Recently substantial progress towards this goal has been made by the use of simple models to represent protein conformation and interatomic interactions, together with the knowledge gained form analyses of know protein structures.
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Dashevskii DG, Baranov AP, Medved' TY, Kabachnik MI. Conformational analysis of the bidentate ligand, tetramethylmethylenediphosphine dioxide, in its chelate complexes with metals. THEOR EXP CHEM+ 1978. [DOI: 10.1007/bf00520369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Timofeeva TV, Kravtsov DN, Bokii NG, Struchkov YT. Calculation of the conformation and the barriers to internal rotation in alkyl aryl sulfides, thiophenols, and their organotin derivatives. J STRUCT CHEM+ 1978. [DOI: 10.1007/bf00746110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Baranov AP, Dashevskii VG, Medved' TY, Kabachnik MI. Conformational analysis of tetramethylvinylidene-, vinylene-, and -ethylenediphosphine dioxides and halo derivatives thereof in connection with their complexing selectivity. THEOR EXP CHEM+ 1978. [DOI: 10.1007/bf00519615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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