1
|
Scott RA, Vanderkooi G, Tuttle RW, Shames PM, Scheraga HA. Minimization of polypeptide energy, iii. Application of a rapid energy minimization technique to the calculation of preliminary structures of gramicidin-s. Proc Natl Acad Sci U S A 2010; 58:2204-11. [PMID: 16591582 PMCID: PMC223821 DOI: 10.1073/pnas.58.6.2204] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R A Scott
- DEPARTMENT OF CHEMISTRY, CORNELL UNIVERSITY, ITHACA, NEW YORK
| | | | | | | | | |
Collapse
|
2
|
Rackovsky S, Scheraga HA. Intermolecular anti-parallel beta sheet: Comparison of predicted and observed conformations of gramicidin S. Proc Natl Acad Sci U S A 2010; 77:6965-7. [PMID: 16592928 PMCID: PMC350420 DOI: 10.1073/pnas.77.12.6965] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recently determined x-ray structure of the hydrated gramicidin S-urea complex is compared with a structure predicted by conformational energy minimization. It is shown that the two structures are in good general agreement, including the prediction of a hydrogen bond between the side-chain amino group of ornithine and the backbone carbonyl of phenylalanine. This agreement demonstrates the power of empirical potential energy methods in conformational analysis and illustrates one method for solution of the multiple-minimum problem for small peptides. It is noted that, in the crystal, gramicidin S is a dimer that forms an intermolecular antiparallel four-stranded beta sheet and that differences between the predicted and x-ray structures can be explained by this intermolecular interaction. The residual conformational asymmetry of the x-ray structure is shown to be due to the formation of the complex with urea.
Collapse
Affiliation(s)
- S Rackovsky
- Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853
| | | |
Collapse
|
3
|
Urry DW. Partial molar rotatory powers and optical activity in proteins and polypeptides, ii. The alpha-helix of poly-L-alanine. Proc Natl Acad Sci U S A 2010; 60:1114-21. [PMID: 16591669 PMCID: PMC224889 DOI: 10.1073/pnas.60.4.1114] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- D W Urry
- INSTITUTE FOR BIOMEDICAL RESEARCH, EDUCATION AND RESEARCH FOUNDATION, AMERICAN MEDICAL ASSOCIATION, CHICAGO, ILLINOIS
| |
Collapse
|
4
|
Tinoco I. Application of optical rotatory dispersion and circular dichrosim to the study of biopolymers. METHODS OF BIOCHEMICAL ANALYSIS 2006; 18:81-203. [PMID: 4909319 DOI: 10.1002/9780470110362.ch3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
5
|
Vila JA, Ripoll DR, Scheraga HA. Atomically detailed folding simulation of the B domain of staphylococcal protein A from random structures. Proc Natl Acad Sci U S A 2003; 100:14812-6. [PMID: 14638943 PMCID: PMC299808 DOI: 10.1073/pnas.2436463100] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The conformational space of the 10-55 fragment of the B-domain of staphylococcal protein A has been investigated by using the electrostatically driven Monte Carlo (EDMC) method. The ECEPP/3 (empirical conformational energy program for peptides) force-field plus two different continuum solvation models, namely SRFOPT (Solvent Radii Fixed with atomic solvation parameters OPTimized) and OONS (Ooi, Oobatake, Némethy, and Scheraga solvation model), were used to describe the conformational energy of the chain. After an exhaustive search, starting from two different random conformations, three of four runs led to native-like conformations. Boltzmann-averaged root-mean-square deviations (RMSD) for all of the backbone heavy atoms with respect to the native structure of 3.35 A and 4.54 A were obtained with SRFOPT and OONS, respectively. These results show that the protein-folding problem can be solved at the atomic detail level by an ab initio procedure, starting from random conformations, with no knowledge except the amino acid sequence. To our knowledge, the results reported here correspond to the largest protein ever folded from a random conformation by an initial-value formulation with a full atomic potential, without resort to knowledge-based information.
Collapse
Affiliation(s)
- Jorge A Vila
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA
| | | | | |
Collapse
|
6
|
Genest M, Marion D, Ptak M. Calculations of the conformations of Iturin A in relation with NMR studies. J Biomol Struct Dyn 1985; 2:849-57. [PMID: 3917121 DOI: 10.1080/07391102.1985.10506328] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Iturin A is an antifungal antibiotic which was isolated from a strain of Bacillus subtilis, and contains a lipophilic beta amino acid closing an heptapeptide cycle with polar L and D residues. Iturin A belongs to a lipopeptide family of which the LDDLLDL sequence is kept constant. NMR spectroscopy and semi-empirical energy calculations are combined to design the conformations of Iturin A in pyridine solution. J coupling constants and nOes (nuclear Overhauser enhancements) are used as guiding line for energy calculations. This preliminary study shows that Iturin A in pyridine appears as rather rigid, especially in the L Pro 5-D Asn 6 region, probably involved in a beta turn. The polar side chains can form different networks of intramolecular hydrogen bonds. The Tyr side chain, relatively mobile, could be involved in interactions with an hydrophobic environment as the beta amino acid side chain found away from the peptide cycle.
Collapse
Affiliation(s)
- M Genest
- Centre de Biophysique Moléculaire C.N.R.S., Université d'Orléans, France
| | | | | |
Collapse
|
7
|
Rinnert H, Maigret B. Conformational analysis of amphotericin B. I, Isolated molecule. Biochem Biophys Res Commun 1981; 101:853-60. [PMID: 7306117 DOI: 10.1016/0006-291x(81)91828-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
8
|
|
9
|
|
10
|
Levitt M. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976; 104:59-107. [PMID: 957439 DOI: 10.1016/0022-2836(76)90004-8] [Citation(s) in RCA: 783] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
11
|
Némethy G. Analysis of the conformation of polypeptides : the combined use of energy computations and nuclear magnetic resonance studies. Biochimie 1975; 57:471-82. [PMID: 50089 DOI: 10.1016/s0300-9084(75)80334-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review surveys current approaches to the problem of determining the solution conformation of polypeptides. The basic principles of energy computations are described. The utility, problems, and limitations of various theoretical methods are summarized: conformational energy mapping, energy minimization, scanning of selected local conformations, statistical predictive schemes. The need for combining the calculations with experimental studies is pointed out. The information content of various physico-chemical methods is compared for this purpose. The analysis of nmr coupling constants is discussed in more detail. In combination with energy computations, it can furnish specific information on local aspects of the conformation. Examples of such combined studies on small peptides are summarized.
Collapse
|
12
|
|
13
|
Sugano H, Abe H, Miyoshi M, Kato T, Izumiya N. Studies of Peptide Antibiotics. XXX. Syntheses of Gramicidin S Analogs ContainingN-Methylleucine in Place of Leucine. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 1974. [DOI: 10.1246/bcsj.47.698] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
14
|
|
15
|
Sugano H, Abe H, Miyoshi M, Kato T, Izumiya N. Gramicidin S analogs containing N-methylleucine in place of leucine. EXPERIENTIA 1973; 29:1488-9. [PMID: 4134369 DOI: 10.1007/bf01943872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
16
|
|
17
|
Santis PD, D'Ilario L, Lamanna G, Morosletti S, Savino M. Circular dichroism and molecular conformation of copper(II)-gramicidin S complexes. Biopolymers 1973. [DOI: 10.1002/bip.1973.360120217] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
18
|
Bayley P. The analysis of circular dichroism of biomolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1973. [DOI: 10.1016/0079-6107(73)90003-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
19
|
|
20
|
|
21
|
Hermans J, Ferro D. Representation of a protein molecule as a tree and application to modular computer programs which calculate and modify atomic coordinates. Biopolymers 1971; 10:1121-38. [PMID: 5095087 DOI: 10.1002/bip.360100704] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
22
|
|
23
|
Knaell KK, Scott RA. Mone Carlo calculations on polypeptide chains. I. A three-state hard-sphere model for randomly coiling poly-L-alanine. J Chem Phys 1971; 54:566-75. [PMID: 5544782 DOI: 10.1063/1.1674879] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
|
24
|
Dispersion of the optical rotation of derivatives of gramicidin S. Russ Chem Bull 1970. [DOI: 10.1007/bf00853835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
25
|
Ovchinnikov YA, Ivanov VT, Bystrov VF, Miroshnikov AI, Shepel EN, Abdullaev ND, Efremov ES, Senyavina LB. The conformation of gramicidin S and its N,N'-diacetyl derivative in solutions. Biochem Biophys Res Commun 1970; 39:217-25. [PMID: 5439511 DOI: 10.1016/0006-291x(70)90781-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
26
|
Abstract
Energy minimization techniques applied to an arbitrary peptide primary sequence result in a still large number of hypothetical structures of similar energy. Optical activity calculations can, in principle, be used to screen the low-energy conformations. Those conformations which yield a spectrum different from the observed spectrum by a factor greater than the current reliability of the calculation can be excluded. The method is applied to gramicidin S.
Collapse
|
27
|
Sheard B, Bradbury E. Nuclear magnetic resonance in the study of biopolymers and their interaction with ions and small molecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1970. [DOI: 10.1016/0079-6107(70)90016-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
28
|
Roberts GC, Jardetzky O. Nuclear magnetic resonance spectroscopy of amino acids, peptides, and proteins. ADVANCES IN PROTEIN CHEMISTRY 1970; 24:447-545. [PMID: 4912354 DOI: 10.1016/s0065-3233(08)60246-6] [Citation(s) in RCA: 221] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
29
|
Momany FA, Vanderkooi G, Tuttle RW, Scheraga HA. Minimization of polypeptide energy. IV. Further studies of gramicidin S. Biochemistry 1969; 8:744-6. [PMID: 5793723 DOI: 10.1021/bi00830a041] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
30
|
Bradbury EM, Carpenter BG, Crane-Robinson C, Rattle HW. Application of high resolution nuclear magnetic resonance to conformational analyses of polypeptides in solution. Nature 1968; 220:69-72. [PMID: 5677447 DOI: 10.1038/220069b0] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
31
|
Stern A, Gibbons WA, Craig LC. A conformational analysis of gramicidin S-A by nuclear magnetic resonance. Proc Natl Acad Sci U S A 1968; 61:734-41. [PMID: 5246004 PMCID: PMC225221 DOI: 10.1073/pnas.61.2.734] [Citation(s) in RCA: 200] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
|
32
|
Craig LC. Conformation studies with polypeptides by rotatory dispersion and thin-film dialysis. Proc Natl Acad Sci U S A 1968; 61:152-9. [PMID: 4301587 PMCID: PMC285917 DOI: 10.1073/pnas.61.1.152] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
33
|
|
34
|
Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. ADVANCES IN PROTEIN CHEMISTRY 1968; 23:283-438. [PMID: 4882249 DOI: 10.1016/s0065-3233(08)60402-7] [Citation(s) in RCA: 2003] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|
35
|
|
36
|
Quadrifoglio F, Urry DW. Circular dichroism and optical rotatory dispersion of gramicidin S in aqueous solution. Biochem Biophys Res Commun 1967; 29:785-91. [PMID: 6077810 DOI: 10.1016/0006-291x(67)90288-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
37
|
Sternlicht H, Wilson D. Magnetic resonance studies of macromolecules. I. Aromatic-methyl interactions and helical structure effects in lysozyme. Biochemistry 1967; 6:2881-92. [PMID: 6055199 DOI: 10.1021/bi00861a032] [Citation(s) in RCA: 124] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
38
|
Beamer RL, Fickling CS, Ewing JH. Stereospecific hydrogenations using palladium-on-poly-L-leucine. J Pharm Sci 1967; 56:1029-32. [PMID: 6035334 DOI: 10.1002/jps.2600560829] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|