1
|
Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| |
Collapse
|
2
|
Leach AR. A Survey of Methods for Searching the Conformational Space of Small and Medium-Sized Molecules. REVIEWS IN COMPUTATIONAL CHEMISTRY 2007. [DOI: 10.1002/9780470125793.ch1] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
3
|
Kolossváry I, Guida WC. Torsional flexing: Conformational searching of cyclic molecules in biased internal coordinate space. J Comput Chem 2004. [DOI: 10.1002/jcc.540140610] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
4
|
Mattern RH, Tran TA, Goodman M. Conformational analyses of cyclic hexapeptide analogs of somatostatin containing arylalkyl peptoid and naphthylalanine residues. J Pept Sci 1999; 5:161-75. [PMID: 10323196 DOI: 10.1002/(sici)1099-1387(199904)5:4<161::aid-psc177>3.0.co;2-f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We report the conformational analysis by 1H-NMR in DMSO and computer simulations involving distance geometry and molecular dynamics simulations of peptoid analogs of the cyclic hexapeptide c-[Phe11-Pro6-Phe7-D-Trp8-Lys9-Thr10] L-363,301 (the numbering refers to the positions in native somatostatin). The compounds c-[Phe11-Nphe6-Nal7-D-Trp8-Lys9-Thr10] (Nphe6-Nal7 analog 1), c-[Nal11-Nphe6-Phe7-D-Trp8-Lys9-Thr10] (Nal11-Nphe6 analog 2) and c-[Phe11-Nnal6-Phe7-D-Trp8-Lys9-Thr10] (Nnal6 analog 3), where Nphe denotes N-benzylglycine and Nnal denotes N-(1-naphthylmethyl)glycine, are subjected to SAR studies in order to investigate the influence of the bulky naphthyl aromatic ring on the conformation. The Nal11-Nphe6 and Nphe6-Nal7 analogs exhibit potent binding to the hsst2, hsst3 and hsst5 receptors, whereas the Nnal6 analog has decreased binding affinity to all receptors but is more selective towards the hsst2 than the other two analogs and L-363,301. The conformational search employing distance geometry, energy minimization and molecular dynamic simulations gives insight into the conformational flexibility of these analogs. The molecules adopt both cis and trans orientations of the peptide bond between residues 11 and 6. The cis isomers of these analogs adopt type II' beta-turns with D-Trp in the i + 1 position and type VIalpha beta-turns with the cis peptide bond between residues 6 and 11. The results of free and distance restrained molecular dynamics simulations at 300 K indicate that the Nphe6-Nal7 and Nal11-Nphe6 compounds adopt a preferred backbone conformation which can be described as 'folded' about residues 7 and 10. The Nnal6 analog, which binds less effectively to the hsst receptors, has a more flexible backbone structure than the Nal11-Nphe6 and Nphe6-Nal7 analogs and prefers a 'flat' structure with regard to the orientations about Phe7 and Thr10 during molecular dynamics simulations.
Collapse
Affiliation(s)
- R H Mattern
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0343, USA
| | | | | |
Collapse
|
5
|
Mattern RH, Tran TA, Goodman M. Conformational analyses by 1H NMR and computer simulations of cyclic hexapeptides related to somatostatin containing acidic and basic peptoid residues. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 53:146-60. [PMID: 10195452 DOI: 10.1034/j.1399-3011.1999.00003.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We report the conformational analysis by 1H NMR in DMSO and computer simulations involving distance geometry and molecular dynamics simulations at 300K of peptoid analogs of the cyclic hexapeptide c-[Phe11-Pro6-Phe7-D-Trp8-Lys9-Thr10]. The analogs c-[Phe11-Nasp6-Phe7-D-Trp8-Lys9-Thr10](1), c-[Phe11-Ndab6Phe7-D-Trp8-Lys9-Thr10] (2) and c-[Phen11-Nlys6-Phe7-D-Trp8-Lys9-Thr10](3) where Nasp denotes N-(2-carboxyethyl) glycine, Ndab N-(2-aminoethyl) glycine and Nlys N-(4-aminobutyl) glycine are subject to conformational studies. The results of free and restrained molecular dynamics simulations at 300K are reported and give insight into the conformational behaviour of these analogs. The compounds show two sets of nuclear magnetic resonance signals corresponding to the cis and trans orientations of the peptide bond between residues 11 and 6. The backbone conformation of the cis isomers that we believe are the bioactive isomers of the three compounds are very similar to each other while there are larger variations amongst the trans isomers. The binding data to the isolated receptors show that the introduction of the Nlys residue in analog 3 leads to an enhancement of binding potency to the hsst5 receptor compared with analog 2 while maintaining identical binding potency to the hsst2 receptor. The Nasp6 analog 1 binds weakly to the hsst2 and is essentially inactive towards the other receptors. Comparison of the conformations and binding activities of these three analogs indicates that the Nlys residue extends sufficiently far to allow binding to a negatively charged binding domain on the hsst5 receptor. According to this model, the Ndab analog 2 cannot extend far enough to allow for binding to the receptor pocket. The loss of activity observed for the Nasp6 compound 1 indicates that the presence of a negatively charged residue in position 6 is unfavorable for binding to the hsst receptors.
Collapse
Affiliation(s)
- R H Mattern
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0343, USA
| | | | | |
Collapse
|
6
|
Mattern RH, Tran TA, Goodman M. Conformational analyses of somatostatin-related cyclic hexapeptides containing peptoid residues. J Med Chem 1998; 41:2686-92. [PMID: 9667959 DOI: 10.1021/jm970392t] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
We report the conformational analysis by 1H NMR in DMSO and computer simulations involving distance geometry and molecular dynamics simulations of a series of peptoid analogues of the cyclic hexapeptide c[Phe11-Pro6-Phe7-d-Trp8-Lys9-Thr10] (1). The proline residue in compound 1 is replaced with the peptoid residues N-benzylglycine (Nphe) (compound 2), N-(S)-alpha-methylbenzylglycine [(S)-beta-MeNphe] (compound 3), and N-(R)-alpha-methylbenzylglycine [(R)-beta-MeNphe] (compound 4). The peptoid analogues 2 and 4 exhibit potent binding activities to the hsst2 receptor, while the binding affinities to the hsst5 and to the hsst3 receptors are reduced compared to that of the parent compound 1. Compound 3 shows reduced binding activities to the hsst2, hsst3, and hsst5 receptors compared to compound 1. The results of in vivo assays indicate that these compounds inhibit the growth hormone release but do not affect the insulin release. These peptoid-containing analogues show two sets of NMR signals corresponding to cis and trans conformations of the peptide bond between Phe11 and Nxaa6. We demonstrate that the backbone conformation and the orientation of the relevant side chains of compound 1 are maintained in the cis isomers of the peptoid analogues which adopt a type VI beta-turn centered around residues 11 and 6 and a type II' beta-turn with d-Trp in the i+1 position. The enhanced selectivity of the peptoid-containing analogues compared to compound 1 and the results of the conformational analysis suggest that the presence of a conformationally constrained hydrophobic group in position 6 in complementary topology to the Phe11 side chain enhances selective binding to the hsst2 receptor.
Collapse
Affiliation(s)
- R H Mattern
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0343, USA
| | | | | |
Collapse
|
7
|
Carpenter KA, Schiller PW, Schmidt R, Wilkes BC. Distinct conformational preferences of three cyclic beta-casomorphin-5 analogs determined using NMR spectroscopy and theoretical analysis. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1996; 48:102-11. [PMID: 8844269 DOI: 10.1111/j.1399-3011.1996.tb01112.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The conformational properties of three cyclic beta-casomorphin analogs based on the general formula H-Tyr-c[-D-Orn-2-Nal-D-Pro-Xaa-] (2-Nal = 2-naphthylalanine; Xaa = D-Ala, Sar or NMe-Ala) in DMSO solution were investigated using NMR spectroscopy in conjunction with molecular modeling techniques. The D-Ala5- and Sar5-analogs (compounds 1 and 2 respectively) are potent mixed mu-agonist/delta-antagonists with high mu- and delta-opioid receptor affinities, whereas the NMe-Ala5-analog (compound 3) is a potent mu-agonist and a weak partial delta-agonist. Distinct conformational differences emerged for the three compounds studied. Flexibility in the bare ring structures was found to increase in the order 3 < 2 < 1. The increased structural rigidity of 3 may be responsible for its low delta-receptor affinity as compared to the two other analogs. A low fractional population of conformers containing two cis peptide bonds was found for compound 2 but not for analog 1 or 3. Initial evidence for this observation was obtained from NMR differential line-broadening experiments and later confirmed by molecular mechanics simulations. Comparison of the temperature dependence of amide proton chemical shifts acquired for the three cyclic analogs indicate a large degree of intramolecular hydrogen bonding for 1 but not for the other two peptides.
Collapse
Affiliation(s)
- K A Carpenter
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, Quebec, Canada
| | | | | | | |
Collapse
|
8
|
Kolossváry I, Guida WC. Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis: Application to Cyclic and Acyclic Alkanes and Cyclic Peptides. J Am Chem Soc 1996. [DOI: 10.1021/ja952478m] [Citation(s) in RCA: 350] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- István Kolossváry
- Contribution from the Department of Chemical Information Technology, Technical University of Budapest, Szt. Gellért tér 4, 1111 Budapest, Hungary, and Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901
| | - Wayne C. Guida
- Contribution from the Department of Chemical Information Technology, Technical University of Budapest, Szt. Gellért tér 4, 1111 Budapest, Hungary, and Research Department, Pharmaceuticals Division, Ciba-Geigy Corporation, Summit, New Jersey 07901
| |
Collapse
|
9
|
Chapter 28. Structure-Based Design from Flexible Ligands. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1995. [DOI: 10.1016/s0065-7743(08)60941-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|
10
|
On searching the conformational space of cyclic molecules. Conformational interconversion pathways in trans-cyclosilkenes. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0166-1280(94)80095-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
11
|
|
12
|
Bruccoleri RE. Application of Systematic Conformational Search to Protein Modeling. MOLECULAR SIMULATION 1993. [DOI: 10.1080/08927029308022163] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
13
|
Bogusky MJ, Naylor AM, Pitzenberger SM, Nutt RF, Brady SF, Colton CD, Sisko JT, Anderson PS, Veber DF. NMR and molecular modeling characterization of RGD containing peptides. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1992; 39:63-76. [PMID: 1634331 DOI: 10.1111/j.1399-3011.1992.tb01557.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The tripeptide sequence arginine-glycine-aspartic acid (RGD) has been shown to be the key recognition segment in numerous cell adhesion proteins. The solution conformation and dynamics in DMSO-d6 of the cyclic pentapeptides, [formula: see text], a potent fibrinogen receptor antagonist, and [formula: see text], a weak fibrinogen receptor antagonist, have been characterized by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. 1H-1H distance constraints derived from two-dimensional NOE spectroscopy and torsional angle constraints obtained from 3JNH-H alpha coupling constants, combined with computer-assisted modeling using conformational searching algorithms and energy minimization have allowed several low energy conformations of the peptides to be determined. Low temperature studies in combination with molecular dynamics simulations suggest that each peptide does not exist in a single, well-defined conformation, but as an equilibrating mixture of conformers in fast exchange on the NMR timescale. The experimental results can be fit by considering pairs of low energy conformers. Despite this inherent flexibility, distinct conformational preferences were found which may be related to the biological activity of the peptides.
Collapse
Affiliation(s)
- M J Bogusky
- Medicinal Chemistry Department, Merck Sharp & Dohme Research Laboratories, West Point, Pennsylvania
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Wilkes BC, Schiller PW. Comparative conformational analysis of [D-Pen2,D-Pen5]enkephalin (DPDPE): a molecular mechanics study. J Comput Aided Mol Des 1991; 5:293-302. [PMID: 1795179 DOI: 10.1007/bf00126664] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A theoretical conformational analysis (molecular mechanics study) of the delta opioid receptor-selective enkephalin analog H-Tyr-D-Pen-Gly-Phe-D-Pen-OH (DPDPE) was performed, based on the use of the SYBYL software. The study led to the identification of several conformers that were significantly lower in energy than previously reported candidate conformers of DPDPE which, for comparative purposes, were also minimized by using the standard SYBYL force field. The results revealed a considerable degree of conformational flexibility of the DPDPE molecule, and suggested that incorporation of further conformational constraints into this enkephalin analog will be necessary in order to elucidate its receptor-bound conformation.
Collapse
Affiliation(s)
- B C Wilkes
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, Quebec, Canada
| | | |
Collapse
|
15
|
Spivak CE, Waters JA, Yadav JS, Shang WC, Hermsmeier M, Liang RF, Gund TM. (+-)-Octahydro-2-methyl-trans-5 (1H)-isoquinolone methiodide: a probe that reveals a partial map of the nicotinic receptor's recognition site. JOURNAL OF MOLECULAR GRAPHICS 1991; 9:105-10, 100-1. [PMID: 1768639 DOI: 10.1016/0263-7855(91)85006-k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A new, semirigid, nicotinic agonist (+-)-octahydro-2-methyl-trans-5 (1H)-isoquinolone methiodide was synthesized. The disposition of this agonist's nitrogen and carbonyl group conforms well to the prevailing notion of a pharmacophore for the nicotinic receptor. Comparing its structure and electrostatic potential surfaces, we predicted that its activity would be similar to that of carbamylcholine at the frog neuromuscular junction. Instead, the potency of the isoquinolone was only 0.015 times as potent as (+)-carbamylcholine. We conclude, after eliminating other possibilities, that the vicinity of the carbonyl group of an agonist must be planar to fit a confined space within the receptor's recognition site. The isoquinolone is a weak agonist because its methylene group beta to the carbonyl intrudes on this space.
Collapse
Affiliation(s)
- C E Spivak
- Addiction Research Center, National Institute on Drug Abuse, Baltimore, MD 21224
| | | | | | | | | | | | | |
Collapse
|
16
|
Braun W. Distance geometry in distance and torsion angle space: Flexibility, convergence and sampling properties. Proteins 1991. [DOI: 10.1007/978-94-010-9063-6_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
17
|
Carrupt PA, el Tayar N, Karlén A, Testa B. Molecular electrostatic potentials for characterizing drug-biosystem interactions. Methods Enzymol 1991; 203:638-77. [PMID: 1662332 DOI: 10.1016/0076-6879(91)03033-d] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
18
|
|
19
|
Senn H, Loosli HR, Sanner M, Braun W. Conformational studies of cyclic peptide structures in solution from 1H-Nmr data by distance geometry calculation and restrained energy minimization. Biopolymers 1990; 29:1387-400. [PMID: 2361151 DOI: 10.1002/bip.360291006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The three-dimensional structure of a cyclic bouvardin analogue, cyclo (-Pro-MeTyr-Ala-MeTyr-MeTyr-D-Ala-) has been determined by distance geometry calculation and restrained energy minimization from nmr data. The preparation of the input for the distance geometry calculations, the modification of the amino acid library, and the analysis of the structures were done with the aid of a recently developed software package, GEOM. A great variety of different initial structures were explored to check the uniqueness of the determined solution structure. Calculations with 500 different initial structures and two different strategies led to a uniquely determined backbone conformation with a root mean square deviations value of 0.4 A. The backbone structure consists of two beta-turns, a beta-II turn at Pro1-MeTyr2, and a beta-VI turn at MeTyr4-MeTyr5. The efficiency of the two calculation strategies were compared in order to propose an optimal means for performing distance geometry calculations with cyclic structures.
Collapse
Affiliation(s)
- H Senn
- Sandoz Ltd., Preclinical Research, CH-4002 Basle, Switzerland
| | | | | | | |
Collapse
|
20
|
Abstract
A theoretical conformational analysis (molecular mechanics study) of nine cyclic tetrapeptides, structurally related to the highly mu-receptor-selective dermorphin analogue H-Tyr-D-Orn-Phe-Asp-NH2, was performed. These compounds display considerable diversity in their mu-receptor affinity and selectivity. A systematic search and subsequent energy minimization in absence of the exocyclic Tyr1 residue and Phe3 side chain revealed the constrained nature of the 11-13-membered ring structures contained in these analogues. No more than four low-energy conformers (within 2 kcal/mol of the lowest energy conformation) were found in each case. After attachment of the Tyr1 moiety and Phe3 side chain to the "bare" low-energy ring structures, a systematic search and energy minimization of these exocyclic moieties resulted in a limited number of low-energy conformational families for all compounds. Five analogues with high mu-receptor affinity--H-Tyr-D-Orn-Phe-Asp-NH2, H-Tyr-D-Orn-Phe-D-Asp-NH2, H-Tyr-D-Asp-Phe-Orn-NH2, H-Tyr-D-Asp-Phe-A2bu-NH2 (A2 bu: alpha, gamma-diaminobutyric acid) and H-Tyr-D-Cys-Phe-Cys-NH2--all showed a tilted stacking interaction between the Tyr1 and Phe3 aromatic rings in the lowest or second lowest energy conformation found. The same kind of stacking was not possible in low-energy conformers of the four analogues with poor affinity for the mu-receptor [H-Tyr-L-Orn-Phe-Asp-NH2, H-Tyr-D-Orn-D-Phe-Asp-NH2, H-Tyr-D-Orn-Phe(NMe)-Asp-NH2 [Phe(NMe): N alpha-methylphenylalanine], and H-Tyr-D-Orn-Phg-Asp-NH2 (Phg: phenylglycine)].(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- B C Wilkes
- Laboratory of Chemical Biology and Peptide Research, Clinical Research Institute of Montreal, Quebec, Canada
| | | |
Collapse
|
21
|
Peishoff CE, Dixon JS, Kopple KD. Application of the distance geometry algorithm to cyclic oligopeptide conformation searches. Biopolymers 1990. [DOI: 10.1002/bip.360300107] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
22
|
Sanner M, Widmer A, Senn H, Braun W. GEOM: a new tool for molecular modelling based on distance geometry calculations with NMR data. J Comput Aided Mol Des 1989; 3:195-210. [PMID: 2585001 DOI: 10.1007/bf01533068] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
GEOM is a new graphics tool which allows the use of distance geometry to compute linear and cyclic structures typically arising in drug design situations. Modified amino acids or monomeric organic entities can be easily constructed in an interactive way and deposited in the library of the distance geometry program together with geometric information required for structure calculation in dihedral angle space. In addition, GEOM is able to produce all files needed to calculate a structure based on NMR data (NOE and J-coupling constraints) and it permits the graphic analysis and comparison of computed structures. The application of GEOM is demonstrated in three examples: modelling of cyclosporin A structures with and without a limited set of H-bond constraints and modelling of a cyclic hexapeptide with a full NMR data set.
Collapse
Affiliation(s)
- M Sanner
- Sandoz AG, Preclinical Research, Basel, Switzerland
| | | | | | | |
Collapse
|
23
|
|
24
|
Tonge AP, Murray-rust P, Gibbons WA, McLachlan LK. Determination of the major solution conformation of tyrocidine A, using molecular mechanics energy minimization and NMR-derived distance and torsion angle constraints. J Comput Chem 1988. [DOI: 10.1002/jcc.540090511] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
25
|
Pepermans H, Tourwé D, Van Binst G, Boelens R, Scheek RM, Van Gunsteren WF, Kaptein R. The combined use of NMR, distance geometry, and restrained molecular dynamics for the conformational study of a cyclic somatostatin analogue. Biopolymers 1988; 27:323-38. [PMID: 3359005 DOI: 10.1002/bip.360270211] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
|
26
|
Wilkes BC, Schiller PW. Theoretical conformational analysis of a mu-selective cyclic opioid peptide analog. Biopolymers 1987; 26:1431-44. [PMID: 2822163 DOI: 10.1002/bip.360260817] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
27
|
Braun W. Distance geometry and related methods for protein structure determination from NMR data. Q Rev Biophys 1987; 19:115-57. [PMID: 3310077 DOI: 10.1017/s0033583500004108] [Citation(s) in RCA: 184] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Computational tools have been developed in the last few years, to allow a direct determination of protein structures from NMR data. Numerical calculations with simulated and experimental NMR constraints for distances and torsional angles show that data sets available with present NMR techniques carry enough information to determine reliably the global fold of a small protein. The maximum size of a protein for which the direct method can be applied is not limited by the computational tools but rather by the resolution of the two-dimensional spectra. A general estimate of the maximum size would be a molecular weight of about 10,000 (Markley et al. 1984), but parts of larger proteins might be accessible with the method. Effort for improvement of the NMR structures should be concentrated more on the local conformation rather than the global features. The r.m.s. D values for variations of the polypeptide backbone fold are on the order of 1.5-2 A for several of the studied proteins, indicating that the global structure is well determined by the present NMR data and their interpretation. The local structures are sometimes rather poor, with standard deviations for the backbone torsion angles of about 50 degrees. Possible improvements would be stereospecific resonance assignments of individual methylene protons and individual assignments of the methyl groups of the branched side-chains. Accurate estimates of the short-range NOE distance constraints by calibrating the distance constraints, including segmental flexibility effects, and combined use of distance geometry, energy minimization and molecular dynamics calculations, are further tools for improving the structures.
Collapse
Affiliation(s)
- W Braun
- Institut für Molekularbiologie u. Biophysik, Eidgenössische Technische Hochschule, Zürich, Switzerland
| |
Collapse
|
28
|
Chapter 27 Molecular Modeling as an Aid to Drug Design and Discovery. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1987. [DOI: 10.1016/s0065-7743(08)61175-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
|
29
|
Chapter 6 Neuropeptides and Their Processing: Targets for Drug Design. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1987. [DOI: 10.1016/s0065-7743(08)61154-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
|