1
|
Park HS, Byun BJ, Kang YK. Exploring Conformational Preferences of Leu-enkephalin Using the Conformational Search and Double-Hybrid DFT Energy Calculations. ACS OMEGA 2022; 7:27755-27768. [PMID: 35967045 PMCID: PMC9366962 DOI: 10.1021/acsomega.2c03942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The conformational preferences of Leu-enkephalin (Leu-Enk) were explored by the conformational search and density functional theory (DFT) calculations. By a combination of low-energy conformers of each residue, the initial structures of the neutral Leu-Enk were generated and optimized using the ECEPP3 force field in the gas phase. These structures were reoptimized at the HF/3-21G(d) and M06-2X levels of theory with 6-31G(d) and 6-31+G(d) basis functions. We finally located the 139 structures with the relative energy <10 kcal mol-1 in the gas phase, from which the structures of the corresponding zwitterionic Leu-Enk were generated and reoptimized at the M06-2X/6-31+G(d) level of theory using the implicit solvation model based on density (SMD) in water. The conformational preferences of Leu-Enk were analyzed using Gibbs free energies corrected by single-point energies calculated at the double-hybrid DSD-PBEP86-D3BJ/def2-TZVP level of theory in the gas phase and in water. The neutral Leu-Enk dominantly adopted a folded structure in the gas phase stabilized by three H-bonds with a βII'-bend-like motif at the Gly3-Phe4 sequence and a close contact between the side chains of Phe4 and Leu5. The zwitterionic Leu-Enk exhibited a folded structure in water stabilized by three H-bonds with double β-bends such as a βII' bend at the Gly2-Gly3 sequence and a βI bend at the Gly3-Phe4 sequence. The calculated ensemble-averaged distance between CGly2 α and CLeu5 α of the zwitterionic Leu-Enk in water is consistent with the value estimated from the simulated annealing using the distance constraints derived from nuclear Overhauser effect spectroscopy (NOESY) spectra in water. Interestingly, the preferred conformations of the neutral and zwitterionic Leu-Enk are new folded structures not predicted by earlier computational studies. According to the refined model of the zwitterionic Leu-Enk bound to δ-opioid receptor (δOR), there were favorable interactions of the terminal charged groups of Leu-Enk with the side chains of charged residues of δOR as well as a favorable CAryl···H interaction of the Phe4 residue of Leu-Enk with Trp284 of δOR. Hence, these favorable interactions would induce the folded structure of the zwitterionic Leu-Enk with double β-bends isolated in water into the "bioactive conformation" like an extended structure when binding to δOR.
Collapse
Affiliation(s)
- Hae Sook Park
- Department
of Nursing, Cheju Halla University, 38 Halladaehak-ro, Jeju, Jeju-do 63092, Republic of Korea
| | - Byung Jin Byun
- Drug
Discovery Center, JW Pharmaceutical Co.
Ltd., 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725, Republic
of Korea
| | - Young Kee Kang
- Department
of Chemistry, Chungbuk National University, 1 Chungdae-ro,
Seowon-gu, Cheongju, Chungbuk 28644, Republic of Korea
| |
Collapse
|
2
|
Root-Bernstein R, Churchill B. Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities. Life (Basel) 2021; 11:life11111217. [PMID: 34833093 PMCID: PMC8623292 DOI: 10.3390/life11111217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Cross-talk between opioid and adrenergic receptors is well-characterized and involves second messenger systems, the formation of receptor heterodimers, and the presence of extracellular allosteric binding regions for the complementary ligand; however, the evolutionary origins of these interactions have not been investigated. We propose that opioid and adrenergic ligands and receptors co-evolved from a common set of modular precursors so that they share binding functions. We demonstrate the plausibility of this hypothesis through a review of experimental evidence for molecularly complementary modules and report unexpected homologies between the two receptor types. Briefly, opioids form homodimers also bind adrenergic compounds; opioids bind to conserved extracellular regions of adrenergic receptors while adrenergic compounds bind to conserved extracellular regions of opioid receptors; opioid-like modules appear in both sets of receptors within key ligand-binding regions. Transmembrane regions associated with homodimerization of each class of receptors are also highly conserved across receptor types and implicated in heterodimerization. This conservation of multiple functional modules suggests opioid–adrenergic ligand and receptor co-evolution and provides mechanisms for explaining the evolution of their crosstalk. These modules also suggest the structure of a primordial receptor, providing clues for engineering receptor functions.
Collapse
|
3
|
Peggion C, Moretto A, Formaggio F, Crisma M, Toniolo C. Multiple, consecutive, fully-extended 2.0₅-helix peptide conformation. Biopolymers 2016; 100:621-36. [PMID: 23893391 DOI: 10.1002/bip.22267] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 02/01/2023]
Abstract
The peptide 2.0(5)-helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α)-tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α)-atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and three-dimensional (3D)-structural features. The infrared absorption and the nuclear magnetic resonance parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 3(10)-helix, thus generating an attractive molecular spring.
Collapse
Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131, Padova, Italy
| | | | | | | | | |
Collapse
|
4
|
Pawlak T, Potrzebowski MJ. Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography. J Phys Chem B 2014; 118:3298-309. [PMID: 24605867 DOI: 10.1021/jp500379e] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.
Collapse
Affiliation(s)
- Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences , Sienkiewicza 112, 90-363 Lodz, Poland
| | | |
Collapse
|
5
|
Rochon K, Proteau-Gagné A, Bourassa P, Nadon JF, Côté J, Bournival V, Gobeil F, Guérin B, Dory YL, Gendron L. Preparation and evaluation at the delta opioid receptor of a series of linear leu-enkephalin analogues obtained by systematic replacement of the amides. ACS Chem Neurosci 2013; 4:1204-16. [PMID: 23650868 PMCID: PMC3750687 DOI: 10.1021/cn4000583] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/07/2013] [Indexed: 12/16/2022] Open
Abstract
Leu-enkephalin analogues, in which the amide bonds were sequentially and systematically replaced either by ester or N-methyl amide bonds, were prepared using classical organic chemistry as well as solid phase peptide synthesis (SPPS). The peptidomimetics were characterized using competition binding, ERK1/2 phosphorylation, receptor internalization, and contractility assays to evaluate their pharmacological profile over the delta opioid receptor (DOPr). The lipophilicity (LogD7.4) and plasma stability of the active analogues were also measured. Our results revealed that the last amide bond can be successfully replaced by either an ester or an N-methyl amide bond without significantly decreasing the biological activity of the corresponding analogues when compared to Leu-enkephalin. The peptidomimetics with an N-methyl amide function between residues Phe and Leu were found to be more lipophilic and more stable than Leu-enkephalin. Findings from the present study further revealed that the hydrogen-bond donor properties of the fourth amide of Leu-enkephalin are not important for its biological activity on DOPr. Our results show that the systematic replacement of amide bonds by isosteric functions represents an efficient way to design and synthesize novel peptide analogues with enhanced stability. Our findings further suggest that such a strategy can also be useful to study the biological roles of amide bonds.
Collapse
Affiliation(s)
- Kristina Rochon
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Arnaud Proteau-Gagné
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Philippe Bourassa
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Jean-François Nadon
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Jérome Côté
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Véronique Bournival
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Fernand Gobeil
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Brigitte Guérin
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Yves L. Dory
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| | - Louis Gendron
- Département de Physiologie
et Biophysique, Laboratoire de Synthèse Supramoléculaire, Département
de Chimie, Département de pharmacologie, and Département de Médecine
Nucléaire et Radiobiologie, Institut de Pharmacologie, Université de Sherbrooke, 3001, 12 Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada
| |
Collapse
|
6
|
Magic angle spinning NMR study of interaction of N-terminal sequence of dermorphin (Tyr-d-Ala-Phe-Gly) with phospholipids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2579-87. [DOI: 10.1016/j.bbamem.2012.06.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 06/05/2012] [Accepted: 06/18/2012] [Indexed: 01/02/2023]
|
7
|
Ramya L, Gautham N. Conformational space exploration of met- and Leu-enkephalin using the mols method, molecular dynamics, and Monte Carlo simulation-a comparative study. Biopolymers 2011; 97:165-76. [DOI: 10.1002/bip.21721] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 09/16/2011] [Accepted: 09/16/2011] [Indexed: 11/09/2022]
|
8
|
Ramya L, Nehru Viji S, Arun Prasad P, Kanagasabai V, Gautham N. MOLS sampling and its applications in structural biophysics. Biophys Rev 2010; 2:169-179. [PMID: 28510038 DOI: 10.1007/s12551-010-0039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Accepted: 10/19/2010] [Indexed: 12/01/2022] Open
Abstract
This review describes the MOLS method and its applications. This computational method has been developed in our laboratory primarily to explore the conformational space of small peptides and identify features of interest, particularly the minima, i.e., the low energy conformations. A systematic "brute-force" search through the vast conformational space for such features faces the insurmountable problem of combinatorial explosion, whilst other techniques, e.g., Monte Carlo searches, are somewhat limited in their region of exploration and may be considered inexhaustive. The MOLS method, on the other hand, uses a sampling technique commonly employed in experimental design theory to identify a small sample of the conformational space that nevertheless retains information about the entire space. The information is extracted using a technique that is a variant of the self-consistent mean field technique, which has been used to identify, for example, the optimal set of side-chain conformations in a protein. Applications of the MOLS method to understand peptide structure, predict the structures of loops in proteins, predict three-dimensional structures of small proteins, and arrive at the best conformation, orientation, and positions of a small molecule ligand in a protein receptor site have all yielded satisfactory results.
Collapse
Affiliation(s)
- L Ramya
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, 600025, India
| | - Shankaran Nehru Viji
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, 600025, India
| | - Pandurangan Arun Prasad
- Institute of Structural and Molecular Biology and Crystallography, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Vadivel Kanagasabai
- Department of Orthopaedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Namasivayam Gautham
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, 600025, India.
| |
Collapse
|
9
|
Proteau-Gagné A, Bournival V, Rochon K, Dory YL, Gendron L. Exploring the Backbone of Enkephalins To Adjust Their Pharmacological Profile for the δ-Opioid Receptor. ACS Chem Neurosci 2010; 1:757-69. [PMID: 22778812 DOI: 10.1021/cn1000759] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Accepted: 09/08/2010] [Indexed: 12/23/2022] Open
Abstract
The role of each of the four amide bonds in Leu(5)-enkephalin was investigated by systematically and sequentially replacing each with its corresponding trans-alkene. Six Leu(5)-enkephalin analogs based on six dipeptide surrogates and two Met(5)-enkephalin analogs were synthesized and thoroughly tested using a δ-opioid receptor internalization assay, an ERK1/2 activation assay, and a competition binding assay to evaluate their biological properties. We observed that an E-alkene can efficiently replace the first amide bond of Leu(5)- and Met(5)-enkephalin without significantly affecting biological activity. By contrast, the second amide bond was found to be highly sensitive to the same modification, suggesting that it is involved in biologically essential intra- or intermolecular interactions. Finally, we observed that the affinity and activity of analogs containing an E-alkene at either the third or fourth position were partially reduced, indicating that these amide bonds are less important for these intra- or intermolecular interactions. Overall, our study demonstrates that the systematic and sequential replacement of amide bonds by E-alkene represents an efficient way to explore peptide backbones.
Collapse
Affiliation(s)
| | | | | | - Yves L. Dory
- Laboratoire de synthèse supramoléculaire, Département de chimie,
| | | |
Collapse
|
10
|
Revilla-López G, Torras J, Curcó D, Casanovas J, Calaza MI, Zanuy D, Jiménez AI, Cativiela C, Nussinov R, Grodzinski P, Alemán C. NCAD, a database integrating the intrinsic conformational preferences of non-coded amino acids. J Phys Chem B 2010; 114:7413-22. [PMID: 20455555 PMCID: PMC2896893 DOI: 10.1021/jp102092m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Peptides and proteins find an ever-increasing number of applications in the biomedical and materials engineering fields. The use of non-proteinogenic amino acids endowed with diverse physicochemical and structural features opens the possibility to design proteins and peptides with novel properties and functions. Moreover, non-proteinogenic residues are particularly useful to control the three-dimensional arrangement of peptidic chains, which is a crucial issue for most applications. However, information regarding such amino acids--also called non-coded, non-canonical, or non-standard--is usually scattered among publications specialized in quite diverse fields as well as in patents. Making all these data useful to the scientific community requires new tools and a framework for their assembly and coherent organization. We have successfully compiled, organized, and built a database (NCAD, Non-Coded Amino acids Database) containing information about the intrinsic conformational preferences of non-proteinogenic residues determined by quantum mechanical calculations, as well as bibliographic information about their synthesis, physical and spectroscopic characterization, conformational propensities established experimentally, and applications. The architecture of the database is presented in this work together with the first family of non-coded residues included, namely, alpha-tetrasubstituted alpha-amino acids. Furthermore, the NCAD usefulness is demonstrated through a test-case application example.
Collapse
Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - David Curcó
- Departament d’Enginyeria Química, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona E-08028, Spain
| | - Jordi Casanovas
- Departament de Química, Escola Politècnica Superior, Universitat de Lleida, c/ Jaume II n°69, Lleida E-25001, Spain
| | - M. Isabel Calaza
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - David Zanuy
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
| | - Ana I. Jiménez
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Carlos Cativiela
- Departamento de Química Orgánica, Instituto de Ciencia de Materiales de Aragón, Universidad de Zaragoza – CSIC, 50009 Zaragoza, Spain
| | - Ruth Nussinov
- Basic Science Program, SAIC-Frederick, Inc. Center for Cancer Research Nanobiology Program, NCI, Frederick, MD 21702, USA
- Department of Human Genetics Sackler, Medical School, Tel Aviv University, Tel Aviv 69978, Israel
| | - Piotr Grodzinski
- Alliance for Nanotechnology in Cancer, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
| |
Collapse
|
11
|
Ramya L, Gautham N. Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin. J Chem Theory Comput 2009; 5:2180-90. [DOI: 10.1021/ct9000087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- L. Ramya
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, 600025, India
| | - N. Gautham
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Chennai, 600025, India
| |
Collapse
|
12
|
Vadivel K, Namasivayam G. An estimate of the numbers and density of low-energy structures (or decoys) in the conformational landscape of proteins. PLoS One 2009; 4:e5148. [PMID: 19357778 PMCID: PMC2663821 DOI: 10.1371/journal.pone.0005148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Accepted: 03/02/2009] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The conformational energy landscape of a protein, as calculated by known potential energy functions, has several minima, and one of these corresponds to its native structure. It is however difficult to comprehensively estimate the actual numbers of low energy structures (or decoys), the relationships between them, and how the numbers scale with the size of the protein. METHODOLOGY We have developed an algorithm to rapidly and efficiently identify the low energy conformers of oligo peptides by using mutually orthogonal Latin squares to sample the potential energy hyper surface. Using this algorithm, and the ECEPP/3 potential function, we have made an exhaustive enumeration of the low-energy structures of peptides of different lengths, and have extrapolated these results to larger polypeptides. CONCLUSIONS AND SIGNIFICANCE We show that the number of native-like structures for a polypeptide is, in general, an exponential function of its sequence length. The density of these structures in conformational space remains more or less constant and all the increase appears to come from an expansion in the volume of the space. These results are consistent with earlier reports that were based on other models and techniques.
Collapse
Affiliation(s)
- Kanagasabai Vadivel
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Tamilnadu, India
| | - Gautham Namasivayam
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Tamilnadu, India
- * E-mail:
| |
Collapse
|
13
|
DOI MITSUNOBU, TAKEHARA SHIGERU, ISHIDA TOSHIMASA, INOUE MASATOSHI. Effects of thioamide substitution for the enkephalin conformation. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1989.tb00704.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]
|
14
|
Prasad PA, Kanagasabai V, Arunachalam J, Gautham N. Exploring conformational space using a mean field technique with MOLS sampling. J Biosci 2007; 32:909-20. [PMID: 17914233 DOI: 10.1007/s12038-007-0091-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The computational identification of all the low energy structures of a peptide given only its sequence is not an easy task even for small peptides,due to the multiple-minima problem and combinatorial explosion. We have developed an algorithm, called the MOLS technique,that addresses this problem, and have applied it to a number of different aspects of the study of peptide and protein structure. Conformational studies of oligopeptides, including loop sequences in proteins have been carried out using this technique. In general the calculations identified all the folds determined by previous studies,and in addition picked up other energetically favorable structures. The method was also used to map the energy surface of the peptides. In another application, we have combined the MOLS technique, using it to generate a library of low energy structures of an oligopeptide, with a genetic algorithm to predict protein structures. The method has also been applied to explore the conformational space of loops in protein structures.Further, it has been applied to the problem of docking a ligand in its receptor site, with encouraging results.
Collapse
Affiliation(s)
- P Arun Prasad
- Department of Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | | | | | | |
Collapse
|
15
|
TSUCHIYA K, TERAMAE H, WATANABE T, ISHIMOTO T, NAGASHIMA U. Conformation Analysis of Enkephalin Using Hamiltonian Algorithm– Effect of Mixing Coefficient in HA –. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2007. [DOI: 10.2477/jccj.6.275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
16
|
Ivanova BB, Kolev T, Zareva SY. Solid-state IR-LD spectroscopic and theoretical analysis of glycine-containing peptides and their hydrochlorides. Biopolymers 2006; 82:587-96. [PMID: 16552765 DOI: 10.1002/bip.20512] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
As part of an investigation on the coordination ability of peptides, structural analyses of the solid di-, tri, and tetrapeptides glycyl-glycine (GG), glycyl-glycyl-glycine (GGG), glycyl-glycyl-glycyl-glycine (GGGG), and their protonated hydrochlorides glycyl-glycine.HCl (GGH), glycyl-glycyl-glycine.HCl (GGGH), and glycyl-glycyl-glycyl-glycine.HCl (GGGGH) have been carried out. The quantum chemical calculations (Hartree-Fock/6-31++G**) and linear-dichroic infrared (IR-LD) spectroscopy predict a near to linear structure of the pure ligands, but the experimental IR-LD data are in accordance with a cross-linked disposition of amide fragments in the protonated forms.
Collapse
Affiliation(s)
- Bojidarka B Ivanova
- Sofia University, St. Kl. Ohridsky,Faculty of Chemistry,1164 Sofia, Bulgaria.
| | | | | |
Collapse
|
17
|
Wu YC, Hsieh JY, Lin HC, Hwang CC. Conformational stability and three-dimensional model of the δ-opioid pharmacophore for the extended antiparallel dimer structure of Met-enkephalin in water. J Mol Model 2006; 13:171-7. [PMID: 16972066 DOI: 10.1007/s00894-006-0139-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Accepted: 07/04/2006] [Indexed: 12/01/2022]
Abstract
The conformational stability of the extended antiparallel dimer structure of Met-enkephalin in water was analyzed by examining the hydration structure of enkephalin using molecular dynamics simulations. The result shows that, despite of the hydrophicility of the terminal atoms in the pentapeptide, the main contributor for the stability of the dimer in water is the four intermolecular hydrogen bonds between the Gly(2) and Phe(4) groups. The three-dimensional model of the delta-opioid pharmacophore for this dimer structure was also established. Such a model was demonstrated to match the delta-opioid pharmacophore query derived from the non-peptides SIOM, TAN-67, and OMI perfectly. This result thus strongly supports the assumption that the dimer structure of Met-enkephalin is a possible delta-receptor binding conformation.
Collapse
Affiliation(s)
- Yng-Ching Wu
- Department of Engineering Science, National Cheng Kung University, Tainan, 701, Taiwan
| | | | | | | |
Collapse
|
18
|
Ivanova BB, Arnaudov MG. Solid state linear-dichroic infrared spectral and theoretical analysis of methionine-containing tripeptides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 65:56-61. [PMID: 16458055 DOI: 10.1016/j.saa.2005.09.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 09/17/2005] [Accepted: 09/19/2005] [Indexed: 05/06/2023]
Abstract
Stereo structural characterization of methionine-containing tripeptides glycine-glycine-methionine (Gly-Gly-Met) and methionine-glycine-glycine (Met-Gly-Gly) is carried out by means of linear-dichroic infrared spectral analysis of oriented as nematic liquid crystal suspension solid samples. Thus obtained data are compared with theoretical ones received by ab initio calculations (Hartree-Fock level of theory and 6-31G** basis set). An IR-spectral characterization of both tripeptides is included as well.
Collapse
Affiliation(s)
- Bojidarka B Ivanova
- Sofia University, St. Kl. Ohridski, Faculty of Chemistry, 1164-Sofia, Bulgaria.
| | | |
Collapse
|
19
|
Liu S, Shibata A, Ueno S, Xu F, Baba Y, Jiang D, Li Y. Investigation of interaction of Leu-enkephalin with lipid membranes. Colloids Surf B Biointerfaces 2006; 48:148-58. [PMID: 16542826 DOI: 10.1016/j.colsurfb.2006.02.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 01/26/2006] [Accepted: 02/07/2006] [Indexed: 10/24/2022]
Abstract
Enkephalins are peptides with morphine-like activity. To achieve their biological function, they must be transported from an aqueous phase to the lipid-rich environment of their membrane bound receptor proteins. In our study, zeta potential (ZP) method was used to detect the association of Leu-enkephalin and Leu-enkephalinamide with phospholipid liposomes constituted from egg-phosphatidylcholine (EPC), dioleoyl-phosphatidylethanolamine (DOPE), cholesterol (Chol), sphingomyelin (SM) as well as soybean phospholipid (SBPL). Transfer of the peptides over lipid membranes was examined by electrophysiology technique (ET) and fluorescence spectroscopy (FS), and further confirmed using 4-fluoro-7-nitrobenzofurazan (NBD-F) labeled Leu-enkephalin (NBD-F-enkephalin) with confocal laser scanning microscopy method (CLSM). Results of zeta potential showed that enkephalinamide associated with lipid membranes and gradually saturated on the membranes either hydrophobically or electrostatically or both. Data from electrophysiology technique indicated that Leu-enkephalin could cause transmembrane currents, suggesting the transfer of peptides across lipid membranes. Transfer examined by fluorescence spectroscopy implied that it could be separated into three steps, adsorption, transportation and desorption, which was afterward reaffirmed by confocal laser scanning microscopy. Transfer efficiencies of enkephalin across SBPL, EPC/DOPE, EPC/DOPE/SM, EPC/SM and EPC/Chol lipid bilayer membranes were evaluated with ET and CLSM experiments. Results showed that the addition of either sphingomyelin or cholesterol, or negatively charged lipid in lipid membrane composition could lower the transfer efficiency.
Collapse
Affiliation(s)
- Shaoqian Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China.
| | | | | | | | | | | | | |
Collapse
|
20
|
Koleva BB, Kolev TM, Spiteller M. Structural and spectroscopic analysis of hydrogensquarates of glycine-containing tripeptides. Biopolymers 2006; 83:498-507. [PMID: 16886213 DOI: 10.1002/bip.20581] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The hydrogensquarates of glycine-containing tripeptides glycylglycylglycine (H-Gly-Gly-Gly-OH), glycylglycylmethionine (H-Gly-Gly-Met-OH), and methionylglycylglycine (H-Met-Gly-Gly-OH) have been characterized structurally. Quantum chemical ab initio calculations, solid-state linear-dichroic infrared (IR-LD) spectroscopy, 1H and 13C NMR data, ESI-MS, HPLC-MS/MS, TGV, and DSC methods were employed. The structures consist in a positively charged peptide moiety and a negative hydrogensquarate anion (HSq), stabilized by strong intermolecular hydrogen bonds.
Collapse
Affiliation(s)
- Bojidarka B Koleva
- Sofia University St. Kl. Ohridsky Faculty of Chemistry, Department of Analytical Chemistry, 1164 Sofia, Bulgaria
| | | | | |
Collapse
|
21
|
Hnizdo V, Darian E, Fedorowicz A, Demchuk E, Li S, Singh H. Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules. J Comput Chem 2006; 28:655-68. [PMID: 17195154 DOI: 10.1002/jcc.20589] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A method for estimating the configurational (i.e., non-kinetic) part of the entropy of internal motion in complex molecules is introduced that does not assume any particular parametric form for the underlying probability density function. It is based on the nearest-neighbor (NN) distances of the points of a sample of internal molecular coordinates obtained by a computer simulation of a given molecule. As the method does not make any assumptions about the underlying potential energy function, it accounts fully for any anharmonicity of internal molecular motion. It provides an asymptotically unbiased and consistent estimate of the configurational part of the entropy of the internal degrees of freedom of the molecule. The NN method is illustrated by estimating the configurational entropy of internal rotation of capsaicin and two stereoisomers of tartaric acid, and by providing a much closer upper bound on the configurational entropy of internal rotation of a pentapeptide molecule than that obtained by the standard quasi-harmonic method. As a measure of dependence between any two internal molecular coordinates, a general coefficient of association based on the information-theoretic quantity of mutual information is proposed. Using NN estimates of this measure, statistical clustering procedures can be employed to group the coordinates into clusters of manageable dimensions and characterized by minimal dependence between coordinates belonging to different clusters.
Collapse
Affiliation(s)
- Vladimir Hnizdo
- National Institute for Occupational Safety and Health, Morgantown, West Virginia 26505, USA.
| | | | | | | | | | | |
Collapse
|
22
|
Abstract
Structure and function are intimately related. Nowhere is this more important than the area of bioactive molecules. It has been shown that the enantioselectivity of an enzyme is directly related to its chirality. X-ray crystallography is the only method for determining the "absolute" configuration of a molecule and is the most comprehensive technique available to determine the structure of any molecule at atomic resolution. Results from crystallographic studies provide unambiguous, accurate, and reliable 3-dimensional structural parameters, which are prerequisites for rational drug design and structure-based functional studies.
Collapse
Affiliation(s)
- Jeffrey R Deschamps
- Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375, USA.
| |
Collapse
|
23
|
Watson TM, Hirst * JD. Theoretical studies of the amide I vibrational frequencies of [Leu]-enkephalin. Mol Phys 2005. [DOI: 10.1080/00268970500052387] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
24
|
Tyndall JDA, Pfeiffer B, Abbenante G, Fairlie DP. Over One Hundred Peptide-Activated G Protein-Coupled Receptors Recognize Ligands with Turn Structure. Chem Rev 2005; 105:793-826. [PMID: 15755077 DOI: 10.1021/cr040689g] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Joel D A Tyndall
- Center for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
| | | | | | | |
Collapse
|
25
|
Abstract
Conformational studies of two linear enkephalin molecules, Met-enkephalin and Leu-enkephalin, have been carried using the mutually orthogonal Latin squares (MOLS) technique with the ECEPP/3 force field. This technique was developed recently in our laboratory to perform an unbiased search of the conformational space of peptides and to locate low energy conformations. The present study identified all the folds predicted by other studies, and in addition picked up other energetically favorable structures. The results suggest that the peptide backbone exists as a mixture of folded and unfolded forms (approximately 50% each). The study also provides information on the distribution of the low energy conformations that we have classified on the basis of structural motifs, backbone hydrogen-bonding patterns, and root mean square deviations in atomic positions.
Collapse
Affiliation(s)
- K Vengadesan
- Department of Crystallography and Biophysics, University of Madras, Chennai 600 025, India
| | | |
Collapse
|
26
|
Jalkanen K, Elstner M, Suhai S. Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2003.12.045] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
27
|
Marcotte I, Separovic F, Auger M, Gagné SM. A multidimensional 1H NMR investigation of the conformation of methionine-enkephalin in fast-tumbling bicelles. Biophys J 2004; 86:1587-600. [PMID: 14990485 PMCID: PMC1303993 DOI: 10.1016/s0006-3495(04)74226-5] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2003] [Accepted: 11/07/2003] [Indexed: 11/22/2022] Open
Abstract
Enkephalins are pentapeptides found in the central nervous system. It is believed that these neuropeptides interact with the nerve cell membrane to adopt a conformation suitable for their binding to an opiate receptor. In this work, we have determined the three-dimensional structure of methionine-enkephalin (Menk) in fast-tumbling bicelles using multidimensional (1)H NMR. Bicelles were selected as model membranes because both their bilayer organization and composition resemble those of natural biomembranes. The effect of the membrane composition on the peptide conformation was explored using both zwitterionic (PC bicelles) and negatively charged bicelles (Bic/PG). Pulsed field gradient experiments allowed the determination of the proportion of Menk bound to the model membranes. Approximately 60% of the water-soluble enkephalin was found to associate to the bicellar systems. Structure calculations from torsion angle and NOE-based distance constraints suggest the presence of both micro - and delta-selective conformers of Menk in each system and slightly different conformers in PC bicelles and Bic/PG. As opposed to previous studies of enkephalins in membrane mimetic systems, our results show that these opiate peptides could adopt several conformations in a membrane environment, which is consistent with the flexibility and poor selectivity of enkephalins.
Collapse
Affiliation(s)
- Isabelle Marcotte
- Département de Chimie, Centre de Recherche en Sciences et Ingénierie des Macromolécules, Université Laval, Québec, Québec, Canada, G1K 7P4
| | | | | | | |
Collapse
|
28
|
Chatterjee C, Mukhopadhyay C. Structural alterations of enkephalins in the presence of GM1 ganglioside micelles. Biopolymers 2003; 70:512-21. [PMID: 14648762 DOI: 10.1002/bip.10509] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The enkephalins are endogenous neurotransmitters and bind with high affinity at the delta-receptor. Gangliosides, the major glycans of nerve cells, known to interact both with receptors and ligands on the cell surface, have been implicated to modulate the actions of opioid receptors by allosteric regulation (Wu, G.; Lu, Z. H.; Wei, T. J.; Howells, R. D.; Christoffers, K.; Leeden R. W. Ann NY Acad Sci 1998, 845, 126-138). We have studied the interactions between enkephalins and monosialylated ganglioside GM1 using NMR spectroscopy and fluorescence. The structural models of enkephalins in the presence of GM1 micelles were generated using two-dimensional (1)H-ROESY experiments along with restrained molecular dynamics simulations. We report a conformational alteration of enkephalins in the presence of GM1 micelles.
Collapse
Affiliation(s)
- Chiradip Chatterjee
- Department of Chemistry, University of Calcutta, 92, A. P. C. Rd., Kolkata-700 009, India
| | | |
Collapse
|
29
|
Nielsen BG, Jensen MØ, Bohr HG. The probability distribution of side-chain conformations in [Leu] and [Met]enkephalin determines the potency and selectivity to μ and δ opiate receptors. Biopolymers 2003; 71:577-92. [PMID: 14635098 DOI: 10.1002/bip.10539] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The structure of enkephalin, a small neuropeptide with five amino acids, has been simulated on computers using molecular dynamics. Such simulations exhibit a few stable conformations, which also have been identified experimentally. The simulations provide the possibility to perform cluster analysis in the space defined by potentially pharmacophoric measures such as dihedral angles, side-chain orientation, etc. By analyzing the statistics of the resulting clusters, the probability distribution of the side-chain conformations may be determined. These probabilities allow us to predict the selectivity of [Leu]enkephalin and [Met]enkephalin to the known mu- and delta-type opiate receptors to which they bind as agonists. Other plausible consequences of these probability distributions are discussed in relation to the way in which they may influence the dynamics of the synapse.
Collapse
Affiliation(s)
- Bjørn G Nielsen
- Quantum Protein Centre (QuP), Physics Institute, Technical University of Denmark, B309, Anker Engelundsvej 1, DK-2800 Lyngby, Denmark.
| | | | | |
Collapse
|
30
|
Vengadesan K, Gautham N. Enhanced sampling of the molecular potential energy surface using mutually orthogonal latin squares: application to peptide structures. Biophys J 2003; 84:2897-906. [PMID: 12719222 PMCID: PMC1302853 DOI: 10.1016/s0006-3495(03)70017-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The computational identification of the optimal three-dimensional fold of even a small peptide chain from its sequence, without reference to other known structures, is a complex problem. There have been several attempts at solving this by sampling the potential energy surface of the molecule in a systematic manner. Here we present a new method to carry out the sampling, and to identify low energy conformers of the molecule. The method uses mutually orthogonal Latin squares to select (of the order of) n(2) points from the multidimensional conformation space of size m(n), where n is the number of dimensions (i.e., the number of conformational variables), and m specifies the fineness of the search grid. The sampling is accomplished by first calculating the value of the potential energy function at each one of the selected points. This is followed by analysis of these values of the potential energy to obtain the optimal value for each of the n-variables separately. We show that the set of the n-optimal values obtained in this manner specifies a low energy conformation of the molecule. Repeated application of the method identifies other low energy structures. The computational complexity of this algorithm scales as the fourth power of the size of the molecule. We applied this method to several small peptides, such as the neuropeptide enkephalin, and could identify a set of low energy conformations for each. Many of the structures identified by this method have also been previously identified and characterized by experiment and theory. We also compared the best structures obtained for the tripeptide (Ala)(3) by the present method, with those obtained by an exhaustive grid search, and showed that the algorithm is successful in identifying all the low energy conformers of this molecule.
Collapse
Affiliation(s)
- K Vengadesan
- Department of Crystallography and Biophysics, University of Madras, Chennai 600 025, India
| | | |
Collapse
|
31
|
|
32
|
Bond JP, Deverin SP, Inouye H, el-Agnaf OMA, Teeter MM, Kirschner DA. Assemblies of Alzheimer's peptides A beta 25-35 and A beta 31-35: reverse-turn conformation and side-chain interactions revealed by X-ray diffraction. J Struct Biol 2003; 141:156-70. [PMID: 12615542 DOI: 10.1016/s1047-8477(02)00625-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Alzheimer's beta amyloid protein (A beta) is a 39 to 43 amino acid peptide that is a major component in the neuritic plaques of Alzheimer's disease (AD). The assemblies constituted from residues 25-35 (A beta 25-35), which is a sequence homologous to the tachykinin or neurokinin class of neuropeptides, are neurotoxic. We used X-ray diffraction and electron microscopy to investigate the structure of the assemblies formed by A beta 25-35 peptides and of various length sequences therein, and of tachykinin-like analogues. Most solubilized peptides after subsequent drying produced diffraction patterns characteristic of beta-sheet structure. Moreover, the peptides A beta 31-35 (Ile-Ile-Gly-Leu-Met) and tachykinin analogue A beta(Phe(31))31-35 (Phe-Ile-Gly-Leu-Met) gave powder diffraction patterns to 2.8A Bragg spacing. The observed reflections were indexed by an orthogonal unit cell having dimensions of a=9.36 A, b=15.83 A, and c=20.10 A for the native A beta 31-35 peptide, and a=9.46 A, b=16.22 A, and c=11.06 A for the peptide having the Ile31Phe substitution. The initial model was a beta strand where the hydrogen bonding, chain, and intersheet directions were placed along the a, b, and c axes. An atomic model was fit to the electron density distribution, and subsequent refinement resulted in R factors of 0.27 and 0.26, respectively. Both peptides showed a reverse turn at Gly33 which results in intramolecular hydrogen bonding between the antiparallel chains. Based on previous reports that antagonists for the tachykinin substance P require a reverse turn, and that A beta is cytotoxic when it is oligomeric or fibrillar, we propose that the tachykinin-like A beta 31-35 domain is a turn exposed at the A beta oligomer surface where it could interact with the ligand-binding site of the tachykinin G-protein-coupled receptor.
Collapse
Affiliation(s)
- Jeremy P Bond
- Department of Biology, Higgins Hall, Boston College, Chestnut Hill, MA 02467, USA
| | | | | | | | | | | |
Collapse
|
33
|
Doi M, Asano A, Komura E, Ueda Y. The structure of an endomorphin analogue incorporating 1-aminocyclohexane-1-carboxlylic acid for proline is similar to the beta-turn of Leu-enkephalin. Biochem Biophys Res Commun 2002; 297:138-42. [PMID: 12220521 DOI: 10.1016/s0006-291x(02)02087-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Endomorphin (EM2, Tyr-Pro-Phe-Phe-NH(2)) can assume various conformations related to cis/trans-rotamers of the amide linkage of Tyr-Pro. To control isomerization, restricted or flexible components have been introduced at the Pro position. We focused on [Chx(2)]EM2, an EM2 analogue substituting 1-aminocyclohexane-1-carboxlylic acid (Chx) for Pro. X-ray diffraction analysis revealed that [Chx(2)]EM2 is folded into the trans-form of Tyr-Chx. The manner of folding resembled that seen in D-TIPP, an EM analogue incorporating tetrahydroisoquinoline carboxylic acid, as well as the beta-turn of Leu-enkephalin. Selectivity for the opioid mu-receptor was fairly well conserved by [Chx(2)]EM, suggesting that the folded form is important for mu-selectivity.
Collapse
Affiliation(s)
- Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | | | | | | |
Collapse
|
34
|
Abstract
The conformations of Leu enkephalin in aqueous solution have been investigated as a function of pH using molecular dynamics simulations. The simulations suggest the peptide backbone exists as a mixture of folded and unfolded forms (approximately 50% each) at neutral pH, but is always unfolded at low or high pH. The folded form at neutral pH possesses a 2 --> 5 hydrogen bond and a close head to tail separation. No significant intramolecular hydrogen bonding of the carbonyl oxygens was observed in either the folded or unfolded forms of the peptide. Analysis of the Gly carbonyl oxygens and terminal groups indicated that, while the conformational population distribution of Leu enkephalin did vary noticeably as a function of pH, their hydration was essentially independent of pH and in agreement with the available NMR data. Further study indicated that the unfolded state of the peptide was not random in nature and consisted of one major unfolded backbone arrangement stabilized by a persistent hydrophobic interaction between the side chains of Tyr and Leu.
Collapse
Affiliation(s)
- Mahalaxmi Aburi
- Department of Biochemistry, Kansas State University, Manhattan, KS 66506-3702, USA
| | | |
Collapse
|
35
|
Ishikawa K, Nakamura T, Koga Y. Cross-checking of nanoelectrospray ionization mass spectrometry and computer simulation for the evaluation of the interaction strength of non-covalently bound enkephalins in solution. JOURNAL OF MASS SPECTROMETRY : JMS 2001; 36:937-942. [PMID: 11523094 DOI: 10.1002/jms.197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Nanoelectrospray ionization mass spectrometry (nanoESI-MS) and computer simulation were applied to the characterization of non-covalent interactions of [Leu5]-enkephalin (LE) and its optical isomers, [D-Tyr1, Leu5]-enkephalin (Y-LE), [D-Phe4, Leu5]-enkephalin (F-LE) and [D-Tyr1, D-Phe4, Leu5]-enkephalin (YF-LE). The dimer formation tendencies of the optical isomers of LE were evaluated by nanoESI-MS using quadruply deuterated LE (H2N-Tyr-(2,2-d2)Gly-(2,2-d2)Gly-Phe-Leu-COOH, d4-LE) as an internal standard. The relative interaction strengths of the optical isomers of LE were estimated to be Y-LE < F-LE < LE < YF-LE. Geometry optimization calculations were performed for interactions in vacuo and in water using a semi-empirical SCF method (PM3). The initial coordinate of the dimer structure of LE was taken from that obtained from single-crystalline x-ray diffraction analysis. Estimates of the interaction strengths of the dimer complexes were based on the heats of formation of a dimer complex (Hd) and the corresponding monomers (Hm) using the equation DeltaH = Hd - 2Hm. The values of DeltaH obtained from the calculations for interactions in water decreased in the order Y-LE > F-LE > LE > YF-LE. Since the smaller values of DeltaH correspond to stronger interactions between peptides, the results from computer simulations were qualitatively consistent with those obtained from the nanoESI experiments. The possibility of cross-checking these independent techniques was demonstrated using medium-sized molecules of biological importance. The agreement of the results from the two techniques suggested that nanoESI experiments, at least qualitatively, reflected the relative interaction strengths of non-covalently bound enkephalins in aqueous solution.
Collapse
Affiliation(s)
- K Ishikawa
- National Institute of Materials and Chemical Research, Higashi, Tsukuba, Ibaraki 305-8565, Japan.
| | | | | |
Collapse
|
36
|
Křı́ž Z, Carlsen P, Koča J. Conformational features of linear and cyclic enkephalins. A computational study. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00728-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
37
|
Jin AY, Leung FY, Weaver DF. Three variations of genetic algorithm for searching biomolecular conformation space: Comparison of GAP 1.0, 2.0, and 3.0. J Comput Chem 1999. [DOI: 10.1002/(sici)1096-987x(199910)20:13<1329::aid-jcc1>3.0.co;2-h] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
38
|
Kamihira M, Naito A, Tuzi S, Saitô H. Phenyl Ring Dynamics of Enkephalin Molecules and Behavior of Bound Solvents in the Crystalline States by 2H NMR Spectroscopy. J Phys Chem A 1999. [DOI: 10.1021/jp983222g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Miya Kamihira
- Department of Life Science, Himeji Institute of Technology. Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Akira Naito
- Department of Life Science, Himeji Institute of Technology. Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Satoru Tuzi
- Department of Life Science, Himeji Institute of Technology. Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Hazime Saitô
- Department of Life Science, Himeji Institute of Technology. Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| |
Collapse
|
39
|
Nishimura K, Naito A, Tuzi S, Saitô H, Hashimoto C, Aida M. Determination of the Three-Dimensional Structure of Crystalline Leu-Enkephalin Dihydrate Based on Six Sets of Accurately Determined Interatomic Distances from 13C-REDOR NMR and the Conformation-Dependent 13C Chemical Shifts. J Phys Chem B 1998. [DOI: 10.1021/jp981683w] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Katsuyuki Nishimura
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Akira Naito
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Satoru Tuzi
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Hazime Saitô
- Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo 678-1297, Japan
| | - Chikao Hashimoto
- Department of Chemistry, The Jikei University School of Medicine, Kokuryo-cho, Chofu-shi, Tokyo 182-0022, Japan
| | - Misako Aida
- Biophysics Division, National Cancer Center Research Institute, Tukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan
| |
Collapse
|
40
|
Kamihira M, Naito A, Nishimura K, Tuzi S, Saitô H. High-Resolution Solid-State 13C and 15N NMR Study on Crystalline Leu- and Met-enkephalins: Distinction of Polymorphs, Backbone Dynamics, and Local Conformational Rearrangements Induced by Dehydration or Freezing of Motions of Bound Solvent Molecules. J Phys Chem B 1998. [DOI: 10.1021/jp970106p] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miya Kamihira
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Akira Naito
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Katsuyuki Nishimura
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Satoru Tuzi
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| | - Hazime Saitô
- Laboratory of Molecular Biophysics II, Department of Life Science, Himeji Institute of Technology, Harima Science Garden City, Kamigori, Hyogo, Japan 678-1297
| |
Collapse
|
41
|
Carlacci L. Conformational analysis of [Met5]-enkephalin: solvation and ionization considerations. J Comput Aided Mol Des 1998; 12:195-213. [PMID: 9690177 DOI: 10.1023/a:1007993118927] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
[Met5]-Enkephalin has the sequence Tyr-Gly-Gly-Phe-Met. Only the extended conformation of the peptide has been observed by X-ray crystallography. Nuclear magnetic resonance spectroscopy supports the presence of a turn at Gly 3 and Phe 4 in dimethyl sulfoxide. In this study, the peptide conformational states and thermodynamic properties are understood in terms of ionization state and solvent environment. In the calculation, final conformations obtained from multiple independent Monte Carlo simulated annealing conformational searches are starting points for molecular dynamics simulations. In an aqueous environment given by the use of solvation free energy and the zwitterionic state, dominant structural motifs computed are G-P Type II' bend, G-G Type II' bend, and G-G Type I' bend motifs, in order of increasing free energy. In the calculation of the peptide with neutral N- and C-termini and solvation free energy, the extended conformer dominates (by at least a factor of 2.5), and the conformation of another low free energy conformer superimposes well on the pharmacophoric groups of morphine. Neutralization of charge and solvation induce and stabilize the extended conformation, respectively. A mechanism of inter-conversion between the extended conformer and three bent conformers is supported by phi/psi-scatter plots, and by the conformer relative free energies. An estimate of the entropy change of receptor unbinding is 8.3 cal K-1 mol-1, which gives rise to a -2.5 kcal/mol entropy contribution to the free energy of unbinding at 25 degrees C. The conformational analysis methodology described here should be useful in studies on short peptides and flexible protein surface loops that have important biological implications.
Collapse
Affiliation(s)
- L Carlacci
- Department of Chemistry, University of South Florida, Tampa 33620-5250, USA
| |
Collapse
|
42
|
Deschamps JR, George C, Flippen-Anderson JL. Structural studies of opioid peptides: a review of recent progress in x-ray diffraction studies. Biopolymers 1996; 40:121-39. [PMID: 8541444 DOI: 10.1002/bip.360400102] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The solid state structures of many opioid peptide agonists have been elucidated by x-ray diffraction analysis. Recently, the first structure of an opioid peptide antagonist has been determined. Theoretically, linear peptides can have many different backbone conformations, yet early x-ray studies (1983-1987) on enkephalin and its analogues showed only two different backbone conformations: extended and single beta-bend. In 1989 enkephalin was observed in a third conformation, a double beta-bend. Since that time diffraction studies have been completed on the rationally designed linear opioid peptide agonists DTLET (Tyr-D-Thr-Gly-Phe-Leu-Thr) and DADLE (D-Ala2,D-Leu5-enkephalin) as well as on several cyclic enkephalin analogues including DPDPE (Tyr-[D-Pen-Gly-Phe-D-Pen]) and JOM-13 (Tyr-[D-Cys-Phe-D-Pen]). The most recent review of the x-ray studies on this class of compounds was written in 1988. This paper will update that review to include the results of studies completed since that time.
Collapse
Affiliation(s)
- J R Deschamps
- Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC 20375, USA
| | | | | |
Collapse
|
43
|
Doi M, In Y, Inoue M, Ishida T. Characteristic molecular packing in the crystal structure of tert-butoxycarbonyl-L-phenylalanyl-L-methionine methyl ester. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 44:532-8. [PMID: 7705974 DOI: 10.1111/j.1399-3011.1994.tb01141.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The molecular conformation and association of the peptide Boc-L-Phe-L-Met-OMe have been studied in the solid state by X-ray diffraction. The peptide crystallizes in the orthorhombic system, space group P2(1)2(1)2(1), with cell parameters of a = 9.821(2), b = 25.394(6), c = 28.714(8) A, V = 7161(3) A3. The structure has been solved by direct methods and refined to a final R of 0.079 for 5464 independent reflections with Fo > or = sigma(Fo). The crystal consists of three independent molecular conformations per asymmetric unit. Respective peptide backbones adopt an extended conformation with the side-chains of Phe and Met residues being arranged below and above the backbone chains. Contrary to the sheet structure most frequently observed in the crystal packing of the extended peptide conformations, three independent molecules lie spirally along the c-axis and form a pin-wheel-like crystal packing. The sheet structures formed by two of three independent molecules are almost at right angles to the backbone of the remaining molecule. This molecular packing mode would provide a possible interaction model between the intersecting beta-sheet structure and single-strand structure of polypeptide.
Collapse
Affiliation(s)
- M Doi
- Osaka University of Pharmaceutical Sciences, Japan
| | | | | | | |
Collapse
|
44
|
Flippen-Anderson JL, George C, Deschamps JR, Reddy PA, Lewin AH, Brine GA. X-ray structures of the ? opioid antagonist TIPP and a protected derivative of the ? opioid antagonist ICI 174,864. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/bf00128528] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
45
|
Mitra SN, Subramanian E. Observation of a sterically unfavorable side-chain conformation in a leucyl residue: crystal and molecular structure of L-leucyl-L-leucine.DMSO solvate. Biopolymers 1994; 34:1139-43. [PMID: 7948727 DOI: 10.1002/bip.360340903] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The crystal structure of a dipeptide L-leucyl-L-leucine (C12H24N2O3) has been determined. The crystals are monoclinic, space group P2(1), with a = 5.434(4) A, b = 15.712(7) A, c = 11.275(2) A, beta = 100.41(1) degrees, and Z = 2. The crystals contain one molecule of dimethyl sulfoxide (DMSO) as solvent of crystallization for each dipeptide molecule. The structure has been solved by direct methods and refined to a final R index of 0.059 for 920 reflections (sin theta/lambda < or = 0.60 A-1) with I > or = 2 sigma (I). The trans peptide unit shows substantial degree of non-planarity (delta omega = 14 degrees). The peptide backbone adopts an extended conformation with torsion angles of psi 1 = 138(1) degrees, omega 1 = 166(1) degrees, phi 2 = -149.3(7) degrees, psi 21 = 164.2(7) degrees, and psi 22 = -15(1) degrees. For the first leucyl residue, the side-chain conformation is specified by the torsion angles 1 chi 1 = 176.7(7) degrees, 1 chi 21 = 62(1) degrees, 1 chi 22 = -177.4(8) degrees; the second leucyl residue adopts a sterically unfavorable conformation with 2 chi 1 = 61(1) degrees, 2 chi 21 = 97(1) degrees, and 2 chi 22 = -151(1) degrees. The packing involves head-to-tail interaction of peptide molecules and segregation of polar and nonpolar regions. The DMSO molecule is strongly hydrogen bonded to the terminal NH3+ group.
Collapse
Affiliation(s)
- S N Mitra
- Department of Crystallography and Biophysics, University of Madras, India
| | | |
Collapse
|
46
|
Flippen-Anderson JL, Deschamps JR, Ward KB, George C, Houghten R. Crystal structure of deltakephalin: a delta-selective opioid peptide with a novel beta-bend-like conformation. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 44:97-104. [PMID: 7982763 DOI: 10.1111/j.1399-3011.1994.tb00563.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The solid-state structure of deltakephalin (Tyr-DThr-Gly-Phe-Leu-Thr) has been determined by single-crystal X-ray diffraction. Deltakephalin (DTLET) is a synthetic opioid peptide which differs from enkephalin in that a D-Thr has been substituted for Gly2 and a sixth residue, L-Thr, has been added. Clear colorless plates obtained using vapor diffusion and macro-seeding crystallization techniques were monoclinic; space group C2 with a = 27.389(5), b = 9.205(2), c = 16.788(2) A, beta = 98.87(2) degrees and V = 4181.4(14) A3. The asymmetric unit contained one molecule of DTLET and six molecules of water, giving a calculated density of 1.28 g cm-3. The crystal structure revealed that DTLET has a pseudo type I' beta-bend which is stabilized by an intramolecular side-chain to backbone hydrogen bond. This is the first reported observation of a pseudo beta-bend conformation in a solid-state structure of an enkephalin analog.
Collapse
Affiliation(s)
- J L Flippen-Anderson
- Laboratory for the Structure of Matter, Naval Research Laboratory, Washington, DC
| | | | | | | | | |
Collapse
|
47
|
Montcalm T, Cui W, Zhao H, Guarnieri F, Wilson SR. Simulated annealing of met-enkephalin: low energy states and their relevance to membrane-bound, solution and solid-state conformations. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0166-1280(94)80093-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
48
|
Doi M, Ishibe A, Shinozaki H, Urata H, Inoue M, Ishida T. Conserved and novel structural characteristics of enantiomorphic Leu-enkephalin. X-ray crystal analysis of Leu-enkephalin enantiomer, L-Tyr-Gly-Gly-L-Phe-L-Leu and D-Tyr-Gly-Gly-D-Phe-D-Leu. INTERNATIONAL JOURNAL OF PEPTIDE AND PROTEIN RESEARCH 1994; 43:325-31. [PMID: 8045677 DOI: 10.1111/j.1399-3011.1994.tb00526.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The crystal of the Leu-enkephalin racemate (L-Tyr-Gly-Gly-L-Phe-L-Leu and D-Tyr-Gly-Gly-D-Phe-D-Leu) was obtained as a centrosymmetric space group. Crystal data: C28H37N5O7 x 1.5H2O, Mw = 582.6, triclinic, space group P1, a = 11.176(3), b = 16.115(3), c = 10.204(4) A, alpha = 92.41(3), beta = 104.86(2), gamma = 85.35(2)degrees, V = 1770(1)A3, Z = 2; F(000) = 640, mu(CuK alpha) = 6.50 cm-1, D chi = 1.081 g cm-3. The structure was determined by X-ray diffraction. The conformation of the Leu-enkephalin racemate was classified into the extended form which has been often observed in natural enkephalin. The symmetry-related molecules were connected by hydrogen bonds and arranged in an antiparallel fashion. The molecular packing showed a sheet structure similar to that of natural enkephalin.
Collapse
Affiliation(s)
- M Doi
- Osaka University of Pharmaceutical Sciences, Japan
| | | | | | | | | | | |
Collapse
|
49
|
Dorofeyev VE, Mazur AK. Investigation of conformational equilibrium of polypeptides by internal coordinate stochastic dynamics. Met5-enkephalin. J Biomol Struct Dyn 1993; 11:143-67. [PMID: 8216941 DOI: 10.1080/07391102.1993.10508714] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The equilibrium population of different conformational states of a polypeptide can in principle be obtained by a very long molecular dynamics simulation. The method of internal coordinate molecular dynamics earlier developed in this laboratory (A.K. Mazur and R.A. Abagyan J. Biomol. Struct. Dyn. 6,833 (1989)) allows one to use time steps much larger than usual for computing molecular trajectories. It is shown here that the sampling of the conformational space can be additionally enhanced by adding a random component to the set of forces applied to atoms. We describe the algorithms by which the random force is introduced and also a special method which excludes the fast rotation of polar hydrogens from equations of motion but keeps them movable. As a result the task stated in the title becomes realistic. Internal coordinate stochastic dynamics is applied for scanning the conformational space of the pentapeptide Met5-enkephalin which is a common test example widely used in theoretical studies. A large number of conformational transitions is observed during the 20 ns simulation starting from the global energy minimum thus allowing us to arrive at a nearly Boltzmann distribution of populations of conformational states. A few states are found which are distinguished by high apparent configurational entropy which turn out to correspond well to experimentally observed conformations of enkephalins.
Collapse
Affiliation(s)
- V E Dorofeyev
- Pacific Institute of Bioorganic Chemistry, Russian Academy of Sciences, Vladivostok
| | | |
Collapse
|
50
|
Vajda S, Jafri MS, Sezerman OU, DeLisi C. Necessary conditions for avoiding incorrect polypeptide folds in conformational search by energy minimization. Biopolymers 1993; 33:173-92. [PMID: 8427934 DOI: 10.1002/bip.360330117] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Low energy conformations have been generated for melittin, pancreatic polypeptide, and ribonuclease S-peptide, both in the vicinity of x-ray structures by energy refinement and by an unconstrained search over the entire conformational space. Since the structural polymorphism of these medium-sized peptides in crystal and solution is moderate, comparing the calculated conformation to x-ray and nmr data provides information on local and global behavior of potential functions. Local analysis includes standardization calculations, which show that models with standard geometry can approximate good resolution x-ray data with less than 0.5 A rms deviation (RMSD). However, the atomic coordinates are shifted up to 2 A RMSD by local energy minimization, and thus 2 A is generally the smallest RMSD value one can target in a conformational search using the same energy evaluation models. The unconstrained search was performed by a buildup-type method based on dynamic programming. To accelerate the generation of structures in the conformational search, we used the ECEPP potential, defined in terms of standard polypeptide geometry. A number of low energy conformations were further refined by relaxing the assumption of standard bond lengths and bond angles through the use of the CHARMM potential, and the hydrophobic folding energies of Eisenberg and McLachlan were calculated. Each conformation is described in terms of the RMSD from the native, hydrogen-bonding structure, solvent-accessible surface area, and the ratio of surfaces corresponding to nonpolar and polar residues. The unconstrained search finds conformations that are different from the native, sometimes substantially, and in addition, have lower conformational energies than the native. The origin of deviations is different for each of the three peptides, but in all examples the refined x-ray structures have lower energies than the calculated incorrect folds when (1) the assumption of standard bond lengths and bond angles is relaxed; (2) a small and constant effective dielectric permittivity (epsilon < 10) is used; and (3) the hydrophobic folding energy is incorporated into the potential.
Collapse
Affiliation(s)
- S Vajda
- Department of Biomedical Engineering, Boston University, Massachusetts 02215
| | | | | | | |
Collapse
|