1
|
Ono S, Naylor MR, Townsend CE, Okumura C, Okada O, Lee HW, Lokey RS. Cyclosporin A: Conformational Complexity and Chameleonicity. J Chem Inf Model 2021; 61:5601-5613. [PMID: 34672629 DOI: 10.1021/acs.jcim.1c00771] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chameleonic behavior of cyclosporin A (CsA) was investigated through conformational ensembles employing multicanonical molecular dynamics simulations that could sample the cis and trans isomers of N-methylated amino acids; these assessments were conducted in explicit water, dimethyl sulfoxide, acetonitrile, methanol, chloroform, cyclohexane (CHX), and n-hexane (HEX) using AMBER ff03, AMBER10:EHT, AMBER12:EHT, and AMBER14:EHT force fields. The conformational details were discussed employing the free-energy landscapes (FELs) at T = 300 K; it was observed that the experimentally determined structures of CsA were only a part of the conformational space. Comparing the ROESY measurements in CHX-d12 and HEX-d14, the major conformations in those apolar solvents were essentially the same as that in CDCl3 except for the observation of some sidechain rotamers. The effects of the metal ions on the conformations, including the cis/trans isomerization, were also investigated. Based on the analysis of FELs, it was concluded that the AMBER ff03 force field best described the experimentally derived conformations, indicating that CsA intrinsically formed membrane-permeable conformations and that the metal ions might be the key to the cis/trans isomerization of N-methylated amino acids before binding a partner protein.
Collapse
Affiliation(s)
- Satoshi Ono
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Matthew R Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chieko Okumura
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Okimasa Okada
- Modality Laboratories, Innovative Research Division, Mitsubishi Tanabe Pharma Corporation, 1000 Kamoshida-cho, Aoba-ku, Yokohama, Kanagawa 227-0033, Japan
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| |
Collapse
|
2
|
Lam KHB, Le Blanc JCY, Campbell JL. Separating Isomers, Conformers, and Analogues of Cyclosporin using Differential Mobility Spectroscopy, Mass Spectrometry, and Hydrogen–Deuterium Exchange. Anal Chem 2020; 92:11053-11061. [DOI: 10.1021/acs.analchem.0c00191] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- K. H. Brian Lam
- Department of Chemistry and Centre for Research in Mass Spectrometry, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
| | | | - J. Larry Campbell
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
3
|
Improving oral bioavailability of cyclic peptides by N-methylation. Bioorg Med Chem 2018; 26:2766-2773. [DOI: 10.1016/j.bmc.2017.08.031] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 01/19/2023]
|
4
|
Wang CK, Swedberg JE, Harvey PJ, Kaas Q, Craik DJ. Conformational Flexibility Is a Determinant of Permeability for Cyclosporin. J Phys Chem B 2018; 122:2261-2276. [DOI: 10.1021/acs.jpcb.7b12419] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Conan K. Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Peta J. Harvey
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| |
Collapse
|
5
|
Witek J, Keller BG, Blatter M, Meissner A, Wagner T, Riniker S. Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States. J Chem Inf Model 2016; 56:1547-62. [DOI: 10.1021/acs.jcim.6b00251] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jagna Witek
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Bettina G. Keller
- Department
of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Markus Blatter
- Novartis
Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Axel Meissner
- Novartis
Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Trixie Wagner
- Novartis
Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| |
Collapse
|
6
|
Niven RW. Toward managing chronic rejection after lung transplant: the fate and effects of inhaled cyclosporine in a complex environment. Adv Drug Deliv Rev 2011; 63:88-109. [PMID: 20950661 DOI: 10.1016/j.addr.2010.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 09/09/2010] [Accepted: 10/05/2010] [Indexed: 10/19/2022]
Abstract
The fate and effects of inhaled cyclosporine A (CsA) are considered after deposition on the lung surface. Special emphasis is given to a post-lung transplant environment and to the potential effects of the drug on the various cell types it is expected to encounter. The known stability, metabolism, pharmacokinetics and pharmacodynamics of the drug have been reviewed and discussed in the context of the lung microenvironment. Arguments support the contention that the immuno-inhibitory and anti-inflammatory effects of CsA are not restricted to T-cells. It is likely that pharmacologically effective concentrations of CsA can be sustained in the lungs but due to the complexity of uptake and action, the elucidation of effective posology must ultimately rely on clinical evidence.
Collapse
|
7
|
Horne W, Olsen C, Beierle J, Montero A, Ghadiri M. Probing the Bioactive Conformation of an Archetypal Natural Product HDAC Inhibitor with Conformationally Homogeneous Triazole‐Modified Cyclic Tetrapeptides. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805900] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
8
|
MORELLI MCASTIGLIONE, PASTORE A, PEDONE C, TEMUSSI P, ZANOTTI G, TANCREDI T. Conformational study of cyclolinopeptide A. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1991.tb00087.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Horne WS, Olsen CA, Beierle JM, Montero A, Reza Ghadiri M. Probing the bioactive conformation of an archetypal natural product HDAC inhibitor with conformationally homogeneous triazole-modified cyclic tetrapeptides. Angew Chem Int Ed Engl 2009; 48:4718-24. [PMID: 19267380 PMCID: PMC3041267 DOI: 10.1002/anie.200805900] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fooling enzymes with mock amides: Analogues of apicidin, a cyclic-tetrapeptide inhibitor of histone deacetylase (HDAC), were designed with a 1,4- or 1,5-disubstituted 1,2,3-triazole in place of a backbone amide bond to fix the bond in question in either a trans-like or a cis-like configuration. Thus, the binding affinity of distinct peptide conformations (see picture) could be probed. One analogue proved in some cases to be superior to apicidin as an HDAC inhibitor.
Collapse
Affiliation(s)
| | | | - John M. Beierle
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Ana Montero
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - M. Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| |
Collapse
|
10
|
Luy B, Frank A, Kessler H. Conformational Analysis of Drugs by Nuclear Magnetic Resonance Spectroscopy. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/9783527621286.ch9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
11
|
Klages J, Neubauer C, Coles M, Kessler H, Luy B. Structure Refinement of Cyclosporin A in Chloroform by Using RDCs Measured in a Stretched PDMS-Gel. Chembiochem 2005; 6:1672-8. [PMID: 16138307 DOI: 10.1002/cbic.200500146] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
New developments concerning alignment media for apolar solvents like chloroform make it possible to measure anisotropic parameters such as residual dipolar couplings (RDCs) at relatively low concentrations and natural isotopic abundance. As RDCs provide structural restraints with respect to an external coordinate system, long-range structural arrangements of the time-averaged structure can be determined with high precision. The method is demonstrated on the well-studied cyclo-undecapeptide Cyclosporin A (CsA), for which crystal and conventionally derived NMR structures are available. Neither crystal nor NMR structure are consistent with heteronuclear D(CH) RDCs measured in a stretched poly(dimethylsiloxane) gel, and refinement by using the anisotropic parameter results in a highly defined structure with a slightly changed backbone conformation. The applied methods and interpretation of the structural model are discussed.
Collapse
Affiliation(s)
- Jochen Klages
- Department Chemie, Lehrstuhl für Organische Chemie II, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | | | | | | | | |
Collapse
|
12
|
Seebach D, Ko SY, Kessler H, Köck M, Reggelin M, Schmieder P, Walkinshaw MD, Bölsterli JJ, Bevec D. Thiocyclosporins: Preparation, Solution and Crystal Structure, and Immunosuppressive Activity. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19910740833] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
13
|
Kessler H, Köck M, Wein T, Gehrke M. Reinvestigation of the Conformation of Cyclosporin A in Chloroform. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19900730703] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
14
|
Volter KE, Embrey KJ, Pierens GK, Quinn RJ. A study of the binding requirements of calyculin A and dephosphonocalyculin A with PP1, development of a molecular recognition model for the binding interactions of the okadaic acid class of compounds with PP1. Eur J Pharm Sci 2001; 12:181-94. [PMID: 11113637 DOI: 10.1016/s0928-0987(00)00116-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The interactions of the okadaic acid class of compounds, with special emphasis on the solution structures of calyculin A and dephosphonocalyculin A with PP1 are reported. After examination of the interactions of all docked structures, a receptor based pharmacophore model for the interactions of the protein phosphatase inhibitors has been developed. Calyculin A or dephosphonocalyculin A can interact with the enzyme in either a manner similar to the reported crystal structure, or in an extended form. The inhibitors require two essential regions interacting with the hydrophobic region and the central metal binding regions of the enzyme. This simplified model is consistent with previously published models of the okadaic acid class of compounds with PP1.
Collapse
Affiliation(s)
- K E Volter
- AstraZeneca R&D, Griffith University, Brisbane 4111, Australia
| | | | | | | |
Collapse
|
15
|
Lu BZ, Wang CX, Chen WZ, Wan SZ, Shi YY. A Stochastic Dynamics Simulation Study Associated with Hydration Force and Friction Memory Effect. J Phys Chem B 2000. [DOI: 10.1021/jp994349o] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ben Zhuo Lu
- Center for Biomedical Engineering, Beijing Polytechnic University, Beijing 100022, People's Republic of China, and School of Life Science, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Cun Xin Wang
- Center for Biomedical Engineering, Beijing Polytechnic University, Beijing 100022, People's Republic of China, and School of Life Science, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Wei Zu Chen
- Center for Biomedical Engineering, Beijing Polytechnic University, Beijing 100022, People's Republic of China, and School of Life Science, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Shun Zhou Wan
- Center for Biomedical Engineering, Beijing Polytechnic University, Beijing 100022, People's Republic of China, and School of Life Science, University of Science and Technology of China, Hefei 230026, People's Republic of China
| | - Yun Yu Shi
- Center for Biomedical Engineering, Beijing Polytechnic University, Beijing 100022, People's Republic of China, and School of Life Science, University of Science and Technology of China, Hefei 230026, People's Republic of China
| |
Collapse
|
16
|
Koppitz M, Mathä B, Kessler H. Structure investigation of amphiphilic cyclopeptides in isotropic and anisotropic environments-A model study simulating peptide-membrane interactions. J Pept Sci 1999; 5:507-18. [PMID: 10587314 DOI: 10.1002/(sici)1099-1387(199911)5:11<507::aid-psc219>3.0.co;2-u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
It has been proposed that the membrane allows a much more efficient binding of certain small or medium-sized amphiphilic messenger molecules to their receptor, not only by accumulation of the drug, but also by induction of orientations and conformations that are much more favorable for receptor docking than structures adopted in isotropic phases. A series of eight amphiphilic cyclic peptides containing lipophilic (L-alpha-aminodecanoic acid = Ada, L-alpha-aminohexadecanoic acid = Ahd, Nhdg = N-hexadecylglycine) and hydrophilic (Lys, Asp) amino acids were synthesized and examined by means of NMR spectroscopy and molecular dynamics (MD) simulations in isotropic (CDCl3) and membrane-mimicking anisotropic (SDS/H2O) solvents to study the influence of the environment on their individual conformations. NMR data of cyclo(-Gly1-D-Asp2-Ahd3-Ahd4-Asp5-Gly6+ ++-) (C4), cyclo(-Lys1-D-Pro2-Lys3-Ada4-Pro5-Ada6-) (C5) and cyclo(-Lys1-Pro2-Lys3-Ada4-D-Pro5-Ada6-) (C6) clearly indicate that those compounds are too rigid to perform a conformational change upon transition from an isotropic to an anisotropic environment. On the other hand, the experimental data of cyclo (-Gly1-Asp2-Ahd3-Ahd4-Asp5-Gly6-) (C1), cyclo(-Asp1-Ala2-Nhdg3-Ala4-D-Asp5-) (C7), and cyclo(-D-Asp1-Ala2-Nhdg3-Ala4-Asp5-) (C8) suggest highly flexible unstructured molecules in both environments. However, for cyclo(-Asp1-Asp2-Gly3-Ahd4-Ahd5-Gly6-) (C2) we observed a structure inducing effect of a membrane-like environment. The compound populates three different conformations in SDS/H2O, whereas in CDCI3 no preferred conformation can be detected. cyclo(-D-Asp1-Asp2-Gly3-Ahd4-Ahd5-Gly6-) (C3) clearly exhibits two different conformations with a shifted beta,beta-turn motif in CDCI3 and SDS/H2O solutions. The conformational change could be reproduced in a restraint-free MD simulation using the biphasic membrane mimetic CCl4/H2O. Our results give clear evidence that membrane interactions may not only lead to structure inductions, but can also induce major conformational changes in compounds already exhibiting a defined structure in isotropic solution.
Collapse
Affiliation(s)
- M Koppitz
- Institute of Organic Chemistry and Biochemistry, Technische Universität München, Garching, Germany
| | | | | |
Collapse
|
17
|
Peters GH, Toxvaerd S, Andersen KV, Svendsen A. Analysis of the dynamics of rhizomucor miehei lipase at different temperatures. J Biomol Struct Dyn 1999; 16:1003-18. [PMID: 10333171 DOI: 10.1080/07391102.1999.10508310] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The dynamics of Rhizomucor miehei lipase has been studied by molecular dynamics simulations at temperatures ranging from 200-500K. Simulations carried out in periodic boundary conditions and using explicit water molecules were performed for 400 ps at each temperature. Our results indicate that conformational changes and internal motions in the protein are significantly influenced by the temperature increase. With increasing temperature, the number of internal hydrogen bonds decreases, while surface accessibility, radius of gyration and the number of residues in random coil conformation increase. In the temperature range studied, the motions can be described in a low dimensional subspace, whose dimensionality decreases with increasing temperature. Approximately 80% of the total motion is described by the first (i) 80 eigenvectors at T=200K, (ii) 30 eigenvectors at T=300K and (iii) 10 eigenvectors at T=400K. At high temperature, the alpha-helix covering the active site in the native Rhizomucor miehei lipase, the helix at which end the active site is located, and in particular, the loop (Gly35-Lys50) show extensive flexibility.
Collapse
Affiliation(s)
- G H Peters
- Chem. Dept. III, H.C. Orsted Institutet, University of Copenhagen, Denmark.
| | | | | | | |
Collapse
|
18
|
Volter KE, Pierens GK, Quinn RJ, Wakimoto T, Matsunaga S, Fusetani N. The solution structures of calyculin A and dephosphonocalyculin A by NMR. Bioorg Med Chem Lett 1999; 9:717-22. [PMID: 10201835 DOI: 10.1016/s0960-894x(99)00066-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The NMR solution structure of calyculin A (1) in chloroform exhibits intramolecular interactions, resembling the original crystal structure. In methanol, calyculin A has the hydrogen bonding moieties solvent exposed. Dephosphonocalyculin A in chloroform resembles calyculin A in chloroform and the crystal structure of calyculin A. Dephosphonocalyculin A in methanol resembles calyculin A in methanol.
Collapse
Affiliation(s)
- K E Volter
- Queensland Pharmaceutical Research Institute, Griffith University, Nathan, Brisbane, Australia
| | | | | | | | | | | |
Collapse
|
19
|
SHUN ZHOU WAN CUN XIN WANG YUN YU S. Generalized Langevin dynamics simulation: numerical integration and application of the generalized Langevin equation with an exponential model for the friction kernel. Mol Phys 1998. [DOI: 10.1080/002689798168592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
20
|
Hünenberger PH, Granwehr JK, Aebischer JN, Ghoneim N, Haselbach E, van Gunsteren WF. Experimental and Theoretical Approach to Hydrogen-Bonded Diastereomeric Interactions in a Model Complex. J Am Chem Soc 1997. [DOI: 10.1021/ja970503d] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
21
|
Matter H, Szilágyi L, Forgó P, Marinić Ž, Klaić B. Structure and Dynamics of a Peptidoglycan Monomer in Aqueous Solution Using NMR Spectroscopy and Simulated Annealing Calculations. J Am Chem Soc 1997. [DOI: 10.1021/ja962776z] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
22
|
Wang CX, Wan SZ, Xiang ZX, Shi YY. Incorporating Hydration Force Determined by Boundary Element Method into Stochastic Dynamics. J Phys Chem B 1997. [DOI: 10.1021/jp9615565] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cun Xin Wang
- Center for Fundamental Physics and Department of Biology, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Shun Zhou Wan
- Center for Fundamental Physics and Department of Biology, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Zhe Xin Xiang
- Center for Fundamental Physics and Department of Biology, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Yun Yu Shi
- Center for Fundamental Physics and Department of Biology, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| |
Collapse
|
23
|
Peters GH, van Aalten DM, Edholm O, Toxvaerd S, Bywater R. Dynamics of proteins in different solvent systems: analysis of essential motion in lipases. Biophys J 1996; 71:2245-55. [PMID: 8913568 PMCID: PMC1233717 DOI: 10.1016/s0006-3495(96)79428-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
We have investigated the effect of different solvents on the dynamics of Rhizomucor miehei lipase. Molecular dynamics simulations were performed in water, methyl hexanoate, and cyclohexane. Analysis of the 400-ps trajectories showed that the solvent has a pronounced effect on the geometrical properties of the protein. The radius of gyration and total accessibility surface decrease in organic solvents, whereas the number of hydrogen bonds increases. The essential motions of the protein in different solvents can be described in a low-dimensional "essential subspace," and the dynamic behavior in this subspace correlates with the polarity of the solvent. Methyl hexanoate, which is a substrate for R. miehei lipase, significantly increases the fluctuations in the active-site loop. During the simulation, a methyl hexanoate entered the active-site groove. This observation provides insight into the possible docking mechanism of the substrate.
Collapse
Affiliation(s)
- G H Peters
- Chemistry Department III, H.C. Orsted Institutet, University of Copenhagen, Denmark.
| | | | | | | | | |
Collapse
|
24
|
Affiliation(s)
- S. Toba
- Contribution from the Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - David S. Hartsough
- Contribution from the Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Kenneth M. Merz
- Contribution from the Department of Chemistry, 152 Davey Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802
| |
Collapse
|
25
|
Abstract
In the past years, much effort has been put on the development of new methodologies and algorithms for the prediction of protein secondary and tertiary structures from (sequence) data; this is reviewed in detail. New approaches for these predictions such as neural network methods, genetic algorithms, machine learning, and graph theoretical methods are discussed. Secondary structure prediction algorithms were improved mostly by considering families of related proteins; however, for the reliable tertiary structure modeling of proteins, knowledge-based techniques are still preferred. Methods and examples with more or less successful results are described. Also, programs and parameterizations for energy minimisations, molecular dynamics, and electrostatic interactions have been improved, especially with respect to their former limits of applicability. Other topics discussed in this review include the use of traditional and on-line databases, the docking problem and surface properties of biomolecules, packing of protein cores, de novo design and protein engineering, prediction of membrane protein structures, the verification and reliability of model structures, and progress made with currently available software and computer hardware. In summary, the prediction of the structure, function, and other properties of a protein is still possible only within limits, but these limits continue to be moved.
Collapse
Affiliation(s)
- G Böhm
- Institut für Biotechnologie, Martin-Luther-Universität Halle-Wittenberg, Germany
| |
Collapse
|
26
|
O'Donohue MF, Burgess AW, Walkinshaw MD, Treutlein HR. Modeling conformational changes in cyclosporin A. Protein Sci 1995; 4:2191-202. [PMID: 8535256 PMCID: PMC2142979 DOI: 10.1002/pro.5560041025] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
NMR and X-ray structures for the immunosuppressant cyclosporin A (CsA) reveal a remarkable difference between the unbound (free) conformation in organic solvents and the conformation bound to cyclophilin. We have performed computer simulations of the molecular dynamics of CsA under a variety of conditions and confirmed the stability of these two conformations at room temperature in water and in vacuum. However, when the free conformation was modeled in vacuum at 600 K, a transition pathway leading to the bound conformation was observed. This involved a change in the cis MeLeu-9 peptide bond to a trans conformation and the movement of the side chains forming the dominant hydrophobic cluster (residues MeBmt-1, MeLeu-4, MeLeu-6, and MeLeu-10) to the opposite side of the plane formed by the backbone atoms in the molecular ring. The final conformation had a backbone RMS deviation from the bound conformation of 0.53 A and was as stable in dynamics simulations as the bound conformation. Our calculations allowed us to make a detailed analysis of a transition pathway between the free and the bound conformations of CsA and to identify two distinct regions of coordinated movement in CsA, both of which underwent transitions independently.
Collapse
Affiliation(s)
- M F O'Donohue
- Ludwig Institute of Cancer Research, P.O. Royal Melbourne Hospital, Parkville, Vic, Australia
| | | | | | | |
Collapse
|
27
|
Kovacs H, Mark AE, Johansson J, van Gunsteren WF. The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfactant protein C in chloroform, methanol and water. J Mol Biol 1995; 247:808-22. [PMID: 7723032 DOI: 10.1016/s0022-2836(05)80156-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A series of three molecular dynamics simulations at 300 K in explicit solvent environments of chloroform, methanol and water has been performed on the pulmonary surfactant lipoprotein, SP-C, comprising several consecutive valine residues in order to investigate the stability of the alpha-helical conformation. Two additional simulations were performed on truncated SP-C with a five-residue N-terminal deletion at 300 K and 500 K in water, the high temperature run in order to increase the rate of peptide denaturation. Indications of destabilization appear in chloroform during 1 ns while the SP-C alpha-helix is remarkably stable during 1 ns in methanol and water. In particular the polyvalyl part comprising residues Val15 to Val21 remains intact even at elevated temperature, and the valines do not disrupt the alpha-helical conformation. The valyl-rotamer sampling is partly restricted. Unfolding takes place successively along the primary sequence starting from the C-terminal end. Factors affecting polypeptide stability in molecular dynamics simulations are addressed. The intrinsic helix-forming tendency of valine residues and its dependence on the sequence context, and the role of the solvent environment in stabilizing or destabilizing an alpha-helical fold, are discussed.
Collapse
Affiliation(s)
- H Kovacs
- Laboratory of Physical Chemistry, ETH-Zentrum CH-8092, Zürich, Switzerland
| | | | | | | |
Collapse
|
28
|
Varnek AA, Wipff G, Glebov AS, Feil D. An application of the Miertus-Scrocco-Tomasi solvation model in molecular mechanics and dynamics simulations. J Comput Chem 1995. [DOI: 10.1002/jcc.540160102] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
29
|
|
30
|
|
31
|
Improta S, Pastore A, Mammi S, Peggion E. Conformation and molecular dynamics calculations on uteroglobin fragment 18-47. Biopolymers 1994; 34:773-82. [PMID: 8025221 DOI: 10.1002/bip.360340609] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The conformational properties of fragment 18-47 of rabbit uteroglobin in aqueous solution containing SDS micelles were investigated by two-dimensional nmr spectroscopy and molecular dynamics calculations. The fragment comprises helices II and III and the beta-turn connecting the two helices. The nmr results and nmr-restrained molecular dynamics calculations showed that in the isolated fragment the elements of secondary structure present in the intact protein are preserved only in part. Specifically, a well-defined alpha-helix was found in the sequence 33-44, corresponding to helix III of uteroglobin, while the regions of helix II and beta-turn are characterized by high flexibility in the fragment.
Collapse
Affiliation(s)
- S Improta
- Department of Organic Chemistry, University of Padova, Italy
| | | | | | | |
Collapse
|
32
|
Shaw RA, Mantsch HH, Chowdhry BZ. Conformational changes in the cyclic undecapeptide cyclosporin induced by interaction with metal ions. An FTIR study. Int J Biol Macromol 1994; 16:143-8. [PMID: 7981161 DOI: 10.1016/0141-8130(94)90041-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Infra-red spectra have been measured for the cyclic undecapeptide cyclosporin A (CsA) and three analogues CsC, CsD and CsH in acetonitrile and in the presence of 10:1 molar excess of Mg2+, Ca2+, Na+ or Li+ in the same solvent. Interaction with each of these ions is suggested by marked changes in band positions over the amide I region (1600-1700 cm-1). The formation of complexes of cyclosporin with calcium and magnesium ions is indicated by the presence of C = O stretching bands well outside the range normally expected for the amide I absorptions of free peptides. Although they share this characteristic, the spectra indicate that the mode and/or strength of Ca2+ binding is quite different from that of Mg2+ binding. In contrast, the two monovalent ions interact with CsA, CsC and CsD to yield spectra that are very similar to one another. The spectra are consistent with binding of the monovalent ions simultaneously to several carbonyl groups of the loop structure.
Collapse
Affiliation(s)
- R A Shaw
- Institute for Biodiagnostics, National Research Council of Canada, Winnipeg, Manitoba
| | | | | |
Collapse
|
33
|
Mierke DF, Kessler H. Improved molecular dynamics simulations for the determination of peptide structures. Biopolymers 1993; 33:1003-17. [PMID: 8343582 DOI: 10.1002/bip.360330703] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this article a few methods or modifications proven to be useful in the conformational examination of peptides and related molecules by molecular dynamics are illustrated. The first is the explicit use of organic solvents in the simulations. For many cases such solvents are appropriate since the nmr measurements (or other experimental observations) were carried out in the same solvent. Here, the use of dimethylsulfoxide and chloroform in molecular dynamics is described, with some advantages of the use of these solvents high-lighted. A constant allowing for the scaling of the nonbonded interactions of the force field, an idea previously employed in distance geometry and simulated annealing, has been implemented. The usefulness of this method is that when the nonbonded term is turned to zero, atoms can pass through each other, while the connectivity of the molecule is maintained. It will be shown that such simulations, if a sufficient driving force is present (i.e., nuclear Overhauser effects restraints), can produce the correct stereoconfiguration (i.e., chiral center) as well as configurational isomer (i.e., cis/trans isomers). Lastly, a penalty term for coupling constants directly related to the Karplus curve has been implemented into the potential energy force field. The advantages of this method over the commonly used dihedral angle restraining are discussed. In particular, it is shown that with more than one coupling constant about a dihedral angle a great reduction of the allowed conformational space is obtained.
Collapse
Affiliation(s)
- D F Mierke
- Organisch Chemisches Institut, Technische Universität München, Garching, Germany
| | | |
Collapse
|
34
|
Wüthrich K, von Freyberg B, Weber C, Wider G, Traber R, Widmer H, Braun W. Receptor-induced conformation change of the immunosuppressant cyclosporin A. Science 1991; 254:953-4. [PMID: 1948082 DOI: 10.1126/science.1948082] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- K Wüthrich
- Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule-Hönggerberg, Zürich, Switzerland
| | | | | | | | | | | | | |
Collapse
|
35
|
Kessler H, Gehrke M, Lautz J, Köck M, Seebach D, Thaler A. Complexation and medium effects on the conformation of cyclosporin A studied by NMR spectroscopy and molecular dynamics calculations. Biochem Pharmacol 1990; 40:169-73. [PMID: 2164815 DOI: 10.1016/0006-2952(90)90192-n] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The conformation of cyclosporin A was investigated in different environments. Whereas there was no distinct difference between the structure of CSA in CDCl3 and THF, the addition of LiCl caused a conformational change. Also, using polar solvents (DMSO, water) induced conformational changes in the backbone as well as the side chains.
Collapse
Affiliation(s)
- H Kessler
- Institut für Organische Chemie, J.W. Goethe-Universität, Frankfurt am Main, F.R.G
| | | | | | | | | | | |
Collapse
|