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Role of intramolecular hydrogen bonds in promoting electron flow through amino acid and oligopeptide conjugates. Proc Natl Acad Sci U S A 2021; 118:2026462118. [PMID: 33707214 DOI: 10.1073/pnas.2026462118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Elucidating the factors that control charge transfer rates in relatively flexible conjugates is of importance for understanding energy flows in biology as well as assisting the design and construction of electronic devices. Here, we report ultrafast electron transfer (ET) and hole transfer (HT) between a corrole (Cor) donor linked to a perylene-diimide (PDI) acceptor by a tetrameric alanine (Ala)4 Selective photoexcitation of the donor and acceptor triggers subpicosecond and picosecond ET and HT. Replacement of the (Ala)4 linker with either a single alanine or phenylalanine does not substantially affect the ET and HT kinetics. We infer that electronic coupling in these reactions is not mediated by tetrapeptide backbone nor by direct donor-acceptor interactions. Employing a combination of NMR, circular dichroism, and computational studies, we show that intramolecular hydrogen bonding brings the donor and the acceptor into proximity in a "scorpion-shaped" molecular architecture, thereby accounting for the unusually high ET and HT rates. Photoinduced charge transfer relies on a (Cor)NH…O=C-NH…O=C(PDI) electronic-coupling pathway involving two pivotal hydrogen bonds and a central amide group as a mediator. Our work provides guidelines for construction of effective donor-acceptor assemblies linked by long flexible bridges as well as insights into structural motifs for mediating ET and HT in proteins.
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Xu P, Guidez EB, Bertoni C, Gordon MS. Perspective:Ab initioforce field methods derived from quantum mechanics. J Chem Phys 2018. [DOI: 10.1063/1.5009551] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Peng Xu
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
| | - Emilie B. Guidez
- Department of Chemistry, University of Colorado Denver, Denver, Colorado 80217, USA
| | - Colleen Bertoni
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, USA
| | - Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames, Iowa 50011, USA
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Kaminský J, Jensen F. Conformational Interconversions of Amino Acid Derivatives. J Chem Theory Comput 2016; 12:694-705. [PMID: 26691979 DOI: 10.1021/acs.jctc.5b00911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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Shi Y, Ren P, Schnieders M, Piquemal JP. Polarizable Force Fields for Biomolecular Modeling. REVIEWS IN COMPUTATIONAL CHEMISTRY 2015. [DOI: 10.1002/9781118889886.ch2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Affiliation(s)
- Julie Grouleff
- Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
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Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. J Chem Theory Comput 2007; 3:1960-1986. [PMID: 18978934 PMCID: PMC2367138 DOI: 10.1021/ct700134r] [Citation(s) in RCA: 279] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
We present an overview of the SIBFA polarizable molecular mechanics procedure, which is formulated and calibrated on the basis of quantum chemistry (QC). It embodies nonclassical effects such as electrostatic penetration, exchange-polarization, and charge transfer. We address the issues of anisotropy, nonadditivity, and transferability by performing parallel QC computations on multimolecular complexes. These encompass multiply H-bonded complexes and polycoordinated complexes of divalent cations. Recent applications to the docking of inhibitors to Zn-metalloproteins are presented next, namely metallo-beta-lactamase, phosphomannoisomerase, and the nucleocapsid of the HIV-1 retrovirus. Finally, toward third-generation intermolecular potentials based on density fitting, we present the development of a novel methodology, the Gaussian electrostatic model (GEM), which relies on ab initio-derived fragment electron densities to compute the components of the total interaction energy. As GEM offers the possibility of a continuous electrostatic model going from distributed multipoles to densities, it allows an inclusion of short-range quantum effects in the molecular mechanics energies. The perspectives of an integrated SIBFA/GEM/QM procedure are discussed.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université René-Descartes, 45, rue des Saints-Pères, 75006 Paris, France, Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, and Laboratoire de Chimie Théorique, Université Pierre-et-Marie-Curie, UMR 7616 CNRS, case courrier 137, 4, place Jussieu, 75252 Paris, France
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Kaminský J, Jensen F. Force Field Modeling of Amino Acid Conformational Energies. J Chem Theory Comput 2007; 3:1774-88. [DOI: 10.1021/ct700082f] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakub Kaminský
- Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark, and Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense, Denmark, and Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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Piquemal JP, Chevreau H, Gresh N. Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential. J Chem Theory Comput 2007; 3:824-37. [DOI: 10.1021/ct7000182] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jean-Philip Piquemal
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case courrier 137, 4, place Jussieu, F. 75252 Paris, Cedex 05, France, and Laboratoire de Pharmacochimie Moléculaire et Structurale, U648 INSERM, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France
| | - Hilaire Chevreau
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case courrier 137, 4, place Jussieu, F. 75252 Paris, Cedex 05, France, and Laboratoire de Pharmacochimie Moléculaire et Structurale, U648 INSERM, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France
| | - Nohad Gresh
- Laboratoire de Chimie Théorique, UMR 7616, Université P. & M. Curie, Case courrier 137, 4, place Jussieu, F. 75252 Paris, Cedex 05, France, and Laboratoire de Pharmacochimie Moléculaire et Structurale, U648 INSERM, IFR Biomédicale, 45, Rue des Saints-Pères, 75006, Paris, France
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Gascon JA, Leung SSF, Batista ER, Batista VS. A Self-Consistent Space-Domain Decomposition Method for QM/MM Computations of Protein Electrostatic Potentials. J Chem Theory Comput 2005; 2:175-86. [DOI: 10.1021/ct050218h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jose A. Gascon
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Siegfried S. F. Leung
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Enrique R. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107, and Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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Papamokos GV, Demetropoulos IN. Vibrational Frequencies of Amides and Amide Dimers: The Assessment of PW91XC Functional. J Phys Chem A 2004. [DOI: 10.1021/jp049563d] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- George V. Papamokos
- Department of Chemistry, Sector of Physical Chemistry, University of Ioannina, Panepistemioupoli Dourouti, 45110 Ioannina, Greece
| | - Ioannis N. Demetropoulos
- Department of Chemistry, Sector of Physical Chemistry, University of Ioannina, Panepistemioupoli Dourouti, 45110 Ioannina, Greece
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Gresh N, Kafafi SA, Truchon JF, Salahub DR. Intramolecular interaction energies in model alanine and glycine tetrapeptides. Evaluation of anisotropy, polarization, and correlation effects. A parallel ab initio HF/MP2, DFT, and polarizable molecular mechanics study. J Comput Chem 2004; 25:823-34. [PMID: 15011254 DOI: 10.1002/jcc.20012] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An extension of the SIBFA polarizable molecular mechanics procedure to flexible oligopeptides is reported. The procedure is evaluated by computing the relative conformational energies, deltaE(conf), of the alanine tetrapeptide in 10 representative conformations, which were originally derived by Beachy et al. (J Am Chem Soc 1997, 119, 5908) to benchmark molecular mechanics procedures with respect to ab initio computations. In the present study, a particular emphasis is on the separable nature of the components of the energy and the particular impact of the polarization energy component on deltaE(conf). We perform comparisons with respect to single-point HF, DFT, LMP2, and MP2 computations done at the SIBFA-derived energy minima. Such comparisons are made first for the 10 conformers derived from phi/psi torsional angle energy-minimization (the rigid rotor approach), and, in a second step, after allowing additional relaxation of the C(alpha) centered valence angles. In both series of energy-minimization, the SIBFA deltaE(conf) compared best with the LMP2 results using the 6-311G** basis set, the rms being 1.3 kcal/mol. In the absence of the polarization component, the rms is 3.5 kcal/mol. In both series of minimizations, the magnitudes of deltaE(conf), computed as differences with respect to the most stable conformer taken as energy zero, decrease along the series: HF > DFT > LMP2 > SIBFA > MP2, indicative of increasing stabilization of the most highly folded conformers.
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Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, FRE 2718 CNRS, Université René-Descartes, IFR Biomédicale, 45, Rue des Saints-Pères, 75006 Paris, France.
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Affiliation(s)
- Jay W Ponder
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Antony J, Gresh N, Olsen L, Hemmingsen L, Schofield CJ, Bauer R. Binding of D- and L-captopril inhibitors to metallo-beta-lactamase studied by polarizable molecular mechanics and quantum mechanics. J Comput Chem 2002; 23:1281-96. [PMID: 12210153 DOI: 10.1002/jcc.10111] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The bacterial Zn2+ metallo-beta-lactamase from B. fragilis is a zinc-enzyme with two potential metal ion binding sites. It cleaves the lactam ring of antibiotics, thus contributing to the acquired resistance of bacteria against antibiotics. The present study bears on the binuclear form of the enzyme. We compare several possible binding modes of captopril, a mercaptocarboxamide inhibitor of several zinc-metalloenzymes. Two diastereoisomers of captopril were considered, with either a D- or an L-proline residue. We have used the polarizable molecular mechanics procedure SIBFA (Sum of Interactions Between Fragments ab initio computed). Two beta-lactamase models were considered, encompassing 104 and 188 residues, respectively. The energy balances included the inter and intramolecular interaction energies as well as the contribution from solvation computed using a continuum reaction field procedure. The thiolate ion of the inhibitor is binding to both metal ions, expelling the bridging solvent molecule from the uncomplexed enzyme. Different competing binding modes of captopril were considered, either where the inhibitor binds in a monodentate mode to the zinc cations only with its thiolate ion, or in bidentate modes involving additional zinc binding by its carboxylate or ketone carbonyl groups. The additional coordination by the inhibitor's carboxylate or carbonyl group always occurs at the zinc ion, which is bound by a histidine, a cysteine, and an aspartate side chain. For both diastereomers, the energy balances favor monodentate binding of captopril via S-. The preference over bidentate binding is small. The interaction energies were recomputed in model sites restricted to captopril, the Zn2+ cations, and their coordinating end side chains from beta-lactamase (98 atoms). The interaction energies and their ranking among competing arrangements were consistent with those computed by ab initio HF and DFT procedures.
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Affiliation(s)
- Jens Antony
- Department of Mathematics and Physics, The Royal Veterinary and Agricultural University, DK-1871 Frederiksberg C, Denmark
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Tiraboschi G, Fournié-Zaluski MC, Roques BP, Gresh N. Intramolecular chelation of Zn2+by α- and β-mercaptocarboxamides. A parallelab initioand polarizable molecular mechanics investigation. Assessment of the role of multipole transferability. J Comput Chem 2001. [DOI: 10.1002/jcc.1064] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Guo H, Gresh N, Roques BP, Salahub DR. Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics. J Phys Chem B 2000. [DOI: 10.1021/jp0012247] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hong Guo
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Nohad Gresh
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Bernard P. Roques
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
| | - Dennis R. Salahub
- Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, Quebec H3X 2H9, Canada; Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques and Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France; and Département de Chimie, Université de Montréal, C.P. 6128, succursale A, Montréal, Québec, Canada, and Steacie Institute for Molecular Sciences, National Research Council, 100 Sussex Drive, Ottawa,
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Yu CH, Schäfer L, Ramek M. Local Geometry Trends and Torsional Sensitivity in N-Formyl-l-alanyl-l-alanine Amide and the Limitations of the Dipeptide Approximation. J Phys Chem A 1999. [DOI: 10.1021/jp992166w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ching-Hsing Yu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Lothar Schäfer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701
| | - Michael Ramek
- Institut für Physikalische und Theoretische Chemie, Technische Universität Graz, A-8010 Graz, Austria
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Gresh N, Guo H, Salahub DR, Roques BP, Kafafi SA. Critical Role of Anisotropy for the Dimerization Energies of Two Protein−Protein Recognition Motifs: cis-N-Methylacetamide versus a β-Sheet Conformer of Alanine Dipeptide. A Joint ab Initio, Density Functional Theory, and Molecular Mechanics Investigation. J Am Chem Soc 1999. [DOI: 10.1021/ja9742489] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nohad Gresh
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Hong Guo
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Dennis R. Salahub
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Bernard P. Roques
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
| | - Sherif A. Kafafi
- Contribution from the Département de Pharmacochimie Moléculaire et Structurale, INSERM U266, CNRS UMR 8600, UFR des Sciences Pharmaceutiques & Biologiques, 4, Avenue de l'Observatoire, 75270 Paris Cedex 06, France, Centre de Recherche en Calcul Appliqué, Bureau 400, 5160, Boulevard Décarie, Montréal, QUEBEC H3X 2H9 Canada, Département de Chimie, Université de Montréal, C.P. 6128, succursale A Montréal, Québec, Canada, and Center for Advanced Research in Biotechnology, Maryland Biotechnology Institute,
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Cramer CJ, Truhlar DG. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev 1999; 99:2161-2200. [PMID: 11849023 DOI: 10.1021/cr960149m] [Citation(s) in RCA: 1722] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Cramer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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Abstract
Ac-(Aib-Ala)3-OH (a protected segment of the peptaibols gliodeliquescin and paracelsin), Z-Leu-Aib-Val-Aib-Gly-OtBu (a segment of [Leu]7-gliodeliquescin), Z-Val-Aib-Aib-Gln-OtBu (a common segment of alamethicin, paracelsin, and hypelcin), and Ac-Aib-Pro-(Aib-Ala)2-OMe and Z-Aib-Pro-(Aib-Ala)2-OMe, which represent differently N(alpha)-protected 1-6 segments of alamethicin and hypelcin, have been synthesized by solution methods. The crystal-state conformations of these five Aib-containing peptides have been determined by X-ray diffraction analysis. We have confirmed that the 3(10)-helical structure is preferentially adopted by Aib-rich short peptides. An experimentally unambiguous proof for the 3(10)-->alpha-helix conversion has been provided by the two differently N-blocked -Aib-Pro-(Aib-Ala)2-OMe hexapeptides. The beta-bend ribbon conformation, commonly observed in the (Aib-Pro)n sequential oligopeptides, is not found in the -Aib-Pro-Aib-Ala-Aib-Ala-sequence. As expected on the basis of the L-configuration of the C(alpha)-monoalkylated residues, a right-handed helix screw sense was found in all peptides investigated.
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Affiliation(s)
- A Aubry
- CNRS-URA-809, University Henri Poincaré, Vandoeuvre les Nancy, France
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