1
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Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences. Top Catal 2021; 65:165-186. [DOI: 10.1007/s11244-021-01521-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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2
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Vazdar M, Heyda J, Mason PE, Tesei G, Allolio C, Lund M, Jungwirth P. Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides. Acc Chem Res 2018; 51:1455-1464. [PMID: 29799185 DOI: 10.1021/acs.accounts.8b00098] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.
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Affiliation(s)
- Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Giulio Tesei
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Christoph Allolio
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Giv’at Ram, Jerusalem 9190401, Israel
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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3
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Roßbach S, Ochsenfeld C. Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA. J Chem Theory Comput 2017; 13:1102-1107. [PMID: 28195707 DOI: 10.1021/acs.jctc.6b00727] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of embedding and coupling schemes on the convergence of the QM size in the QM/MM approach is investigated for the transfer of a proton in a DNA base pair. We find that the embedding scheme (mechanical or electrostatic) has a much greater impact on the convergence behavior than the coupling scheme (additive QM/MM or subtractive ONIOM). To achieve size convergence, QM regions with up to 6000 atoms are necessary for pure QM or mechanical embedding. In contrast, electrostatic embedding converges faster: for the example of the transfer of a proton between DNA base pairs, we recommend including at least five base pairs and 5 Å of solvent (including counterions) into the QM region, i.e., a total of 1150 atoms.
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Affiliation(s)
- Sven Roßbach
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr. 7, D-81377 Munich, Germany.,Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr, 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr. 7, D-81377 Munich, Germany.,Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr, 5-13, D-81377 Munich, Germany
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4
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Fouda A, Ryde U. Does the DFT Self-Interaction Error Affect Energies Calculated in Proteins with Large QM Systems? J Chem Theory Comput 2016; 12:5667-5679. [DOI: 10.1021/acs.jctc.6b00903] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Adam Fouda
- Department of Theoretical
Chemistry, Chemical Centre, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical
Chemistry, Chemical Centre, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden
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5
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Cole DJ, Hine NDM. Applications of large-scale density functional theory in biology. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:393001. [PMID: 27494095 DOI: 10.1088/0953-8984/28/39/393001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.
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Affiliation(s)
- Daniel J Cole
- Theory of Condensed Matter group, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK. School of Chemistry, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
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6
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Taenzler PJ, Sadeghian K, Ochsenfeld C. A Dynamic Equilibrium of Three Hydrogen-Bond Conformers Explains the NMR Spectrum of the Active Site of Photoactive Yellow Protein. J Chem Theory Comput 2016; 12:5170-5178. [DOI: 10.1021/acs.jctc.6b00359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Phillip Johannes Taenzler
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
| | - Keyarash Sadeghian
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry,
Department of Chemistry, University of Munich (LMU), Butenandtstrasse
7, D-81377 Munich, Germany
- Center for Integrated Protein
Science (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Muenchen, Germany
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7
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Zhao Y, Deng L, Yang W, Wang D, Pambou E, Lu Z, Li Z, Wang J, King S, Rogers S, Xu H, Lu JR. Tuning One‐Dimensional Nanostructures of Bola‐Like Peptide Amphiphiles by Varying the Hydrophilic Amino Acids. Chemistry 2016; 22:11394-404. [PMID: 27362441 DOI: 10.1002/chem.201601309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Yurong Zhao
- Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Changjiang West Road Qingdao 266580 P. R. China
| | - Li Deng
- Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Changjiang West Road Qingdao 266580 P. R. China
| | - Wei Yang
- Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Changjiang West Road Qingdao 266580 P. R. China
| | - Dong Wang
- Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Changjiang West Road Qingdao 266580 P. R. China
| | - Elias Pambou
- School of Physics and Astronomy The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Zhiming Lu
- School of Physics and Astronomy The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Zongyi Li
- School of Physics and Astronomy The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Jiqian Wang
- Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Changjiang West Road Qingdao 266580 P. R. China
| | - Stephen King
- ISIS Pulsed Neutron Source STFC Rutherford Appleton Laboratory, Harwell Oxford Didcot OX11 0QX UK
| | - Sarah Rogers
- ISIS Pulsed Neutron Source STFC Rutherford Appleton Laboratory, Harwell Oxford Didcot OX11 0QX UK
| | - Hai Xu
- Centre for Bioengineering and Biotechnology China University of Petroleum (East China) Changjiang West Road Qingdao 266580 P. R. China
| | - Jian R. Lu
- School of Physics and Astronomy The University of Manchester Oxford Road Manchester M13 9PL UK
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8
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Harris TV, Szilagyi RK. Protein environmental effects on iron-sulfur clusters: A set of rules for constructing computational models for inner and outer coordination spheres. J Comput Chem 2016; 37:1681-96. [DOI: 10.1002/jcc.24384] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Travis V. Harris
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University; Bozeman Montana 59717
| | - Robert K. Szilagyi
- NAI Astrobiology Biogeocatalysis Research Center, Department of Chemistry and Biochemistry, Montana State University; Bozeman Montana 59717
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9
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Blank ID, Sadeghian K, Ochsenfeld C. A base-independent repair mechanism for DNA glycosylase--no discrimination within the active site. Sci Rep 2015; 5:10369. [PMID: 26013033 PMCID: PMC4445063 DOI: 10.1038/srep10369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/09/2015] [Indexed: 11/09/2022] Open
Abstract
The ubiquitous occurrence of DNA damages renders its repair machinery a crucial requirement for the genomic stability and the survival of living organisms. Deficiencies in DNA repair can lead to carcinogenesis, Alzheimer, or Diabetes II, where increased amounts of oxidized DNA bases have been found in patients. Despite the highest mutation frequency among oxidized DNA bases, the base-excision repair process of oxidized and ring-opened guanine, FapydG (2,6-diamino-4-hydroxy-5-formamidopyrimidine), remained unclear since it is difficult to study experimentally. We use newly-developed linear-scaling quantum-chemical methods (QM) allowing us to include up to 700 QM-atoms and achieving size convergence. Instead of the widely assumed base-protonated pathway we find a ribose-protonated repair mechanism which explains experimental observations and shows strong evidence for a base-independent repair process. Our results also imply that discrimination must occur during recognition, prior to the binding within the active site.
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Affiliation(s)
- Iris D Blank
- 1] Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 Munich, Germany [2] Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Keyarash Sadeghian
- 1] Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 Munich, Germany [2] Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- 1] Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 7, D-81377 Munich, Germany [2] Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU), Butenandtstr. 5-13, D-81377 Munich, Germany
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10
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Sadeghian K, Flaig D, Blank ID, Schneider S, Strasser R, Stathis D, Winnacker M, Carell T, Ochsenfeld C. Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403334] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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11
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Sadeghian K, Flaig D, Blank ID, Schneider S, Strasser R, Stathis D, Winnacker M, Carell T, Ochsenfeld C. Ribose-Protonated DNA Base Excision Repair: A Combined Theoretical and Experimental Study. Angew Chem Int Ed Engl 2014; 53:10044-8. [DOI: 10.1002/anie.201403334] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 05/12/2014] [Indexed: 12/28/2022]
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12
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Maurer SA, Beer M, Lambrecht DS, Ochsenfeld C. Linear-scaling symmetry-adapted perturbation theory with scaled dispersion. J Chem Phys 2013; 139:184104. [DOI: 10.1063/1.4827297] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Vazdar M, Wernersson E, Khabiri M, Cwiklik L, Jurkiewicz P, Hof M, Mann E, Kolusheva S, Jelinek R, Jungwirth P. Aggregation of Oligoarginines at Phospholipid Membranes: Molecular Dynamics Simulations, Time-Dependent Fluorescence Shift, and Biomimetic Colorimetric Assays. J Phys Chem B 2013; 117:11530-40. [DOI: 10.1021/jp405451e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mario Vazdar
- Division
of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, P.O.B.
180, HR-10002 Zagreb, Croatia
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Erik Wernersson
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Morteza Khabiri
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Lukasz Cwiklik
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Piotr Jurkiewicz
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Martin Hof
- J. Heyrovský
Institute of Physical Chemistry, Academy of Sciences of the Czech Republic v.v.i., Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Ella Mann
- Department
of Chemistry and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Sofiya Kolusheva
- Department
of Chemistry and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Raz Jelinek
- Department
of Chemistry and the Ilse Katz Institute for Nanoscale Science and
Technology, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Department
of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
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14
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Sumner S, Söderhjelm P, Ryde U. Effect of Geometry Optimizations on QM-Cluster and QM/MM Studies of Reaction Energies in Proteins. J Chem Theory Comput 2013; 9:4205-14. [DOI: 10.1021/ct400339c] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sophie Sumner
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00
Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00
Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00
Lund, Sweden
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15
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Liao RZ, Thiel W. Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase. J Comput Chem 2013; 34:2389-97. [PMID: 23913757 DOI: 10.1002/jcc.23403] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 07/14/2013] [Accepted: 07/18/2013] [Indexed: 11/06/2022]
Abstract
We report systematic quantum mechanics-only (QM-only) and QM/molecular mechanics (MM) calculations on an enzyme-catalyzed reaction to assess the convergence behavior of QM-only and QM/MM energies with respect to the size of the chosen QM region. The QM and MM parts are described by density functional theory (typically B3LYP/def2-SVP) and the CHARMM force field, respectively. Extending our previous work on acetylene hydratase with QM regions up to 157 atoms (Liao and Thiel, J. Chem. Theory Comput. 2012, 8, 3793), we performed QM/MM geometry optimizations with a QM region M4 composed of 408 atoms, as well as further QM/MM single-point calculations with even larger QM regions up to 657 atoms. A charge deletion analysis was conducted for the previously used QM/MM model (M3a, with a QM region of 157 atoms) to identify all MM residues with strong electrostatic contributions to the reaction energetics (typically more than 2 kcal/mol), which were then included in M4. QM/MM calculations with this large QM region M4 lead to the same overall mechanism as the previous QM/MM calculations with M3a, but there are some variations in the relative energies of the stationary points, with a mean absolute deviation (MAD) of 2.7 kcal/mol. The energies of the two relevant transition states are close to each other at all levels applied (typically within 2 kcal/mol), with the first (second) one being rate-limiting in the QM/MM calculations with M3a (M4). QM-only gas-phase calculations give a very similar energy profile for QM region M4 (MAD of 1.7 kcal/mol), contrary to the situation for M3a where we had previously found significant discrepancies between the QM-only and QM/MM results (MAD of 7.9 kcal/mol). Extension of the QM region beyond M4 up to M7 (657 atoms) leads to only rather small variations in the relative energies from single-point QM-only and QM/MM calculations (MAD typically about 1-2 kcal/mol). In the case of acetylene hydratase, a model with 408 QM atoms thus seems sufficient to achieve convergence in the computed relative energies to within 1-2 kcal/mol.
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Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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16
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Flaig D, Ochsenfeld C. An extrapolation method for the efficient calculation of molecular response properties within Born-Oppenheimer molecular dynamics. Phys Chem Chem Phys 2013; 15:9392-6. [PMID: 23666498 DOI: 10.1039/c3cp50204j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The calculation of molecular response properties in dynamic molecular systems is a major challenge that requires sampling over many steps of, e.g., Born-Oppenheimer molecular dynamics (BO-MD) simulations. We present an extrapolation scheme to accelerate such calculations for multiple steps within BO-MD trajectories or equivalently within other sampling methods of conformational space. The extrapolation scheme is related to the one introduced by Pulay and Fogarasi [Chem. Phys. Lett., 2004, 386, 272] for self-consistent field (SCF) energy calculations. We extend the extrapolation to the quantities within our density matrix-based Laplace-transformed coupled perturbed SCF (DL-CPSCF) method that allows for linear-scaling calculations of response properties for large molecular systems. Here, we focus on the example of calculating NMR chemical shifts for which the number of required DL-CPSCF iterations reduces by roughly 40-70%.
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Affiliation(s)
- Denis Flaig
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Munich, Germany
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17
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Zhang Z, Xu Z, Yang Z, Liu Y, Wang J, Shao Q, Li S, Lu Y, Zhu W. The stabilization effect of dielectric constant and acidic amino acids on arginine-arginine (Arg-Arg) pairings: database survey and computational studies. J Phys Chem B 2013; 117:4827-35. [PMID: 23581492 DOI: 10.1021/jp4001658] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Database survey in this study revealed that about one-third of the protein structures deposited in the Protein Data Bank (PDB) contain arginine-arginine (Arg-Arg) pairing with a carbon···carbon (CZ···CZ) interaction distance less than 5 Å. All the Arg-Arg pairings were found to bury in a polar environment composed of acidic residues, water molecules, and strong polarizable or negatively charged moieties from binding site or bound ligand. Most of the Arg-Arg pairings are solvent exposed and 68.3% Arg-Arg pairings are stabilized by acidic residues, forming Arg-Arg-Asp/Glu clusters. Density functional theory (DFT) was then employed to study the effect of environment on the pairing structures. It was revealed that Arg-Arg pairings become thermodynamically stable (about -1 kcal/mol) as the dielectric constant increases to 46.8 (DMSO), in good agreement with the results of the PDB survey. DFT calculations also demonstrated that perpendicular Arg-Arg pairing structures are favorable in low dielectric constant environment, while in high dielectric constant environment parallel structures are favorable. Additionally, the acidic residues can stabilize the Arg-Arg pairing structures to a large degree. Energy decomposition analysis of Arg-Arg pairings and Arg-Arg-Asp/Glu clusters showed that both solvation and electrostatic energies contribute significantly to their stability. The results reported herein should be very helpful for understanding Arg-Arg pairing and its application in drug design.
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Affiliation(s)
- Zhengyan Zhang
- College of Chemistry, Chemical Engineering and Materials Science of Soochow University, Soochow University, Suzhou, Jiangsu, 215123, China
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18
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Maurer SA, Lambrecht DS, Kussmann J, Ochsenfeld C. Efficient distance-including integral screening in linear-scaling Møller-Plesset perturbation theory. J Chem Phys 2013; 138:014101. [DOI: 10.1063/1.4770502] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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19
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Liao RZ, Thiel W. Comparison of QM-Only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene Hydratase. J Chem Theory Comput 2012; 8:3793-803. [DOI: 10.1021/ct3000684] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rong-Zhen Liao
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470, Mülheim an der Ruhr, Germany
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20
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Vazdar M, Vymětal J, Heyda J, Vondrášek J, Jungwirth P. Like-Charge Guanidinium Pairing from Molecular Dynamics and Ab Initio Calculations. J Phys Chem A 2011; 115:11193-201. [DOI: 10.1021/jp203519p] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mario Vazdar
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Rudjer Bošković Institute, Division of Organic Chemistry and Biochemistry, POB 180, HR-10002 Zagreb, Croatia
| | - Jiři Vymětal
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jan Heyda
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Jiři Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Center for Biomolecules and Complex Molecular Systems, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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