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Lohrman J, Vázquez-Montelongo EA, Pramanik S, Day VW, Hix MA, Bowman-James K, Cisneros GA. Characterizing Hydrogen-Bond Interactions in Pyrazinetetracarboxamide Complexes: Insights from Experimental and Quantum Topological Analyses. Inorg Chem 2018; 57:9775-9778. [DOI: 10.1021/acs.inorgchem.8b00627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jessica Lohrman
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Erik A. Vázquez-Montelongo
- Department of Chemistry, University of North Texas, 1508 W Mulberry Street, Denton, Texas 76201, United States
| | - Subhamay Pramanik
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Victor W. Day
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - Mark A. Hix
- Department of Chemistry, University of North Texas, 1508 W Mulberry Street, Denton, Texas 76201, United States
| | - Kristin Bowman-James
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, 1508 W Mulberry Street, Denton, Texas 76201, United States
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2
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Agback P, Agback T. Direct evidence of a low barrier hydrogen bond in the catalytic triad of a Serine protease. Sci Rep 2018; 8:10078. [PMID: 29973622 PMCID: PMC6031666 DOI: 10.1038/s41598-018-28441-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/21/2018] [Indexed: 11/28/2022] Open
Abstract
Serine proteases are one of the largest groups of enzymes, found in both eukaryotes and prokaryotes, and are responsible for many different functions. The detailed information about the hydrogen-bonds in the catalytic triad (Asp…His…Ser) of these enzymes is of importance in order to fully understand the mechanism of action. The aspartate of the triad is hydrogen bonded to the histidine but the exact nature of this bond has been under discussion for some time. It is either a common short ionic hydrogen bond (SIHB) or a delocalized low barrier hydrogen bond (LBHB) were the hydrogen bond is shorter. So far, the evidence for LBHB in proteins have not been conclusive. Here we show clear NMR evidence that LBHB does exist in NS3, a serine protease from Dengue. The one bond coupling constant between the hydrogen and nitrogen was shown to be only 52 Hz instead of the usual 90 Hz. This together with a 1H chemical shift of 19.93 ppm is evidence that the hydrogen bond distance between His and Asp is shorter than for SIHB. Our result clearly shows the existence of LBHB and will help in understanding the mechanism of the catalytic triad in the important group of serine proteases.
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden.
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Nichols DA, Hargis JC, Sanishvili R, Jaishankar P, Defrees K, Smith E, Wang KK, Prati F, Renslo AR, Woodcock HL, Chen Y. Ligand-Induced Proton Transfer and Low-Barrier Hydrogen Bond Revealed by X-ray Crystallography. J Am Chem Soc 2015; 137:8086-95. [PMID: 26057252 PMCID: PMC4530788 DOI: 10.1021/jacs.5b00749] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ligand binding can change the pKa of protein residues and influence enzyme catalysis. Herein, we report three ultrahigh resolution X-ray crystal structures of CTX-M β-lactamase, directly visualizing protonation state changes along the enzymatic pathway: apo protein at 0.79 Å, precovalent complex with nonelectrophilic ligand at 0.89 Å, and acylation transition state (TS) analogue at 0.84 Å. Binding of the noncovalent ligand induces a proton transfer from the catalytic Ser70 to the negatively charged Glu166, and the formation of a low-barrier hydrogen bond (LBHB) between Ser70 and Lys73, with a length of 2.53 Å and the shared hydrogen equidistant from the heteroatoms. QM/MM reaction path calculations determined the proton transfer barrier to be 1.53 kcal/mol. The LBHB is absent in the other two structures although Glu166 remains neutral in the covalent complex. Our data represents the first X-ray crystallographic example of a hydrogen engaged in an enzymatic LBHB, and demonstrates that desolvation of the active site by ligand binding can provide a protein microenvironment conducive to LBHB formation. It also suggests that LBHBs may contribute to stabilization of the TS in general acid/base catalysis together with other preorganized features of enzyme active sites. These structures reconcile previous experimental results suggesting alternatively Glu166 or Lys73 as the general base for acylation, and underline the importance of considering residue protonation state change when modeling protein-ligand interactions. Additionally, the observation of another LBHB (2.47 Å) between two conserved residues, Asp233 and Asp246, suggests that LBHBs may potentially play a special structural role in proteins.
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Affiliation(s)
- Derek A. Nichols
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
| | | | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - Emmanuel Smith
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
| | - Kenneth K. Wang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Italy
| | - Adam R. Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California San Francisco, 1700 4 Street, Byers Hall S504, San Francisco, CA 94158
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida 33620
| | - Yu Chen
- University of South Florida College of Medicine, Dept of Molecular Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, FL 33612
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4
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Dance I. The pathway for serial proton supply to the active site of nitrogenase: enhanced density functional modeling of the Grotthuss mechanism. Dalton Trans 2015; 44:18167-86. [DOI: 10.1039/c5dt03223g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proton translocation along a chain of eight waters to the active site of nitrogenase is described in detail, using density functional simulations with a 269 atom system that includes surrounding amino acids.
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Affiliation(s)
- Ian Dance
- School of Chemistry
- UNSW Australia
- Sydney 2052
- Australia
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5
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Castro B, Chaudret R, Ricci G, Kurz M, Ochsenbein P, Kretzschmar G, Kraft V, Rossen K, Eisenstein O. Nonclassical CH−π Supramolecular Interactions in Artemisinic Acid Favor a Single Conformation, Yielding High Diastereoselectivity in the Reduction with Diazene. J Org Chem 2014; 79:5939-47. [DOI: 10.1021/jo500233z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Bertrand Castro
- Institut Charles
Gerhardt, CNRS 5253, Université Montpellier 2, cc 1501,
place E. Bataillon, F-34095 Montpellier, France
| | - Robin Chaudret
- IFP Energies Nouvelles, 1 et 4 avenue de Bois-Préau, 92852 Rueil-Malmaison Cedex, France
| | - Gino Ricci
- Sanofi Chimie, 45 chemin
de Meteline 04200 Sisteron, France
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Philippe Ochsenbein
- Sanofi-Aventis R & D, 371 rue du Professeur Joseph Blayac, 34184 Montpellier Cedex 04, France
| | - Gerhard Kretzschmar
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Volker Kraft
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Kai Rossen
- Sanofi-Aventis Deutschland GmbH, Chemistry & Biotechnology Department, Industriepark Höchst, D-65926 Frankfurt am Main, Germany
| | - Odile Eisenstein
- Institut Charles
Gerhardt, CNRS 5253, Université Montpellier 2, cc 1501,
place E. Bataillon, F-34095 Montpellier, France
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6
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Aasheim JH, Fliegl H, Uggerud E, Bonge-Hansen T, Eisenstein O. Stereoselectivity through a network of non-classical CH weak interactions: a prospective study of a bicyclic organocatalytic scaffold. NEW J CHEM 2014. [DOI: 10.1039/c4nj01460j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The preferred stereoisomeric product of this catalytic Diels–Alder reaction is in part determined by noncovalent CH⋯π interactions.
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Affiliation(s)
| | - Heike Fliegl
- Centre for Theoretical and Computational Chemistry (CTCC)
- Department of Chemistry
- University of Oslo
- Blindern, Norway
| | - Einar Uggerud
- Centre for Theoretical and Computational Chemistry (CTCC)
- Department of Chemistry
- University of Oslo
- Blindern, Norway
| | | | - Odile Eisenstein
- Centre for Theoretical and Computational Chemistry (CTCC)
- Department of Chemistry
- University of Oslo
- Blindern, Norway
- Institut Charles Gerhardt
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Dong K, Zhao L, Wang Q, Song Y, Zhang S. Are ionic liquids pairwise in gas phase? A cluster approach and in situ IR study. Phys Chem Chem Phys 2013; 15:6034-40. [PMID: 23493905 DOI: 10.1039/c3cp44493g] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, we discussed the vaporization and gas species of ionic liquids (ILs) by a cluster approach of quantum statistical thermodynamics proposed by R. Luwig (Phys. Chem. Chem. Phys., 10, 4333), which is a controversial issue up to date. Based on the different sized clusters (2-12 ion-pairs) of the condensed phase, the molar enthalpies of vaporization (ΔvapH, 298.15 K, 1bar) of four representative ILs, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([Emim][NTf2]) 1-ethyl-2,3-dimethylimidazolium bis(trifluoromethylsulfonyl)imide ([Emmim][NTf2]) 1-ethyl-3-methylimidazolium chloride ([Emim]Cl) and ethylammonium nitrate ([EtAm][NO3]), were calculated. The predicted ΔvapH were increased remarkably; even the values of [EtAm][NO3] were larger than 700 kJ mol(-1) when the charged isolated ions were assumed to be gas species. However, the ΔvapH were close to experimental measurements when the gas species assumed to be anion-cation pairwise, indicating that the different conformational ion-pairs can coexist in the gas phase when the IL is evaporated. Particularly for the protic IL, [EtAm][NO3], even the neutral precursor molecules by proton transfer can occur in gas phase. In addition, it's found that the effect of hydrogen bonds on the vaporization cannot be negligible by comparing the ΔvapH of [Emim][NTf2] with [Emmim][NTf2]. The in situ and calculated IR spectra provided the further proof that the ions are pairwise in gas phase.
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Affiliation(s)
- Kun Dong
- Beijing Key Laboratory of Ionic Liquids Clean Process, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China
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Popescu AR, Rojo I, Teixidor F, Sillanpää R, Hänninen MM, Viñas C. Chelation of a proton by oxidized diphosphines. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2012.06.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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van Severen MC, Chaudret R, Parisel O, Piquemal JP. Toward a ligand specific of Pb2+ with respect to the Zn2+ and Ca2+ cations: A track from quantum chemistry. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.02.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Chaudret R, Piquemal JP, Cisneros GA. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Phys Chem Chem Phys 2011; 13:11239-47. [PMID: 21566841 DOI: 10.1039/c0cp02550j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA polymerases require two divalent metal ions in the active site for catalysis. Mg(2+) has been confirmed to be the most probable cation utilized by most polymerases in vivo. Other metal ions are either potent mutagens or inhibitors. We used structural and topological analyses based on ab initio QM/MM calculations to study human DNA polymerase λ (Polλ) with different metals in the active site. Our results indicate a slightly longer O3'-Pα distance (∼3.6 Å) for most inhibitor cations compared to the natural and mutagenic metals (∼3.3-3.4 Å). Optimization with a larger basis set for the previously reported transition state (TS) structures (Cisneros et al., DNA Repair, 2008, 7, 1824.) gives barriers of 17.4 kcal mol(-1) and 15.1 kcal mol(-1) for the Mg(2+) and Mn(2+) catalyzed reactions respectively. Relying on the key relation between the topological signature of a metal cation and its selectivity within biological systems (de Courcy et al., J. Chem. Theor. Comput., 2010, 6, 1048.) we have performed electron localization function (ELF) topological analyses. These analyses show that all inhibitor and mutagenic metals considered, except Na(+), present a "split" of the outer-shell density of the metal. This "splitting" is not observed for the non-mutagenic Mg(2+) metal. Population and multipole analyses on the ELF basins reveal that the electronic dipolar and quadrupolar polarization is significantly different with Mg(2+) compared to all other cations. Our results shed light at the atomic level on the subtle differences between Mg(2+), mutagenic, and inhibitor metals in DNA polymerases. These results provide a correlation between the electronic distribution of the cations in the active site and the possible consequences on DNA synthesis.
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Affiliation(s)
- Robin Chaudret
- UPMC Université Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Paris, France
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