1
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Elizebath D, Vedhanarayanan B, Dhiman A, Mishra RK, Ramachandran CN, Lin TW, Praveen VK. Spontaneous Curvature Induction in an Artificial Bilayer Membrane. Angew Chem Int Ed Engl 2024; 63:e202403900. [PMID: 38459961 DOI: 10.1002/anie.202403900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 03/11/2024]
Abstract
Maintaining lipid asymmetry across membrane leaflets is critical for functions like vesicular traffic and organelle homeostasis. However, a lack of molecular-level understanding of the mechanisms underlying membrane fission and fusion processes in synthetic systems precludes their development as artificial analogs. Here, we report asymmetry induction of a bilayer membrane formed by an extended π-conjugated molecule with oxyalkylene side chains bearing terminal tertiary amine moieties (BA1) in water. Autogenous protonation of the tertiary amines in the periphery of the bilayer by water induces anisotropic curvature, resulting in membrane fission to form vesicles and can be monitored using time-dependent spectroscopy and microscopy. Interestingly, upon loss of the induced asymmetry by extensive protonation using an organic acid restored bilayer membrane. The mechanism leading to the compositional asymmetry in the leaflet and curvature induction in the membrane is validated by density functional theory (DFT) calculations. Studies extended to control molecules having changes in hydrophilic (BA2) and hydrophobic (BA3) segments provide insight into the delicate nature of molecular scale interactions in the dynamic transformation of supramolecular structures. The synergic effect of hydrophobic interaction and the hydrated state of BA1 aggregates provide dynamicity and unusual stability. Our study unveils mechanistic insight into the dynamic transformation of bilayer membranes into vesicles.
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Affiliation(s)
- Drishya Elizebath
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Balaraman Vedhanarayanan
- Department of Chemistry, Tunghai University, No. 1727, Section 4, Taiwan Boulevard, Xitun District, Taichung City, 40704, Taiwan
| | - Angat Dhiman
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Rakesh K Mishra
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Department of Chemistry, National Institute of Technology Uttarakhand (NITUK), Srinagar (Garhwal), Uttarakhand, 246174, India
| | - C N Ramachandran
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, 247667, India
| | - Tsung-Wu Lin
- Department of Chemistry, Tunghai University, No. 1727, Section 4, Taiwan Boulevard, Xitun District, Taichung City, 40704, Taiwan
| | - Vakayil K Praveen
- Chemical Sciences and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala, 695019, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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2
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Maghsoud Y, Roy A, Leddin EM, Cisneros GA. Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ. J Chem Inf Model 2024; 64:4231-4249. [PMID: 38717969 PMCID: PMC11181361 DOI: 10.1021/acs.jcim.4c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2024]
Abstract
Human DNA polymerases are vital for genetic information management. Their function involves catalyzing the synthesis of DNA strands with unparalleled accuracy, which ensures the fidelity and stability of the human genomic blueprint. Several disease-associated mutations and their functional impact on DNA polymerases have been reported. One particular polymerase, human DNA polymerase kappa (Pol κ), has been reported to be susceptible to several cancer-associated mutations. The Y432S mutation in Pol κ, associated with various cancers, is of interest due to its impact on polymerization activity and markedly reduced thermal stability. Here, we have used computational simulations to investigate the functional consequences of the Y432S using classical molecular dynamics (MD) and coupled quantum mechanics/molecular mechanics (QM/MM) methods. Our findings suggest that Y432S induces structural alterations in domains responsible for nucleotide addition and ternary complex stabilization while retaining structural features consistent with possible catalysis in the active site. Calculations of the minimum energy path associated with the reaction mechanism of the wild type (WT) and Y432S Pol κ indicate that, while both enzymes are catalytically competent (in terms of energetics and the active site's geometries), the cancer mutation results in an endoergic reaction and an increase in the catalytic barrier. Interactions with a third magnesium ion and environmental effects on nonbonded interactions, particularly involving key residues, contribute to the kinetic and thermodynamic distinctions between the WT and mutant during the catalytic reaction. The energetics and electronic findings suggest that active site residues favor the catalytic reaction with dCTP3- over dCTP4-.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Arkanil Roy
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Emmett M Leddin
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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3
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Das CK, Gupta A, Nair NN. Probing the general base for DNA polymerization in telomerase: a molecular dynamics investigation. Phys Chem Chem Phys 2023; 25:14147-14157. [PMID: 37162325 DOI: 10.1039/d3cp00521f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Telomerase is an RNA-dependent DNA polymerase that plays a role in the maintenance of the 3' end of the eukaryotic chromosome, known as a telomere, by catalyzing the DNA polymerization reaction in cancer and embryonic stem cells. The detailed molecular details of the DNA polymerization by telomerase, especially the general base for deprotonating the terminal 3'-hydroxyl, which triggers the chemical reaction, remain elusive. We conducted a computational investigation using hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations to probe the detailed mechanism of the reaction. Our simulations started with the telomerase:RNA:DNA:dNTP ternary complex, and by using enhanced sampling QM/MM MD simulations, we probed the general base involved directly in the polymerization. We report the participation of an aspartate (Asp344) coordinated to Mg and an active site water molecule, jointly acting as a base during nucleic acid addition. The Asp344 residue remains transiently protonated during the course of the reaction, and later it deprotonates by transferring its proton to the water at the end of the reaction.
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Affiliation(s)
- Chandan Kumar Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
| | - Abhinav Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208016, India.
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4
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Berger MB, Cisneros GA. Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity. J Am Chem Soc 2023; 145:3478-3490. [PMID: 36745735 PMCID: PMC10237177 DOI: 10.1021/jacs.2c11713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA polymerases are responsible for the replication and repair of DNA found in all DNA-based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is composed of over 10 proteins. A subset of these proteins (Pol III*) includes the polymerase (α), exonuclease (ϵ), clamp (β), and accessory protein (θ). Mutations of residues in, or around the active site of the catalytic subunits (α and ϵ), can have a significant impact on catalysis. However, the effects of distal mutations in noncatalytic subunits on the activity of catalytic subunits are less well-characterized. Here, we investigate the effects of two Pol III* variants, β-L82E/L82'E and β-L82D/L82'D, on the proofreading reaction catalyzed by ϵ. MD simulations reveal major changes in the dynamics of Pol III*, which extend throughout the complex. These changes are mostly induced by a shift in the position of the DNA substrate inside the β-clamp, although no major structural changes are observed in the protein complex. Quantum mechanics/molecular mechanics (QM/MM) calculations indicate that the β-L82D/L82'D variant has reduced catalytic proficiency due to highly endoergic reaction energies resulting from structural changes in the active site and differences in the electric field at the active site arising from the protein and substrate. Conversely, the β-L82E/L82'E variant is predicted to maintain proofreading activity, exhibiting a similar reaction barrier for nucleotide excision compared with the WT system. However, significant differences in the reaction mechanism are obtained due to the changes induced by the mutations on the β-clamp.
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Affiliation(s)
- Madison B Berger
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
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5
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Pan X, Van R, Epifanovsky E, Liu J, Pu J, Nam K, Shao Y. Accelerating Ab Initio Quantum Mechanical and Molecular Mechanical (QM/MM) Molecular Dynamics Simulations with Multiple Time Step Integration and a Recalibrated Semiempirical QM/MM Hamiltonian. J Phys Chem B 2022; 126:10.1021/acs.jpcb.2c02262. [PMID: 35653199 PMCID: PMC9715852 DOI: 10.1021/acs.jpcb.2c02262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular dynamics (MD) simulations employing ab initio quantum mechanical and molecular mechanical (ai-QM/MM) potentials are considered to be the state of the art, but the high computational cost associated with the ai-QM calculations remains a theoretical challenge for their routine application. Here, we present a modified protocol of the multiple time step (MTS) method for accelerating ai-QM/MM MD simulations of condensed-phase reactions. Within a previous MTS protocol [Nam J. Chem. Theory Comput. 2014, 10, 4175], reference forces are evaluated using a low-level (semiempirical QM/MM) Hamiltonian and employed at inner time steps to propagate the nuclear motions. Correction forces, which arise from the force differences between high-level (ai-QM/MM) and low-level Hamiltonians, are applied at outer time steps, where the MTS algorithm allows the time-reversible integration of the correction forces. To increase the outer step size, which is bound by the highest-frequency component in the correction forces, the semiempirical QM Hamiltonian is recalibrated in this work to minimize the magnitude of the correction forces. The remaining high-frequency modes, which are mainly bond stretches involving hydrogen atoms, are then removed from the correction forces. When combined with a Langevin or SIN(R) thermostat, the modified MTS-QM/MM scheme remains robust with an up to 8 (with Langevin) or 10 fs (with SIN(R)) outer time step (with 1 fs inner time steps) for the chorismate mutase system. This leads to an over 5-fold speedup over standard ai-QM/MM simulations, without sacrificing the accuracy in the predicted free energy profile of the reaction.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St., LD326, Indianapolis, Indiana 46202, United States
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019-5251, United States
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6
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Fontecilla-Camps JC, Volbeda A. Quinolinate Synthase: An Example of the Roles of the Second and Outer Coordination Spheres in Enzyme Catalysis. Chem Rev 2022; 122:12110-12131. [PMID: 35536891 DOI: 10.1021/acs.chemrev.1c00869] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The activation energy barrier of biochemical reactions is normally lowered by an enzyme catalyst, which directly helps the weakening of the bond(s) to be broken. In many metalloenzymes, this is a first coordination sphere effect. Besides having a direct catalytic action, enzymes can fix their reactive groups and substrates so that they are optimally positioned and also modify the water activity in the system. They can either activate substrates prior to their reaction or bind preactivated substrates, thereby drastically reducing local entropic effects. The latter type is well represented by some bisubstrate reactions, where they have been defined as "entropic traps". These can be described as "second coordination sphere" processes, but enzymes can also control the reactivity beyond this point through local conformational changes belonging to an "outer coordinate sphere" that can be modulated by substrate binding. We have chosen the [4Fe-4S] cluster-dependent enzyme quinolinate synthase to illustrate each one of these processes. In addition, this very old metalloenzyme shows low in vitro substrate binding specificity, atypical reactivity that produces dead-end products, and a unique modulation of its active site volume.
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Affiliation(s)
| | - Anne Volbeda
- Université Grenoble Alpes, CEA, CNRS, IBS, Metalloproteins Unit, F-38000 Grenoble, France
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7
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Pan X, Yang J, Van R, Epifanovsky E, Ho J, Huang J, Pu J, Mei Y, Nam K, Shao Y. Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions. J Chem Theory Comput 2021; 17:5745-5758. [PMID: 34468138 DOI: 10.1021/acs.jctc.1c00565] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing machine-learning-assisted free energy simulation of solution-phase and enzyme reactions at the ab initio quantum-mechanical/molecular-mechanical (ai-QM/MM) level of accuracy. Within our protocol, the MLP is built to reproduce the ai-QM/MM energy and forces on both QM (reactive) and MM (solvent/enzyme) atoms. As an alternative strategy, a delta machine learning potential (ΔMLP) is trained to reproduce the differences between the ai-QM/MM and semiempirical (se) QM/MM energies and forces. To account for the effect of the condensed-phase environment in both MLP and ΔMLP, the DeePMD representation of a molecular system is extended to incorporate the external electrostatic potential and field on each QM atom. Using the Menshutkin and chorismate mutase reactions as examples, we show that the developed MLP and ΔMLP reproduce the ai-QM/MM energy and forces with errors that on average are less than 1.0 kcal/mol and 1.0 kcal mol-1 Å-1, respectively, for representative configurations along the reaction pathway. For both reactions, MLP/ΔMLP-based simulations yielded free energy profiles that differed by less than 1.0 kcal/mol from the reference ai-QM/MM results at only a fraction of the computational cost.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Junjie Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, LD326, Indianapolis, Indiana 46202, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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8
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Feng YX, Wang HJ, Wang JW, Zhang W, Zhang M, Lu TB. Stand-Alone CdS Nanocrystals for Photocatalytic CO 2 Reduction with High Efficiency and Selectivity. ACS APPLIED MATERIALS & INTERFACES 2021; 13:26573-26580. [PMID: 34038075 DOI: 10.1021/acsami.1c03606] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The development of a cost-effective photocatalyst is highly anticipated to achieve efficient photocatalytic CO2 reduction with superior selectivity, which is still facing the lack of valid settlements. Herein, 4-mercaptopyridine (PD) as the building block of a capping ligand is tightly decorated on the surface of CdS nanocrystals (CdS-PD) using a facile ligand-exchange strategy, to exploit a cost-effective photocatalyst for photocatalytic CO2 reduction without any cocatalysts. The conjugated structure of PD can facilitate the delocalization of photogenerated electrons in CdS nanocrystals, bringing forth an improved charge separation efficiency. More importantly, N-protonated PD can enable the easy formation of a six-membered ring intermediate with CO2 assisted by water, which can serve as the efficient active site to achieve photocatalytic CO2 reduction. In the absence of a cocatalyst, stand-alone CdS-PD nanocrystals exhibit an excellent CO yield of 20.35 mmol g-1 h-1 concomitant with a high selectivity of 95.3% for the CO2-to-CO conversion under visible light, which are remarkably superior than those of CdS nanocrystals possessing traditional alkyl-chain and other conjugated capping ligands.
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Affiliation(s)
- You-Xiang Feng
- MOE International Joint Laboratory of Materials Microstructure, Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Hong-Juan Wang
- MOE International Joint Laboratory of Materials Microstructure, Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Jia-Wei Wang
- MOE International Joint Laboratory of Materials Microstructure, Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Wen Zhang
- MOE International Joint Laboratory of Materials Microstructure, Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Min Zhang
- MOE International Joint Laboratory of Materials Microstructure, Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
- Tianjin Key Laboratory of Organic Solar Cells and Photochemical Conversion, School of Chemistry and Chemical Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Tong-Bu Lu
- MOE International Joint Laboratory of Materials Microstructure, Institute for New Energy Materials and Low Carbon Technologies, School of Materials Science and Engineering, Tianjin University of Technology, Tianjin 300384, China
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9
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Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction. Proc Natl Acad Sci U S A 2021; 118:2103990118. [PMID: 34088846 DOI: 10.1073/pnas.2103990118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA synthesis by polymerases is essential for life. Deprotonation of the nucleophile 3'-OH is thought to be the obligatory first step in the DNA synthesis reaction. We have examined each entity surrounding the nucleophile 3'-OH in the reaction catalyzed by human DNA polymerase (Pol) η and delineated the deprotonation process by combining mutagenesis with steady-state kinetics, high-resolution structures of in crystallo reactions, and molecular dynamics simulations. The conserved S113 residue, which forms a hydrogen bond with the primer 3'-OH in the ground state, stabilizes the primer end in the active site. Mutation of S113 to alanine destabilizes primer binding and reduces the catalytic efficiency. Displacement of a water molecule that is hydrogen bonded to the 3'-OH using the 2'-OH of a ribonucleotide or 2'-F has little effect on catalysis. Moreover, combining the S113A mutation with 2'-F replacement, which removes two potential hydrogen acceptors of the 3'-OH, does not reduce the catalytic efficiency. We conclude that the proton can leave the O3' via alternative paths, supporting the hypothesis that binding of the third Mg2+ initiates the reaction by breaking the α-β phosphodiester bond of an incoming deoxyribonucleoside triphosphate (dNTP).
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10
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Liu C, Lv C, Yao YY, Du X, Zhao DX, Yang ZZ. Water-Mediated Oxidation of Guanine by a Repair Enzyme: Simulation Using the ABEEM Polarizable Force Field. J Chem Theory Comput 2021; 17:3525-3538. [PMID: 34018392 DOI: 10.1021/acs.jctc.1c00107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The recognition mechanism of oxidative damage in organisms has long been a research hotspot. Water is an important medium in the recognition process, but its specific role remains unknown. There is a need to develop a suitable force field that can adequately describe the electrostatic, hydrogen bond, and other interactions among the molecules in the complex system of the repair enzyme and oxidized base. The developing ABEEM polarizable force field (PFF) has been used to simulate the repaired enzyme hOGG1 and oxidized DNA (PDB ID: 1EBM) in a biological environment, and the corresponding results are better than those of the fixed-charge force fields OPLS/AA and AMBER OL15. 8-Oxo-G is recognized by Gln315 of hOGG1 mainly through hydrogen bonds mediated by continuous exchange of 2 water molecules. Phe319 and Cys253 are stacked on both sides of the π planes of bases to form sandwich structures. The charge polarization effect gives an important signal to drive the exchange of water molecules and maintains the recognition of oxidation bases by enzymes. The mediated main water molecule A and mediated auxiliary water molecule B together pull Gln315 to recognize 8-oxo-G by hydrogen bond interactions. Then, the charge polarization signal of solvent water molecule C with a large absolute charge causes the absolute charge of O atoms in water molecule A or B to increase by approximately 0.2 e, and water molecule A or B leaves Gln315 and 8-oxo-G. The other water molecule and water molecule C synergistically recognize 8-oxo-G with Gln315. Even though the water molecules between Gln315 and 8-oxo-G are removed, the MD simulation results show that water molecules appear between Gln315 and 8-oxo-G in a very short time (<2 ps). The dwell time of each water molecule is approximately 60 ps. The radial distribution function and dwell time support the correctness of the above mechanism. These polarization effects and hydrogen bonding interactions cannot be simulated by a fixed-charge force field.
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Affiliation(s)
- Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Change Lv
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Yu-Ying Yao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Xue Du
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
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11
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Geronimo I, Vidossich P, Donati E, Vivo M. Computational investigations of polymerase enzymes: Structure, function, inhibition, and biotechnology. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Inacrist Geronimo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Pietro Vidossich
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Elisa Donati
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
| | - Marco Vivo
- Laboratory of Molecular Modelling and Drug Discovery, Istituto Italiano di Tecnologia Genoa Italy
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12
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Park WW, Lee KM, Lee BS, Kim YJ, Joo SH, Kwak SK, Yoo TH, Kwon OH. Hydrogen-Bond Free Energy of Local Biological Water. Angew Chem Int Ed Engl 2020; 59:7089-7096. [PMID: 32112494 DOI: 10.1002/anie.202002025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Indexed: 11/09/2022]
Abstract
Here, we propose an experimental methodology based on femtosecond-resolved fluorescence spectroscopy to measure the hydrogen (H)-bond free energy of water at protein surfaces under isothermal conditions. A demonstration was conducted by installing a non-canonical isostere of tryptophan (7-azatryptophan) at the surface of a coiled-coil protein to exploit the photoinduced proton transfer of its chromophoric moiety, 7-azaindole. The H-bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water, and it was found to be higher than that of bulk water by 0.4 kcal mol-1 . The free-energy difference is dominated by the entropic cost in the H-bond network among water molecules at the hydrophilic and charged protein surface. Our study opens a door to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.
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Affiliation(s)
- Won-Woo Park
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Kyung Min Lee
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Young Jae Kim
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
| | - Se Hun Joo
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering, School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Oh-Hoon Kwon
- Department of Chemistry, School of Natural Science, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.,Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan, 44919, Republic of Korea
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13
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Park W, Lee KM, Lee BS, Kim YJ, Joo SH, Kwak SK, Yoo TH, Kwon O. Hydrogen‐Bond Free Energy of Local Biological Water. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202002025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Won‐Woo Park
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Kyung Min Lee
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Byeong Sung Lee
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Young Jae Kim
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
| | - Se Hun Joo
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Sang Kyu Kwak
- Department of Energy Engineering School of Energy and Chemical Engineering Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology Ajou University Suwon 16499 Republic of Korea
| | - Oh‐Hoon Kwon
- Department of Chemistry School of Natural Science Ulsan National Institute of Science and Technology Ulsan 44919 Republic of Korea
- Center for Soft and Living Matter Institute for Basic Science (IBS) Ulsan 44919 Republic of Korea
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14
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Pan X, Li P, Ho J, Pu J, Mei Y, Shao Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching. Phys Chem Chem Phys 2019; 21:20595-20605. [PMID: 31508625 PMCID: PMC6761017 DOI: 10.1039/c9cp02593f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire an AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced QM/MM free energy profiles at the B3LYP/6-31G* level of theory all within 1 kcal mol-1 with a 20 to 45 fold reduction in the computer time.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China.
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, LD326, Indianapolis, IN 46202, USA.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China. and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
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15
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Darby JF, Hopkins AP, Shimizu S, Roberts SM, Brannigan JA, Turkenburg JP, Thomas GH, Hubbard RE, Fischer M. Water Networks Can Determine the Affinity of Ligand Binding to Proteins. J Am Chem Soc 2019; 141:15818-15826. [DOI: 10.1021/jacs.9b06275] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
| | - Adam P. Hopkins
- Demuris Ltd., The Biosphere, Draymans Way, Newcastle Helix, Newcastle upon Tyne NE4 5BX, United Kingdom
| | | | | | | | | | | | - Roderick E. Hubbard
- Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB21 6GB, United Kingdom
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, and Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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16
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Wilson KA, Holland CD, Wetmore SD. Uncovering a unique approach for damaged DNA replication: A computational investigation of a mutagenic tobacco-derived thymine lesion. Nucleic Acids Res 2019; 47:1871-1879. [PMID: 30605521 PMCID: PMC6393286 DOI: 10.1093/nar/gky1265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/03/2018] [Accepted: 12/06/2018] [Indexed: 01/01/2023] Open
Abstract
4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone is a potent nicotine carcinogen that leads to many DNA lesions, the most persistent being the O2-[4-oxo-4-(3-pyridyl)butyl]thymine adduct (POB-T). Although the experimental mutagenic profile for the minor groove POB-T lesion has been previously reported, the findings are puzzling in terms of the human polymerases involved. Specifically, while pol κ typically replicates minor groove adducts, in vivo studies indicate pol η replicates POB-T despite being known for processing major groove adducts. Our multiscale modeling approach reveals that the canonical (anti) glycosidic orientation of POB-T can fit in the pol κ active site, but only a unique (syn) POB-T conformation is accommodated by pol η. These distinct binding orientations rationalize the differential in vitro mutagenic spectra based on the preferential stabilization of dGTP and dTTP opposite the lesion for pol κ and η, respectively. Overall, by uncovering the first evidence for the replication of a damaged pyrimidine in the syn glycosidic orientation, the current work provides the insight necessary to clarify a discrepancy in the DNA replication literature, expand the biological role of the critical human pol η, and understand the mutational signature in human cancers associated with tobacco exposure.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Carl D Holland
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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17
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Wilson KA, Fernandes PA, Ramos MJ, Wetmore SD. Exploring the Identity of the General Base for a DNA Polymerase Catalyzed Reaction Using QM/MM: The Case Study of Human Translesion Synthesis Polymerase η. ACS Catal 2019. [DOI: 10.1021/acscatal.8b04889] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4 Canada
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4 Canada
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18
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Wilson KA, Garden JL, Wetmore NT, Wetmore SD. Computational insights into the mutagenicity of two tobacco-derived carcinogenic DNA lesions. Nucleic Acids Res 2018; 46:11858-11868. [PMID: 30407571 PMCID: PMC6294509 DOI: 10.1093/nar/gky1071] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/11/2018] [Accepted: 10/18/2018] [Indexed: 01/20/2023] Open
Abstract
4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone is a potent carcinogen found in all tobacco products that leads to a variety of DNA lesions in cells, including O6-[4-oxo-4-(3-pyridyl)butyl]guanine (POB-G) and O6-[4-hydroxy-4-(3-pyridyl)butyl]guanine (PHB-G), which differ by only a single substituent in the bulky moiety. This work uses a multiscale computational approach to shed light on the intrinsic conformational and base-pairing preferences of POB-G and PHB-G, and the corresponding properties in DNA and the polymerase η active site. Our calculations reveal that both lesions form stable pairs with C and T, with the T pairs being the least distorted relative to canonical DNA. This rationalizes the experimentally reported mutational profile for POB-G and validates our computational model. The same approach predicts that PHB-G is more mutagenic than POB-G due to a difference in the bulky moiety hydrogen-bonding pattern, which increases the stability of the PHB-G:T pair. The mutagenicity of PHB-G is likely further increased by stabilization of an intercalated DNA conformation that is associated with deletion mutations. This work thereby uncovers structural explanations for the reported mutagenicity of POB-G, provides the first clues regarding the mutagenicity of PHB-G and complements a growing body of literature highlighting that subtle chemical changes can affect the biological outcomes of DNA adducts.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Josh L Garden
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Natasha T Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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19
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
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20
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Zhou Y, Ojeda-May P, Nagaraju M, Kim B, Pu J. Mapping Free Energy Pathways for ATP Hydrolysis in the E. coli ABC Transporter HlyB by the String Method. Molecules 2018; 23:molecules23102652. [PMID: 30332773 PMCID: PMC6222333 DOI: 10.3390/molecules23102652] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 11/16/2022] Open
Abstract
HlyB functions as an adenosine triphosphate (ATP)-binding cassette (ABC) transporter that enables bacteria to secrete toxins at the expense of ATP hydrolysis. Our previous work, based on potential energy profiles from combined quantum mechanical and molecular mechanical (QM/MM) calculations, has suggested that the highly conserved H-loop His residue H662 in the nucleotide binding domain (NBD) of E. coli HlyB may catalyze the hydrolysis of ATP through proton relay. To further test this hypothesis when entropic contributions are taken into account, we obtained QM/MM minimum free energy paths (MFEPs) for the HlyB reaction, making use of the string method in collective variables. The free energy profiles along the MFEPs confirm the direct participation of H662 in catalysis. The MFEP simulations of HlyB also reveal an intimate coupling between the chemical steps and a local protein conformational change involving the signature-loop residue S607, which may serve a catalytic role similar to an Arg-finger motif in many ATPases and GTPases in stabilizing the phosphoryl-transfer transition state.
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Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Pedro Ojeda-May
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Mulpuri Nagaraju
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Bryant Kim
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., LD326, Indianapolis, IN 46202, USA.
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21
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Stevens DR, Hammes-Schiffer S. Exploring the Role of the Third Active Site Metal Ion in DNA Polymerase η with QM/MM Free Energy Simulations. J Am Chem Soc 2018; 140:8965-8969. [PMID: 29932331 DOI: 10.1021/jacs.8b05177] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The enzyme human DNA polymerase η (Pol η) is critical for bypassing lesions during DNA replication. In addition to the two Mg2+ ions aligning the active site, experiments suggest that a third Mg2+ ion could play an essential catalytic role. Herein the role of this third metal ion is investigated with quantum mechanical/molecular mechanical (QM/MM) free energy simulations of the phosphoryl transfer reaction and a proposed self-activating proton transfer from the incoming nucleotide to the pyrophosphate leaving group. The simulations with only two metal ions in the active site support a sequential mechanism, with phosphoryl transfer followed by relatively fast proton transfer. The simulations with three metal ions in the active site suggest that the third metal ion may play a catalytic role through electrostatic interactions with the leaving group. These electrostatic interactions stabilize the product, making the phosphoryl transfer reaction more thermodynamically favorable with a lower free energy barrier relative to the activated state corresponding to the deprotonated 3'OH nucleophile, and also inhibit the subsequent proton transfer. The possibility that Mg2+-bound hydroxide acts as the base deprotonating the 3'OH nucleophile is also explored.
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Affiliation(s)
- David R Stevens
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06520 , United States
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22
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Govindarajan N, Tiwari A, Ensing B, Meijer EJ. Impact of the Ligand Flexibility and Solvent on the O-O Bond Formation Step in a Highly Active Ruthenium Water Oxidation Catalyst. Inorg Chem 2018; 57:13063-13066. [PMID: 29732882 PMCID: PMC6220359 DOI: 10.1021/acs.inorgchem.8b00619] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
By advanced molecular dynamics simulations, we show that for a highly active ruthenium-based water oxidation catalyst the dangling carboxylate group of the catalyst plays an important role in the crucial O-O bond formation step. The interplay of the flexible group and solvent molecules facilitates two possible pathways: a direct pathway with a single solvent water molecule or a mediated pathway involving two solvent water molecules, which have similar activation barriers. Our results provide an example for which a realistic molecular dynamics approach, incorporating an explicit description of the solvent, is required to reveal the full complexity of an important catalytic reaction in aqueous solvent.
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Affiliation(s)
- Nitish Govindarajan
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
| | - Ambuj Tiwari
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
| | - Bernd Ensing
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
| | - Evert Jan Meijer
- Amsterdam Center for Multiscale Modeling and Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098XH Amsterdam , The Netherlands
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23
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Li Y, Bao L, Zhang R, Tang X, Zhang Q, Wang W. Insights into the error bypass of 1-Nitropyrene DNA adduct by DNA polymerase ι: A QM/MM study. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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24
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Walker AR, Cisneros GA. Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants. Chem Res Toxicol 2017; 30:1922-1935. [PMID: 28877429 PMCID: PMC5696005 DOI: 10.1021/acs.chemrestox.7b00161] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Genetic information is vital in the
cell cycle of DNA-based organisms.
DNA polymerases (DNA Pols) are crucial players in transactions dealing
with these processes. Therefore, the detailed understanding of the
structure, function, and mechanism of these proteins has been the
focus of significant effort. Computational simulations have been applied
to investigate various facets of DNA polymerase structure and function.
These simulations have provided significant insights over the years.
This perspective presents the results of various computational studies
that have been employed to research different aspects of DNA polymerases
including detailed reaction mechanism investigation, mutagenicity
of different metal cations, possible factors for fidelity synthesis,
and discovery/functional characterization of cancer-related mutations
on DNA polymerases.
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Affiliation(s)
- Alice R Walker
- Department of Chemistry, University of North Texas , 1155 Union Circle, Denton, Texas 76203, United States
| | - G Andrés Cisneros
- Department of Chemistry, University of North Texas , 1155 Union Circle, Denton, Texas 76203, United States
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25
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Wilson KA, Wetmore SD. Conformational Flexibility of the Benzyl-Guanine Adduct in a Bypass Polymerase Active Site Permits Replication: Insights from Molecular Dynamics Simulations. Chem Res Toxicol 2017; 30:2013-2022. [PMID: 28810119 DOI: 10.1021/acs.chemrestox.7b00179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Katie A. Wilson
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and
Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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26
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Wilson KA, Wetmore SD. Molecular Insights into the Translesion Synthesis of Benzyl-Guanine from Molecular Dynamics Simulations: Structural Evidence of Mutagenic and Nonmutagenic Replication. Biochemistry 2017; 56:1841-1853. [PMID: 28290677 DOI: 10.1021/acs.biochem.6b01247] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
DNA can be damaged by many compounds in our environment, and the resulting damaged DNA is commonly replicated by translesion synthesis (TLS) polymerases. Because the mechanism and efficiency of TLS are affected by the type of DNA damage, obtaining information for a variety of DNA adducts is critical. However, there is no structural information for the insertion of a dNTP opposite an O6-dG adduct, which is a particularly harmful class of DNA lesions. We used molecular dynamics (MD) simulations to investigate structural and energetic parameters that dictate preferred dNTP insertion opposite O6-benzyl-guanine (Bz-dG) by DNA polymerase IV, a prototypical TLS polymerase. Specifically, MD simulations were completed on all possible ternary insertion complexes and ternary -1 base deletion complexes with different Bz-dG conformations. Our data suggests that the purines are unlikely to be inserted opposite anti- or syn-Bz-dG, and dTTP is unlikely to be inserted opposite syn-Bz-dG, because of changes in the active site conformation, including critical hydrogen-bonding interactions and/or reaction-ready parameters compared to natural dG replication. In contrast, a preserved active site conformation suggests that dCTP can be inserted opposite either anti- or syn-Bz-dG and dTTP can be inserted opposite anti-Bz-dG. This is the first structural explanation for the experimentally observed preferential insertion of dCTP and misincorporation of dTTP opposite Bz-dG. Furthermore, we provide atomic level insight into why Bz-dG replication does not lead to deletion mutations, which is in contrast with the replication outcomes of other adducts. These findings provide a basis for understanding the replication of related O6-dG adducts.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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27
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Genna V, Vidossich P, Ippoliti E, Carloni P, De Vivo M. A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases. J Am Chem Soc 2016; 138:14592-14598. [PMID: 27530537 DOI: 10.1021/jacs.6b05475] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3'-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation. Thus, SAM allows an elegant and efficient closed-loop sequence of chemical and physical steps for Pol catalysis. This is markedly different from previous mechanistic hypotheses. Our proposed mechanism is corroborated via ab initio QM/MM simulations on a specific Pol, the human DNA polymerase-η, an enzyme involved in repairing damaged DNA. The structural conservation of DNA and RNA Pols supports the possible extension of SAM to Pol enzymes from the three domains of life.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia , Via Morego 30, 16163, Genoa, Italy.,IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Pietro Vidossich
- IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Emiliano Ippoliti
- IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Paolo Carloni
- IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia , Via Morego 30, 16163, Genoa, Italy.,IAS-5/INM-9 Computational Biomedicine and JARA-HPC, Forschungszentrum Jülich , Wilhelm-Johnen-Strasse, 52428 Jülich, Germany
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28
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Galano-Frutos JJ, Morón MC, Sancho J. The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin. Phys Chem Chem Phys 2016; 17:28635-46. [PMID: 26443502 DOI: 10.1039/c5cp04504e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Binding/unbinding of small ligands, such as ions, to/from proteins influences biochemical processes such as protein folding, enzyme catalysis or protein/ligand recognition. We have investigated the mechanism of chloride/water exchange at a protein surface (that of the apoflavodoxin from Helicobacter pylori) using classical all-atom molecular dynamics simulations. They reveal a variety of chloride exit routes and residence times; the latter is related to specific coordination modes of the anion. The role of solvent molecules in the mechanism of chloride unbinding has been studied in detail. We see no temporary increase in chloride coordination along the release process. Instead, the coordination of new water molecules takes place in most cases after the chloride/protein atom release event has begun. Moreover, the distribution function of water entrance events into the first chloride solvation shell peaks after chloride protein atom dissociation events. All these observations together seem to indicate that water molecules simply fill the vacancies left by the previously coordinating protein residues. We thus propose a step-by-step dissociation pathway in which protein/chloride interactions gradually break down before new water molecules progressively fill the vacant positions left by protein atoms. As observed for other systems, water molecules associated with bound chloride or with protein atoms have longer residence times than those bound to the free anion. The implications of the exchange mechanism proposed for the binding of the FMN (Flavin Mononucleotide) protein cofactor are discussed.
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Affiliation(s)
- Juan J Galano-Frutos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC). Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
| | - M Carmen Morón
- Instituto de Ciencia de Materiales de Aragón (ICMA), Consejo Superior de Investigaciones Científicas-Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain and Departamento de Física de la Materia Condensada, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain. and Biocomputation and Complex Systems Physics Institute (BIFI), Joint Unit BIFI-IQFR (CSIC). Edificio I + D, Mariano Esquillor, 50018, Zaragoza, Spain
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29
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Grigorenko BL, Knyazeva MA, Nemukhin AV. Analysis of proton wires in the enzyme active site suggests a mechanism of c-di-GMP hydrolysis by the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. [PMID: 27479508 DOI: 10.1002/prot.25108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/30/2016] [Accepted: 07/25/2016] [Indexed: 11/08/2022]
Abstract
We report for the first time a hydrolysis mechanism of the cyclic dimeric guanosine monophosphate (c-di-GMP) by the EAL domain phosphodiesterases as revealed by molecular simulations. A model system for the enzyme-substrate complex was prepared on the base of the crystal structure of the EAL domain from the BlrP1 protein complexed with c-di-GMP. The nucleophilic hydroxide generated from the bridging water molecule appeared in a favorable position for attack on the phosphorus atom of c-di-GMP. The most difficult task was to find a pathway for a proton transfer to the O3' atom of c-di-GMP to promote the O3'P bond cleavage. We show that the hydrogen bond network extended over the chain of water molecules in the enzyme active site and the Glu359 and Asp303 side chains provides the relevant proton wires. The suggested mechanism is consistent with the structural, mutagenesis, and kinetic experimental studies on the EAL domain phosphodiesterases. Proteins 2016; 84:1670-1680. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Bella L Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia.,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia
| | - Marina A Knyazeva
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia
| | - Alexander V Nemukhin
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskiye Gory, Moscow, 119991, Russia. .,N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow, 119334, Russia.
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30
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Albrecht L, Wilson KA, Wetmore SD. Computational Evaluation of Nucleotide Insertion Opposite Expanded and Widened DNA by the Translesion Synthesis Polymerase Dpo4. Molecules 2016; 21:molecules21070822. [PMID: 27347908 PMCID: PMC6273265 DOI: 10.3390/molecules21070822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/08/2016] [Accepted: 06/14/2016] [Indexed: 11/25/2022] Open
Abstract
Expanded (x) and widened (y) deoxyribose nucleic acids (DNA) have an extra benzene ring incorporated either horizontally (xDNA) or vertically (yDNA) between a natural pyrimidine base and the deoxyribose, or between the 5- and 6-membered rings of a natural purine. Far-reaching applications for (x,y)DNA include nucleic acid probes and extending the natural genetic code. Since modified nucleobases must encode information that can be passed to the next generation in order to be a useful extension of the genetic code, the ability of translesion (bypass) polymerases to replicate modified bases is an active area of research. The common model bypass polymerase DNA polymerase IV (Dpo4) has been previously shown to successfully replicate and extend past a single modified nucleobase on a template DNA strand. In the current study, molecular dynamics (MD) simulations are used to evaluate the accommodation of expanded/widened nucleobases in the Dpo4 active site, providing the first structural information on the replication of (x,y)DNA. Our results indicate that the Dpo4 catalytic (palm) domain is not significantly impacted by the (x,y)DNA bases. Instead, the template strand is displaced to accommodate the increased C1’–C1’ base-pair distance. The structural insights unveiled in the present work not only increase our fundamental understanding of Dpo4 replication, but also reveal the process by which Dpo4 replicates (x,y)DNA, and thereby will contribute to the optimization of high fidelity and efficient polymerases for the replication of modified nucleobases.
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Affiliation(s)
- Laura Albrecht
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
| | - Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge Alberta, AB T1K 3M4, Canada.
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31
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Genna V, Gaspari R, Dal Peraro M, De Vivo M. Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η. Nucleic Acids Res 2016; 44:2827-36. [PMID: 26935581 PMCID: PMC4824119 DOI: 10.1093/nar/gkw128] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/19/2016] [Indexed: 12/18/2022] Open
Abstract
Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases.
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Roberto Gaspari
- CONCEPT Lab., Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland Swiss Institute of Bioinformatics (SIB), CH-1015, Lausanne, Switzerland
| | - Marco De Vivo
- Laboratory of Molecular Modeling & Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy IAS-5 / INM-9 Computational Biomedicine Forschungszentrum Jülich, Wilhelm-Johnen-Straße 52428 Jülich, Germany
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32
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Yadav R, Sengupta B, Sen P. Effect of sucrose on chemically and thermally induced unfolding of domain-I of human serum albumin: Solvation dynamics and fluorescence anisotropy study. Biophys Chem 2016; 211:59-69. [PMID: 26930029 DOI: 10.1016/j.bpc.2016.02.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
The present study is devoted to understand the effect of sucrose on the hydration dynamics and rotational relaxation dynamics within the domain-I of HSA during chemically as well as thermally induced unfolding. It has been observed that the average solvation time become slower in the presence of sucrose for the lower concentrations of GnHCl, however at higher concentrations of GnHCl the effect of sucrose is almost negligible. From the time resolved fluorescence anisotropy it has been observed that in the lower concentration region of GnHCl the sucrose induced stabilization is small as compared to the higher concentrations of GnHCl. We have concluded that the hydration dynamics plays an important role in the sucrose induced stabilization process at the low concentration region; whereas environmental restriction is responsible at the higher concentration of GnHCl. However, we have observed a negligible stabilizing effect of sucrose towards the temperature induced unfolding.
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Affiliation(s)
- Rajeev Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India
| | - Bhaswati Sengupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, 208 016, UP, India.
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33
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Toxicology of DNA Adducts Formed Upon Human Exposure to Carcinogens. ADVANCES IN MOLECULAR TOXICOLOGY 2016. [DOI: 10.1016/b978-0-12-804700-2.00007-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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34
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Yao Y, Liu J, Zheng F, Zhan CG. Reaction Pathway for Cocaine Hydrolase-Catalyzed Hydrolysis of (+)-Cocaine. Theor Chem Acc 2016; 135. [PMID: 28250715 DOI: 10.1007/s00214-015-1788-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recently designed and discovered cocaine hydrolase (CocH), engineered from human butyrylcholinesterase (BChE), has been proven promising as a novel enzyme therapy for treatment of cocaine overdose and addiction because it is highly efficient in catalyzing hydrolysis of naturally occurring (-)-cocaine. It has been known that the CocH also has a high catalytic efficiency against (+)-cocaine, a synthetic enantiomer of cocaine. Reaction pathway and the corresponding free energy profile for the CocH-catalyzed hydrolysis of (+)-cocaine have been determined, in the present study, by performing first-principles pseudobond quantum mechanical/molecular mechanical (QM/MM)-free energy (FE) calculations. Acordingt to the QM/MM-FE results, the catalytic hydrolysis process is initiated by the nucleophilic attack on carbonyl carbon of (-)-cocaine benzoyl ester via hydroxyl oxygen of S198 side chain, and the second reaction step (i.e. dissociation of benzoyl ester) is rate-determining. This finding for CocH-catalyzed hydrolysis of (+)-cocaine is remarkably different from that for the (+)-cocaine hydrolysis catalyzed by bacterial cocaine esterase in which the first reaction step of the deacylation is associated with the highest free energy barrier (~17.9 kcal/mol). The overall free energy barrier (~16.0 kcal/mol) calculated for the acylation stage of CocH-catalyzed hydrolysis of (+)-cocaine is in good agreement with the experimental free energy barrier of ~14.5 kcal/mol derivated from the experimental kinetic data.
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Affiliation(s)
- Yuan Yao
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; The Academy of Fundamental and Interdisciplinary Sciences, Harbin Institute of Technology, Harbin 150080, P.R. China
| | - Junjun Liu
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536; Tongji School of Pharmacy, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei 430030, P.R. China
| | - Fang Zheng
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
| | - Chang-Guo Zhan
- Molecular Modeling and Biopharmaceutical Center and Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone, Lexington, KY 40536
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35
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Krueger RA, Vilčiauskas L, Melchior JP, Bester G, Kreuer KD. Mechanism of Efficient Proton Conduction in Diphosphoric Acid Elucidated via First-Principles Simulation and NMR. J Phys Chem B 2015; 119:15866-75. [DOI: 10.1021/acs.jpcb.5b09684] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachel A. Krueger
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
- Division
of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Linas Vilčiauskas
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Department
of Chemical Engineering, University of Texas, Austin, Texas 78712, United States
| | - Jan-Patrick Melchior
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
| | - Gabriel Bester
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
- Department
of Chemistry, University of Hamburg, D-20146 Hamburg, Germany
| | - Klaus-Dieter Kreuer
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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36
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Hahn DK, Tusell JR, Sprang SR, Chu X. Catalytic Mechanism of Mammalian Adenylyl Cyclase: A Computational Investigation. Biochemistry 2015; 54:6252-62. [PMID: 26393535 PMCID: PMC5156327 DOI: 10.1021/acs.biochem.5b00655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adenylyl cyclase (AC) catalyzes the synthesis of cyclic AMP, an important intracellular regulatory molecule, from ATP. We propose a catalytic mechanism for class III mammalian AC based on density functional theory calculations. We employ a model of the AC active site derived from a crystal structure of mammalian AC activated by Gα·GTP and forskolin at separate allosteric sites. We compared the calculated activation free energies for 13 possible reaction sequences involving proton transfer, nucleophilic attack, and elimination of pyrophosphate. The proposed most probable mechanism is initiated by deprotonation of 3'OH and water-mediated transfer of the 3'H to the γ-phosphate. Proton transfer is followed by changes in coordination of the two magnesium ion cofactors and changes in the conformation of ATP to enhance the role of 3'O as a nucleophile and to bring 3'O close to Pα. The subsequent phosphoryl transfer step is concerted and rate-limiting. Comparison of the enzyme-catalyzed and nonenzymatic reactions reveals that the active site residues lower the free energy barrier for both phosphoryl transfer and proton transfer and significantly shift the proton transfer equilibrium. Calculations for mutants K1065A and R1029A demonstrate that K1065 plays a significant role in shifting the proton transfer equilibrium, whereas R1029 is important for making the transition state of concerted phosphoryl transfer tight rather than loose.
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Affiliation(s)
- David K. Hahn
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
| | - Jose R Tusell
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
| | - Stephen R. Sprang
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
| | - Xi Chu
- Center for Biomolecular Structure and Dynamics and Department of Chemistry and Biochemistry, The University of Montana, Missoula, Montana 59812
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37
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Sholder G, Creech A, Loechler EL. How Y-Family DNA polymerase IV is more accurate than Dpo4 at dCTP insertion opposite an N2-dG adduct of benzo[a]pyrene. DNA Repair (Amst) 2015; 35:144-53. [PMID: 26523515 DOI: 10.1016/j.dnarep.2015.09.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/11/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022]
Abstract
To bypass DNA damage, cells have Y-Family DNA polymerases (DNAPs). One Y-Family-class includes DNAP κ and DNAP IV, which accurately insert dCTP opposite N(2)-dG adducts, including from the carcinogen benzo[a]pyrene (BP). Another class includes DNAP η and DNAP V, which insert accurately opposite UV-damage, but inaccurately opposite BP-N(2)-dG. To investigate structural differences between Y-Family-classes, regions are swapped between DNAP IV (a κ/IV-class-member) and Dpo4 (a η/V-class-member); the kinetic consequences are evaluated via primer-extension studies with a BP-N(2)-dG-containing template. Four key structural elements are revealed. (1) Y-Family DNAPs have discreet non-covalent contacts between their little finger-domain (LF-Domain) and their catalytic core-domain (CC-Domain), which we call "non-covalent bridges" (NCBs). Arg37 and Arg38 in DNAP IV's CC-Domain near the active site form a non-covalent bridge (AS-NCB) by interacting with Glu251 and Asp252, respectively, in DNAP IV's LF-Domain. Without these interactions dATP/dGTP/dTTP misinsertions increase. DNAP IV's AS-NCB suppresses misinsertions better than Dpo4's equivalent AS-NCB. (2) DNAP IV also suppresses dATP/dGTP/dTTP misinsertions via a second non-covalent bridge, which is ∼8Å from the active site (Distal-NCB). Dpo4 has no Distal-NCB, rendering it inferior at dATP/dGTP/dTTP suppression. (3) dCTP insertion is facilitated by the larger minor groove opening near the active site in DNAP IV versus Dpo4, which is sensible given that Watson/Crick-like [dCTP:BP-N(2)-dG] pairing requires the BP-moiety to be in the minor groove. (4) Compared to Dpo4, DNAP IV has a smaller major groove opening, which suppresses dGTP misinsertion, implying BP-N(2)-dG bulk in the major groove during Hoogsteen syn-adduct-dG:dGTP pairing. In summary, DNAP IV has a large minor groove opening to enhance dCTP insertion, a plugged major groove opening to suppress dGTP misinsertion, and two non-covalent bridges (near and distal to the active site) to suppress dATP/dGTP/dTTP misinsertions; collectively these four structural features enhance DNAP IV's dNTP insertion fidelity opposite a BP-N(2)-dG adduct compared to Dpo4.
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Affiliation(s)
- Gabriel Sholder
- Biology Department, Boston University, Boston, MA 02215, USA
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38
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Huang NL, Lin JH. Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation. Nucleic Acids Res 2015; 43:6772-86. [PMID: 26150421 PMCID: PMC4538842 DOI: 10.1093/nar/gkv672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 06/19/2015] [Indexed: 01/24/2023] Open
Abstract
Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.
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Affiliation(s)
- Nan-Lan Huang
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan
| | - Jung-Hsin Lin
- Research Center for Applied Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan Institute of Biomedical Sciences, Academia Sinica, Nangang, Taipei 11529, Taiwan School of Pharmacy, National Taiwan University, Taipei 10050, Taiwan
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39
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Saha D, Supekar S, Mukherjee A. Distribution of Residence Time of Water around DNA Base Pairs: Governing Factors and the Origin of Heterogeneity. J Phys Chem B 2015; 119:11371-81. [DOI: 10.1021/acs.jpcb.5b03553] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debasis Saha
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
| | - Shreyas Supekar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Maharashtra 411021, India
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40
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Choudhury S, Mondal PK, Sharma VK, Mitra S, Sakai VG, Mukhopadhyay R, Pal SK. Direct Observation of Coupling between Structural Fluctuation and Ultrafast Hydration Dynamics of Fluorescent Probes in Anionic Micelles. J Phys Chem B 2015; 119:10849-57. [PMID: 25874585 DOI: 10.1021/jp511899q] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The coupling of structural fluctuation and the dynamics of associated water molecules of biological macromolecules is vital for various biological activities. Although a number of molecular dynamics (MD) studies on proteins/DNA predicted the importance of such coupling, experimental evidence of variation of hydration dynamics with controlled structural fluctuation even in model macromolecule is sparse and raised controversies in the contemporary literature. Here, we have investigated dynamics of hydration at the surfaces of two similar anionic micelles sodium dodecyl sulfate (SDS) and sodium dodecylbenzenesulfonate (SDBS) as model macromolecules using coumarin 500 (C500) as spectroscopic probe with femtosecond to picosecond time resolution up to 20 ns time window. The constituting surfactants SDS and SDBS are structurally similar except one benzene moiety in the SDBS may offer additional rigidity to the SDBS micelles through π-stacking and added bulkiness. The structural integrity of the micelles in the aqueous medium is confirmed in dynamic light scattering (DLS) studies. A variety of studies including polarization gated fluorescence spectroscopy and quasielastic neutron scattering (QENS) have been used to confirm differential structural fluctuation of SDS and SDBS micelles. We have also employed femtosecond-resolved Förster resonance energy transfer (FRET) in order to study binding of a cationic organic ligand ethidium bromide (EtBr) salt at the micellar surfaces. The distance distribution of the donor (C500)-acceptor (EtBr) in the micellar media reveals the manifestation of the structural flexibility of the micelles. Our studies on dynamical coupling of the structural flexibility with surface hydration in the nanoscopic micellar media may find the relevance in the "master-slave" type water dynamics in biologically relevant macromolecules.
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Affiliation(s)
- Susobhan Choudhury
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - Prasanna Kumar Mondal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
| | - V K Sharma
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - S Mitra
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - V Garcia Sakai
- Science and Technology Facilities Council, Rutherford Appleton Laboratory , Didcot, OX11 0QX, U.K
| | - R Mukhopadhyay
- Solid State Physics Division, Bhabha Atomic Research Centre , Mumbai 400085, India
| | - Samir Kumar Pal
- Department of Chemical, Biological & Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences , Block JD, Sector III, Salt Lake, Kolkata 700 098, India
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41
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Zhang R, Bhattacharjee A, Field MJ, Salahub DR. Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model. Proteins 2014; 83:268-81. [DOI: 10.1002/prot.24732] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Rui Zhang
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Anirban Bhattacharjee
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
| | - Martin J. Field
- DYNAMOP; Institut de Biologie Structurale, Jean-Pierre Ebel; Grenoble France
| | - Dennis R. Salahub
- Department of Chemistry; Centre for Molecular Simulation, Institute for Quantum Science and Technology, University of Calgary; Calgary Canada
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42
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Lu X, Gaus M, Elstner M, Cui Q. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B 2014; 119:1062-82. [PMID: 25178644 PMCID: PMC4306495 DOI: 10.1021/jp506557r] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report the parametrization of
the approximate density functional
theory, DFTB3, for magnesium and zinc for chemical and biological
applications. The parametrization strategy follows that established
in previous work that parametrized several key main group elements
(O, N, C, H, P, and S). This 3OB set of parameters can thus be used
to study many chemical and biochemical systems. The parameters are
benchmarked using both gas-phase and condensed-phase systems. The
gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization
(MIO). The results indicate that DFTB3/3OB is particularly successful
at predicting structures, including rather complex dinuclear metalloenzyme
active sites, while being semiquantitative (with a typical mean absolute
deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point
calculations with high-level quantum mechanics (QM) methods generally
lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic
properties. DFTB3/MM simulations for solution and two enzyme systems
also lead to encouraging structural and energetic properties in comparison
to available experimental data. The remaining limitations of DFTB3,
such as the treatment of interaction between metal ions and highly
charged/polarizable ligands, are also discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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43
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Lior-Hoffmann L, Ding S, Geacintov NE, Zhang Y, Broyde S. Structural and dynamic characterization of polymerase κ's minor groove lesion processing reveals how adduct topology impacts fidelity. Biochemistry 2014; 53:5683-91. [PMID: 25148552 PMCID: PMC4159208 DOI: 10.1021/bi5007964] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
DNA
lesion bypass polymerases process different lesions with varying
fidelities, but the structural, dynamic, and mechanistic origins of
this phenomenon remain poorly understood. Human DNA polymerase κ
(Polκ), a member of the Y family of lesion bypass polymerases,
is specialized to bypass bulky DNA minor groove lesions in a predominantly
error-free manner, by housing them in its unique gap. We have investigated
the role of the unique Polκ gap and N-clasp structural features
in the fidelity of minor groove lesion processing with extensive molecular
modeling and molecular dynamics simulations to pinpoint their functioning
in lesion bypass. Here we consider the N2-dG covalent adduct derived from the carcinogenic aromatic amine,
2-acetylaminofluorene (dG-N2-AAF), that
is produced via the combustion of kerosene and diesel fuel. Our simulations
reveal how the spacious gap directionally accommodates the lesion
aromatic ring system as it transits through the stages of incorporation
of the predominant correct partner dCTP opposite the damaged guanine,
with preservation of local active site organization for nucleotidyl
transfer. Furthermore, flexibility in Polκ’s N-clasp
facilitates the significant misincorporation of dTTP opposite dG-N2-AAF via wobble pairing. Notably, we show that
N-clasp flexibility depends on lesion topology, being markedly reduced
in the case of the benzo[a]pyrene-derived major adduct
to N2-dG, whose bypass by Polκ is
nearly error-free. Thus, our studies reveal how Polκ’s
unique structural and dynamic properties can regulate its bypass fidelity
of polycyclic aromatic lesions and how the fidelity is impacted by
lesion structures.
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Affiliation(s)
- Lee Lior-Hoffmann
- Department of Biology and ‡Department of Chemistry, New York University , 100 Washington Square East, New York, New York 10003, United States
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44
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Yang Y, Qin Y, Ding Q, Bakhtina M, Wang L, Tsai MD, Zhong D. Ultrafast water dynamics at the interface of the polymerase-DNA binding complex. Biochemistry 2014; 53:5405-13. [PMID: 25105470 PMCID: PMC4148141 DOI: 10.1021/bi500810a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA polymerases slide on DNA during replication, and the interface must be mobile for various conformational changes. The role of lubricant interfacial water is not understood. In this report, we systematically characterize the water dynamics at the interface and in the active site of a tight binding polymerase (pol β) in its binary complex and ternary state using tryptophan as a local optical probe. Using femtosecond spectroscopy, we observed that upon DNA recognition the surface hydration water is significantly confined and becomes bound water at the interface, but the dynamics are still ultrafast and occur on the picosecond time scale. These interfacial water molecules are not trapped but are mobile in the heterogeneous binding nanospace. Combining our findings with our previous observation of ultrafast water motions at the interface of a loose binding polymerase (Dpo4), we conclude that the binding interface is dynamic and the water molecules in various binding clefts, channels, and caves are mobile and even fluid with different levels of mobility for loose or tight binding polymerases. Such a dynamic interface should be general to all DNA polymerase complexes to ensure the biological function of DNA synthesis.
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Affiliation(s)
- Yi Yang
- Department of Physics, ‡Department of Chemistry and Biochemistry, and §Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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45
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Yang W. An overview of Y-Family DNA polymerases and a case study of human DNA polymerase η. Biochemistry 2014; 53:2793-803. [PMID: 24716551 PMCID: PMC4018060 DOI: 10.1021/bi500019s] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
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Y-Family
DNA polymerases specialize in translesion synthesis, bypassing
damaged bases that would otherwise block the normal progression of
replication forks. Y-Family polymerases have unique structural features
that allow them to bind damaged DNA and use a modified template base
to direct nucleotide incorporation. Each Y-Family polymerase is unique
and has different preferences for lesions to bypass and for dNTPs
to incorporate. Y-Family polymerases are also characterized by a low
catalytic efficiency, a low processivity, and a low fidelity on normal
DNA. Recruitment of these specialized polymerases to replication forks
is therefore regulated. The catalytic center of the Y-Family polymerases
is highly conserved and homologous to that of high-fidelity and high-processivity
DNA replicases. In this review, structural differences between Y-Family
and A- and B-Family polymerases are compared and correlated with their
functional differences. A time-resolved X-ray crystallographic study
of the DNA synthesis reaction catalyzed by the Y-Family DNA polymerase
human polymerase η revealed transient elements that led to the
nucleotidyl-transfer reaction.
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Affiliation(s)
- Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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46
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Qin Y, Yang Y, Zhang L, Fowler JD, Qiu W, Wang L, Suo Z, Zhong D. Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex. J Phys Chem A 2013; 117:13926-34. [PMID: 24308461 DOI: 10.1021/jp410051w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the DNA binding interface and active site are dynamically solvent accessible and the interfacial water dynamics are similar to the surface hydration water fluctuations on picosecond time scales. Our molecular dynamics simulations also show the binding interface full of water molecules and nonspecific weak interactions. Such a fluid binding interface facilitates the polymerase sliding on DNA for fast translocation whereas the spacious and mobile hydrated active site contributes to the low fidelity of the lesion-bypass Y-family DNA polymerase.
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Affiliation(s)
- Yangzhong Qin
- Department of Physics, Department of Chemistry and Biochemistry, Programs of Biophysics, Chemical Physics, and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States
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47
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Hwang T, Goldsmith BR, Peters B, Scott SL. Water-Catalyzed Activation of H2O2 by Methyltrioxorhenium: A Combined Computational–Experimental Study. Inorg Chem 2013; 52:13904-17. [DOI: 10.1021/ic401343m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Taeho Hwang
- Department of Chemical Engineering and ‡Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-5080, United States
| | - Bryan R. Goldsmith
- Department of Chemical Engineering and ‡Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-5080, United States
| | - Baron Peters
- Department of Chemical Engineering and ‡Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-5080, United States
| | - Susannah L. Scott
- Department of Chemical Engineering and ‡Department of Chemistry & Biochemistry, University of California, Santa Barbara, California 93106-5080, United States
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48
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Lee SG, Jez JM. Evolution of structure and mechanistic divergence in di-domain methyltransferases from nematode phosphocholine biosynthesis. Structure 2013; 21:1778-87. [PMID: 24012478 PMCID: PMC3797223 DOI: 10.1016/j.str.2013.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/25/2013] [Accepted: 07/28/2013] [Indexed: 10/26/2022]
Abstract
The phosphobase methylation pathway is the major route for supplying phosphocholine to phospholipid biosynthesis in plants, nematodes, and Plasmodium. In this pathway, phosphoethanolamine N-methyltransferase (PMT) catalyzes the sequential methylation of phosphoethanolamine to phosphocholine. In the PMT, one domain (MT1) catalyzes methylation of phosphoethanolamine to phosphomonomethylethanolamine and a second domain (MT2) completes the synthesis of phosphocholine. The X-ray crystal structures of the di-domain PMT from the parasitic nematode Haemonchus contortus (HcPMT1 and HcPMT2) reveal that the catalytic domains of these proteins are structurally distinct and allow for selective methylation of phosphobase substrates using different active site architectures. These structures also reveal changes leading to loss of function in the vestigial domains of the nematode PMT. Divergence of function in the two nematode PMTs provides two distinct antiparasitic inhibitor targets within the same essential metabolic pathway. The PMTs from nematodes, plants, and Plasmodium also highlight adaptable metabolic modularity in evolutionarily diverse organisms.
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Affiliation(s)
- Soon Goo Lee
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
| | - Joseph M. Jez
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO 63130, USA
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49
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Hanaoka K, Shoji M, Kondo D, Sato A, Yang MY, Kamiya K, Shiraishi K. Substrate-mediated proton relay mechanism for the religation reaction in topoisomerase II. J Biomol Struct Dyn 2013; 32:1759-65. [PMID: 24047515 DOI: 10.1080/07391102.2013.834848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The DNA religation reaction of yeast type II topoisomerase (topo II) was investigated to elucidate its metal-dependent general acid/base catalysis. Quantum mechanical/molecular mechanical calculations were performed for the topo II religation reaction, and the proton transfer pathway was examined. We found a substrate-mediated proton transfer of the topo II religation reaction, which involves the 3' OH nucleophile, the reactive phosphate, water, Arg781, and Tyr782. Metal A stabilizes the transition states, which is consistent with a two-metal mechanism in topo II. This pathway may be required for the cleavage/religation reaction of topo IA and II and will provide a general explanation for the catalytic mechanism in the topo IA and II.
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Affiliation(s)
- Kyohei Hanaoka
- a Graduate School of Pure and Applied Sciences, University of Tsukuba , Tennodai 1-1-1, Tsukuba , 305-8571 , Japan
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50
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Zhou Y, Ojeda-May P, Pu J. H-loop histidine catalyzes ATP hydrolysis in the E. coli ABC-transporter HlyB. Phys Chem Chem Phys 2013; 15:15811-5. [PMID: 23955493 DOI: 10.1039/c3cp50965f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters form a family of molecular motor proteins that couple ATP hydrolysis to substrate translocation across cell membranes. Each nucleotide binding domain of ABC-transporters contains a highly conserved H-loop histidine residue, whose precise mechanistic role in motor functions has remained elusive. By using combined quantum mechanical and molecular mechanical (QM/MM) calculations, we showed that the conserved H-loop residue H662 in E. coli HlyB, a bacterial ABC-transporter, can act first as a general acid and then as a general base to facilitate proton transfer in ATP hydrolysis. Without the assistance of H662, direct proton transfer from the lytic water to ATP results in a substantially higher barrier height. Our findings suggest that the essential function of the H-loop residue H662 is to provide a "chemical linchpin" that shuttles protons between reactants through a relay mechanism, thereby catalyzing ATP hydrolysis in HlyB.
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Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St., Indianapolis, IN 46202, USA.
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