1
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Patel S, Hosur RV. Replica exchange molecular dynamics simulations reveal self-association sites in M-crystallin caused by mutations provide insights of cataract. Sci Rep 2021; 11:23270. [PMID: 34857812 PMCID: PMC8639718 DOI: 10.1038/s41598-021-02728-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/09/2021] [Indexed: 11/09/2022] Open
Abstract
Crystallins are ubiquitous, however, prevalence is seen in eye lens. Eye lens crystallins are long-lived and structural intactness is required for maintaining lens transparency and protein solubility. Mutations in crystallins often lead to cataract. In this study, we performed mutations at specific sites of M-crystallin, a close homologue of eye lens crystallin and studied by using replica exchange molecular dynamics simulation with generalized Born implicit solvent model. Mutations were made on the Ca2+ binding residues (K34D and S77D) and in the hydrophobic core (W45R) which is known to cause congenital cataract in homologous γD-crystallin. The chosen mutations caused large motion of the N-terminal Greek key, concomitantly broke the interlocking Greek keys interactions and perturbed the compact core resulting in several folded and partially unfolded states. Partially unfolded states exposed large hydrophobic patches that could act as precursors for self-aggregation. Accumulation of such aggregates is the potential cause of cataract in homologous eye lens crystallins.
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Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098, India.
| | - Ramakrishna V. Hosur
- grid.452882.1UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Vidyanagari, Mumbai, 400098 India
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2
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Vorobjev YN. An effective molecular blocker of ion channel of M2 protein as anti-influenza a drug. J Biomol Struct Dyn 2020; 39:2352-2363. [PMID: 32212957 DOI: 10.1080/07391102.2020.1747550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Design of a drug compound that can effectively bind to the M2 ion channel and block the diffusion of hydrogen ions (H+) through and inhibit influenza A virus replication is an important task. Known anti-influenza drugs amantadine and rimantadine have a weak effect on influenza A virus. A new class of positively charged, +2 e.u., molecules is proposed here to block diffusion of H+ ion through the M2 channel. Several drug candidates, derivatives of a lead compound (diazabicyclooctane), were proposed and investigated. Molecular dynamics of thermal fluctuations of M2 protein structure and ionization-conformation coupling of all the ionizable residues were simulated at physiological pH. The influence of the most probable mutations of key drug-binding amino acid residues in the M2 ion channel were investigated too. It is shown that the suggested new blocker has high binding affinity for the M2 channel. There are two in-channel binding sites of high affinity, the first one has H-bonds with two of four serine residues Ser-31A (B) or Ser-31C(D), and the second one has H-bonds with two of four histidine residues His-37A (B), or His-37C(D). The main advantage of the new drug molecule is the positive charge, +2 e.u., which creates a positive electrostatic potential barrier (in addition to a steric one) for a transfer of H+ ion through M2 channel and may serve as an effective anti-influenza A virus drug.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yury N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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3
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Popov AV, Yudkina AV, Vorobjev YN, Zharkov DO. Catalytically Competent Conformation of the Active Site of Human 8-Oxoguanine-DNA Glycosylase. BIOCHEMISTRY (MOSCOW) 2020; 85:192-204. [PMID: 32093595 DOI: 10.1134/s0006297920020066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
8-Oxoguanine-DNA N-glycosylase (OGG1) is a eukaryotic DNA repair enzyme responsible for the removal of 8-oxoguanine (oxoG), one of the most abundant oxidative DNA lesions. OGG1 catalyzes two successive reactions - N-glycosidic bond hydrolysis (glycosylase activity) and DNA strand cleavage on the 3'-side of the lesion by β-elimination (lyase activity). The enzyme also exhibits lyase activity with substrates containing apurinic/apyrimidinic (AP) sites (deoxyribose moieties lacking the nucleobase). OGG1 is highly specific for the base opposite the lesion, efficiently excising oxoG and cleaving AP sites located opposite to C, but not opposite to A. The activity is also profoundly decreased by amino acid changes that sterically interfere with oxoG binding in the active site of the enzyme after the lesion is everted from the DNA duplex. Earlier, the molecular dynamics approach was used to study the conformational dynamics of such human OGG1 mutants in complexes with the oxoG:C-containing substrate DNA, and the population density of certain conformers of two OGG1 catalytic residues, Lys249 and Asp268, was suggested to determine the enzyme activity. Here, we report the study of molecular dynamics of human OGG1 bound to the oxoG:A-containing DNA and OGG1 mutants bound to the AP:C-containing DNA. We showed that the enzyme low activity is associated with a decrease in the populations of Lys249 and Asp268 properly configured for catalysis. The experimentally measured rate constants for the OGG1 mutants show a good agreement with the models. We conclude that the enzymatic activity of OGG1 is determined majorly by the population density of the catalytically competent conformations of the active site residues Lys249 and Asp268.
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Affiliation(s)
- A V Popov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - A V Yudkina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yu N Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - D O Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
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4
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Li C, Qin Z, Han W. Bottom-up derived flexible water model with dipole and quadrupole moments for coarse-grained molecular simulations. Phys Chem Chem Phys 2020; 22:27394-27412. [DOI: 10.1039/d0cp04185h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bottom-up CG water model is developed to capture the electrostatic multipoles, structural correlation and thermodynamics of water.
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Affiliation(s)
- Chen Li
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zhongyuan Qin
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Wei Han
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
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5
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Patel S, Krishnan B, Hosur RV, Chary KVR. Mechanistic Insights from Replica Exchange Molecular Dynamics Simulations into Mutation Induced Disordered-to-Ordered Transition in Hahellin, a βγ-Crystallin. J Phys Chem B 2019; 123:5086-5098. [DOI: 10.1021/acs.jpcb.9b03845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Sunita Patel
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Hyderabad 500107, India
| | - Bal Krishnan
- Indian Institute of Science Education and Research, Berhampur, 760010, India
| | - Ramakrishna V. Hosur
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai University Campus, Mumbai 400098, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Kandala V. R. Chary
- Tata Institute of Fundamental Research, Hyderabad 500107, India
- Tata Institute of Fundamental Research, Mumbai 400005, India
- Indian Institute of Science Education and Research, Berhampur, 760010, India
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6
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Seo JH, Min WK, Lee SG, Yun H, Kim BG. To the Final Goal: Can We Predict and Suggest Mutations for Protein to Develop Desired Phenotype? BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0064-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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7
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Bejagam KK, Singh S, An Y, Berry C, Deshmukh SA. PSO-Assisted Development of New Transferable Coarse-Grained Water Models. J Phys Chem B 2018; 122:1958-1971. [DOI: 10.1021/acs.jpcb.7b10542] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karteek K. Bejagam
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Samrendra Singh
- CNH Industrial, Burr Ridge, Chicago, Illinois 60527, United States
| | - Yaxin An
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Carter Berry
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sanket A. Deshmukh
- Department
of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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8
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Vorobjev YN, Scheraga HA, Vila JA. Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins. J Biomol Struct Dyn 2018; 36:561-574. [PMID: 28132613 PMCID: PMC6191177 DOI: 10.1080/07391102.2017.1288169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 01/20/2017] [Indexed: 10/25/2022]
Abstract
A computational method, to predict the pKa values of the ionizable residues Asp, Glu, His, Tyr, and Lys of proteins, is presented here. Calculation of the electrostatic free-energy of the proteins is based on an efficient version of a continuum dielectric electrostatic model. The conformational flexibility of the protein is taken into account by carrying out molecular dynamics simulations of 10 ns in implicit water. The accuracy of the proposed method of calculation of pKa values is estimated from a test set of experimental pKa data for 297 ionizable residues from 34 proteins. The pKa-prediction test shows that, on average, 57, 86, and 95% of all predictions have an error lower than 0.5, 1.0, and 1.5 pKa units, respectively. This work contributes to our general understanding of the importance of protein flexibility for an accurate computation of pKa, providing critical insight about the significance of the multiple neutral states of acid and histidine residues for pKa-prediction, and may spur significant progress in our effort to develop a fast and accurate electrostatic-based method for pKa-predictions of proteins as a function of pH.
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Affiliation(s)
- Yury N. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Science, Lavrentiev Avenue 8, Novosibirsk 630090
- Novosibirsk State University, Novosibirsk 630090, Russia
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301
| | - Harold A. Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301
| | - Jorge A. Vila
- IMASL-CONICET, Universidad Nacional de San Luis, Ejército de Los Andes 950, 5700 San Luis, Argentina
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9
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Popov AV, Endutkin AV, Vorobjev YN, Zharkov DO. Molecular dynamics simulation of the opposite-base preference and interactions in the active site of formamidopyrimidine-DNA glycosylase. BMC STRUCTURAL BIOLOGY 2017; 17:5. [PMID: 28482831 PMCID: PMC5422863 DOI: 10.1186/s12900-017-0075-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 04/20/2017] [Indexed: 01/20/2023]
Abstract
Background Formamidopyrimidine-DNA glycosylase (Fpg) removes abundant pre-mutagenic 8-oxoguanine (oxoG) bases from DNA through nucleophilic attack of its N-terminal proline at C1′ of the damaged nucleotide. Since oxoG efficiently pairs with both C and A, Fpg must excise oxoG from pairs with C but not with A, otherwise a mutation occurs. The crystal structures of several Fpg–DNA complexes have been solved, yet no structure with A opposite the lesion is available. Results Here we use molecular dynamic simulation to model interactions in the pre-catalytic complex of Lactococcus lactis Fpg with DNA containing oxoG opposite C or A, the latter in either syn or anti conformation. The catalytic dyad, Pro1–Glu2, was modeled in all four possible protonation states. Only one transition was observed in the experimental reaction rate pH dependence plots, and Glu2 kept the same set of interactions regardless of its protonation state, suggesting that it does not limit the reaction rate. The adenine base opposite oxoG was highly distorting for the adjacent nucleotides: in the more stable syn models it formed non-canonical bonds with out-of-register nucleotides in both the damaged and the complementary strand, whereas in the anti models the adenine either formed non-canonical bonds or was expelled into the major groove. The side chains of Arg109 and Phe111 that Fpg inserts into DNA to maintain its kinked conformation tended to withdraw from their positions if A was opposite to the lesion. The region showing the largest differences in the dynamics between oxoG:C and oxoG:A substrates was unexpectedly remote from the active site, located near the linker joining the two domains of Fpg. This region was also highly conserved among 124 analyzed Fpg sequences. Three sites trapping water molecules through multiple bonds were identified on the protein–DNA interface, apparently helping to maintain enzyme-induced DNA distortion and participating in oxoG recognition. Conclusion Overall, the discrimination against A opposite to the lesion seems to be due to incorrect DNA distortion around the lesion-containing base pair and, possibly, to gross movement of protein domains connected by the linker. Electronic supplementary material The online version of this article (doi:10.1186/s12900-017-0075-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander V Popov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia.,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia
| | - Yuri N Vorobjev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia. .,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk, 630090, Russia. .,Novosibrsk State University, 2 Pirogova St., Novosibirsk, 630090, Russia.
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10
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Danielson ML, Hu B, Shen J, Desai PV. In Silico ADME Techniques Used in Early-Phase Drug Discovery. TRANSLATING MOLECULES INTO MEDICINES 2017. [DOI: 10.1007/978-3-319-50042-3_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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11
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Musiani F, Giorgetti A. Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:49-77. [PMID: 28109331 DOI: 10.1016/bs.ircmb.2016.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment.
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Affiliation(s)
- F Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Bologna, Italy.
| | - A Giorgetti
- Applied Bioinformatics Group, University of Verona, Verona, Italy.
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12
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Hoppins JJ, Gruber DR, Miears HL, Kiryutin AS, Kasymov RD, Petrova DV, Endutkin AV, Popov AV, Yurkovskaya AV, Fedechkin SO, Brockerman JA, Zharkov DO, Smirnov SL. 8-Oxoguanine Affects DNA Backbone Conformation in the EcoRI Recognition Site and Inhibits Its Cleavage by the Enzyme. PLoS One 2016; 11:e0164424. [PMID: 27749894 PMCID: PMC5066940 DOI: 10.1371/journal.pone.0164424] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/23/2016] [Indexed: 12/13/2022] Open
Abstract
8-oxoguanine is one of the most abundant and impactful oxidative DNA lesions. However, the reasons underlying its effects, especially those not directly explained by the altered base pairing ability, are poorly understood. We report the effect of the lesion on the action of EcoRI, a widely used restriction endonuclease. Introduction of 8-oxoguanine inside, or adjacent to, the GAATTC recognition site embedded within the Drew—Dickerson dodecamer sequence notably reduced the EcoRI activity. Solution NMR revealed that 8-oxoguanine in the DNA duplex causes substantial alterations in the sugar—phosphate backbone conformation, inducing a BI→BII transition. Moreover, molecular dynamics of the complex suggested that 8-oxoguanine, although does not disrupt the sequence-specific contacts formed by the enzyme with DNA, shifts the distribution of BI/BII backbone conformers. Based on our data, we propose that the disruption of enzymatic cleavage can be linked with the altered backbone conformation and dynamics in the free oxidized DNA substrate and, possibly, at the protein—DNA interface.
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Affiliation(s)
- Joanna J. Hoppins
- Chemistry Department, Western Washington University, Bellingham, WA, United States of America
| | - David R. Gruber
- Chemistry Department, Western Washington University, Bellingham, WA, United States of America
| | - Heather L. Miears
- Chemistry Department, Western Washington University, Bellingham, WA, United States of America
| | - Alexey S. Kiryutin
- SB RAS International Tomography Center, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Rustem D. Kasymov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Institute of Biochemistry, Stuttgart University, Stuttgart, Germany
| | - Darya V. Petrova
- Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Anton V. Endutkin
- Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Alexander V. Popov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Alexandra V. Yurkovskaya
- SB RAS International Tomography Center, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Stanislav O. Fedechkin
- Chemistry Department, Western Washington University, Bellingham, WA, United States of America
- University of California Santa Cruz, Program in Biomedical Science and Engineering, Santa Cruz, CA, United States of America
| | - Jacob A. Brockerman
- Chemistry Department, Western Washington University, Bellingham, WA, United States of America
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Dmitry O. Zharkov
- Novosibirsk State University, Novosibirsk, Russia
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- * E-mail: (SLS); (DOZ)
| | - Serge L. Smirnov
- Chemistry Department, Western Washington University, Bellingham, WA, United States of America
- * E-mail: (SLS); (DOZ)
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13
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Topham CM, Barbe S, André I. An Atomistic Statistically Effective Energy Function for Computational Protein Design. J Chem Theory Comput 2016; 12:4146-68. [PMID: 27341125 DOI: 10.1021/acs.jctc.6b00090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shortcomings in the definition of effective free-energy surfaces of proteins are recognized to be a major contributory factor responsible for the low success rates of existing automated methods for computational protein design (CPD). The formulation of an atomistic statistically effective energy function (SEEF) suitable for a wide range of CPD applications and its derivation from structural data extracted from protein domains and protein-ligand complexes are described here. The proposed energy function comprises nonlocal atom-based and local residue-based SEEFs, which are coupled using a novel atom connectivity number factor to scale short-range, pairwise, nonbonded atomic interaction energies and a surface-area-dependent cavity energy term. This energy function was used to derive additional SEEFs describing the unfolded-state ensemble of any given residue sequence based on computed average energies for partially or fully solvent-exposed fragments in regions of irregular structure in native proteins. Relative thermal stabilities of 97 T4 bacteriophage lysozyme mutants were predicted from calculated energy differences for folded and unfolded states with an average unsigned error (AUE) of 0.84 kcal mol(-1) when compared to experiment. To demonstrate the utility of the energy function for CPD, further validation was carried out in tests of its capacity to recover cognate protein sequences and to discriminate native and near-native protein folds, loop conformers, and small-molecule ligand binding poses from non-native benchmark decoys. Experimental ligand binding free energies for a diverse set of 80 protein complexes could be predicted with an AUE of 2.4 kcal mol(-1) using an additional energy term to account for the loss in ligand configurational entropy upon binding. The atomistic SEEF is expected to improve the accuracy of residue-based coarse-grained SEEFs currently used in CPD and to extend the range of applications of extant atom-based protein statistical potentials.
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Affiliation(s)
- Christopher M Topham
- Université de Toulouse; INSA, UPS, INP; LISBP , 135 Avenue de Rangueil, F-31077 Toulouse, France.,CNRS, UMR5504 , F-31400 Toulouse, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés , F-31400 Toulouse, France
| | - Sophie Barbe
- Université de Toulouse; INSA, UPS, INP; LISBP , 135 Avenue de Rangueil, F-31077 Toulouse, France.,CNRS, UMR5504 , F-31400 Toulouse, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés , F-31400 Toulouse, France
| | - Isabelle André
- Université de Toulouse; INSA, UPS, INP; LISBP , 135 Avenue de Rangueil, F-31077 Toulouse, France.,CNRS, UMR5504 , F-31400 Toulouse, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés , F-31400 Toulouse, France
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14
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Investigation of Structural Dynamics of Enzymes and Protonation States of Substrates Using Computational Tools. Catalysts 2016; 6. [PMID: 27885336 PMCID: PMC5119520 DOI: 10.3390/catal6060082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This review discusses the use of molecular modeling tools, together with existing experimental findings, to provide a complete atomic-level description of enzyme dynamics and function. We focus on functionally relevant conformational dynamics of enzymes and the protonation states of substrates. The conformational fluctuations of enzymes usually play a crucial role in substrate recognition and catalysis. Protein dynamics can be altered by a tiny change in a molecular system such as different protonation states of various intermediates or by a significant perturbation such as a ligand association. Here we review recent advances in applying atomistic molecular dynamics (MD) simulations to investigate allosteric and network regulation of tryptophan synthase (TRPS) and protonation states of its intermediates and catalysis. In addition, we review studies using quantum mechanics/molecular mechanics (QM/MM) methods to investigate the protonation states of catalytic residues of β-Ketoacyl ACP synthase I (KasA). We also discuss modeling of large-scale protein motions for HIV-1 protease with coarse-grained Brownian dynamics (BD) simulations.
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15
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Miroshnikova AD, Kuznetsova AA, Vorobjev YN, Kuznetsov NA, Fedorova OS. Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1. MOLECULAR BIOSYSTEMS 2016; 12:1527-39. [PMID: 27063150 DOI: 10.1039/c6mb00128a] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Here, we used stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Effects of monovalent (K(+)) and divalent (Mg(2+), Mn(2+), Ca(2+), Zn(2+), Cu(2+), and Ni(2+)) metal ions on DNA binding and catalytic stages were studied. It was shown that the first step of substrate binding (corresponding to formation of a primary enzyme-substrate complex) does not depend on the concentration (0.05-5.0 mM) or the nature of divalent metal ions. In contrast, the initial DNA binding efficiency significantly decreased at a high concentration (5-250 mM) of monovalent K(+) ions, indicating the involvement of electrostatic interactions in this stage. It was also shown that Cu(2+) ions abrogated the DNA binding ability of APE1, possibly, due to a strong interaction with DNA bases and the sugar-phosphate backbone. In the case of Ca(2+) ions, the catalytic activity of APE1 was lost completely with retention of binding potential. Thus, the enzymatic activity of APE1 is increased in the order Zn(2+) < Ni(2+) < Mn(2+) < Mg(2+). Circular dichroism spectra and calculation of the contact area between APE1 and DNA reveal that Mg(2+) ions stabilize the protein structure and the enzyme-substrate complex.
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Affiliation(s)
- Anastasia D Miroshnikova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), Siberian Branch of Russian Academy of Sciences, 8 Lavrentyev Ave., Novosibirsk 630090, Russia.
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16
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Hospital A, Goñi JR, Orozco M, Gelpí JL. Molecular dynamics simulations: advances and applications. Adv Appl Bioinform Chem 2015; 8:37-47. [PMID: 26604800 PMCID: PMC4655909 DOI: 10.2147/aabc.s70333] [Citation(s) in RCA: 233] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is rich enough to shift the usual paradigm of structural bioinformatics from studying single structures to analyze conformational ensembles. Here, we describe the foundations of molecular dynamics and the improvements made in the direction of getting such ensemble. Specific application of the technique to three main issues (allosteric regulation, docking, and structure refinement) is discussed.
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Affiliation(s)
- Adam Hospital
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain
| | - Josep Ramon Goñi
- Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, University of Barcelona, Barcelona, Spain ; Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Josep L Gelpí
- Joint BSC-IRB Research Program in Computational Biology, University of Barcelona, Barcelona, Spain ; Barcelona Supercomputing Center, University of Barcelona, Barcelona, Spain ; Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
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17
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Topham CM, Smith JC. Tri-peptide reference structures for the calculation of relative solvent accessible surface area in protein amino acid residues. Comput Biol Chem 2014; 54:33-43. [PMID: 25544680 DOI: 10.1016/j.compbiolchem.2014.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 11/23/2014] [Accepted: 11/30/2014] [Indexed: 10/24/2022]
Abstract
Relative amino acid residue solvent accessibility values allow the quantitative comparison of atomic solvent-accessible surface areas in different residue types and physical environments in proteins and in protein structural alignments. Geometry-optimised tri-peptide structures in extended solvent-exposed reference conformations have been obtained for 43 amino acid residue types at a high level of quantum chemical theory. Significant increases in side-chain solvent accessibility, offset by reductions in main-chain atom solvent exposure, were observed for standard residue types in partially geometry-optimised structures when compared to non-minimised models built from identical sets of proper dihedral angles abstracted from the literature. Optimisation of proper dihedral angles led most notably to marked increases of up to 54% in proline main-chain atom solvent accessibility compared to literature values. Similar effects were observed for fully-optimised tri-peptides in implicit solvent. The relief of internal strain energy was associated with systematic variation in N, C(α) and C(β) atom solvent accessibility across all standard residue types. The results underline the importance of optimisation of 'hard' degrees of freedom (bond lengths and valence bond angles) and improper dihedral angle values from force field or other context-independent reference values, and impact on the use of standardised fixed internal co-ordinate geometry in sampling approaches to the determination of absolute values of protein amino acid residue solvent accessibility. Quantum chemical methods provide a useful and accurate alternative to molecular mechanics methods to perform energy minimisation of peptides containing non-standard (chemically modified) amino acid residues frequently present in experimental protein structure data sets, for which force field parameters may not be available. Reference tri-peptide atomic co-ordinate sets including hydrogen atoms are made freely available.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 40 Rue Boyssonne, Toulouse 31400, France; Computational Molecular Biophysics, IWR der Universität Heidelberg, Im Neuenheimer Feld 368, Heidelberg D-69120, Germany; University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, TN 37831-6309, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR der Universität Heidelberg, Im Neuenheimer Feld 368, Heidelberg D-69120, Germany; University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008, Oak Ridge, TN 37831-6309, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN 37996, USA
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18
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Kuznetsov NA, Kuznetsova AA, Vorobjev YN, Krasnoperov LN, Fedorova OS. Thermodynamics of the DNA damage repair steps of human 8-oxoguanine DNA glycosylase. PLoS One 2014; 9:e98495. [PMID: 24911585 PMCID: PMC4049573 DOI: 10.1371/journal.pone.0098495] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/03/2014] [Indexed: 11/19/2022] Open
Abstract
Human 8-oxoguanine DNA glycosylase (hOGG1) is a key enzyme responsible for initiating the base excision repair of 7,8-dihydro-8-oxoguanosine (oxoG). In this study a thermodynamic analysis of the interaction of hOGG1 with specific and non-specific DNA-substrates is performed based on stopped-flow kinetic data. The standard Gibbs energies, enthalpies and entropies of specific stages of the repair process were determined via kinetic measurements over a temperature range using the van’t Hoff approach. The three steps which are accompanied with changes in the DNA conformations were detected via 2-aminopurine fluorescence in the process of binding and recognition of damaged oxoG base by hOGG1. The thermodynamic analysis has demonstrated that the initial step of the DNA substrates binding is mainly governed by energy due to favorable interactions in the process of formation of the recognition contacts, which results in negative enthalpy change, as well as due to partial desolvation of the surface between the DNA and enzyme, which results in positive entropy change. Discrimination of non-specific G base versus specific oxoG base is occurring in the second step of the oxoG-substrate binding. This step requires energy consumption which is compensated by the positive entropy contribution. The third binding step is the final adjustment of the enzyme/substrate complex to achieve the catalytically competent state which is characterized by large endothermicity compensated by a significant increase of entropy originated from the dehydration of the DNA grooves.
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Affiliation(s)
- Nikita A. Kuznetsov
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Alexandra A. Kuznetsova
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Yuri N. Vorobjev
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Lev N. Krasnoperov
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Olga S. Fedorova
- Siberian Branch of the Russian Academy of Sciences, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia and Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
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19
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Baler K, Martin OA, Carignano MA, Ameer GA, Vila JA, Szleifer I. Electrostatic unfolding and interactions of albumin driven by pH changes: a molecular dynamics study. J Phys Chem B 2014; 118:921-30. [PMID: 24393011 PMCID: PMC3983335 DOI: 10.1021/jp409936v] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/04/2014] [Indexed: 01/22/2023]
Abstract
A better understanding of protein aggregation is bound to translate into critical advances in several areas, including the treatment of misfolded protein disorders and the development of self-assembling biomaterials for novel commercial applications. Because of its ubiquity and clinical potential, albumin is one of the best-characterized models in protein aggregation research; but its properties in different conditions are not completely understood. Here, we carried out all-atom molecular dynamics simulations of albumin to understand how electrostatics can affect the conformation of a single albumin molecule just prior to self-assembly. We then analyzed the tertiary structure and solvent accessible surface area of albumin after electrostatically triggered partial denaturation. The data obtained from these single protein simulations allowed us to investigate the effect of electrostatic interactions between two proteins. The results of these simulations suggested that hydrophobic attractions and counterion binding may be strong enough to effectively overcome the electrostatic repulsions between the highly charged monomers. This work contributes to our general understanding of protein aggregation mechanisms, the importance of explicit consideration of free ions in protein solutions, provides critical new insights about the equilibrium conformation of albumin in its partially denatured state at low pH, and may spur significant progress in our efforts to develop biocompatible protein hydrogels driven by electrostatic partial denaturation.
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Affiliation(s)
- K. Baler
- Department of Biomedical Engineering, Chemistry
of Life Processes Institute, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - O. A. Martin
- Universidad
Nacional de San Luis, Instituto de Matemática
Aplicada San Luis, CONICET, Avenida
Italia 1556-s5700, San Luis-Argentina
| | - M. A. Carignano
- Department of Biomedical Engineering, Chemistry
of Life Processes Institute, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Qatar
Environment and Energy Research Institute, P.O. Box 5825, Doha, Qatar
| | - G. A. Ameer
- Department of Biomedical Engineering, Chemistry
of Life Processes Institute, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - J. A. Vila
- Universidad
Nacional de San Luis, Instituto de Matemática
Aplicada San Luis, CONICET, Avenida
Italia 1556-s5700, San Luis-Argentina
| | - I. Szleifer
- Department of Biomedical Engineering, Chemistry
of Life Processes Institute, and Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Li J, Mach P, Koehl P. Measuring the shapes of macromolecules - and why it matters. Comput Struct Biotechnol J 2013; 8:e201309001. [PMID: 24688748 PMCID: PMC3962087 DOI: 10.5936/csbj.201309001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 11/22/2022] Open
Abstract
The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing numerical and analytical approaches that solve these problems. We cover in more details our own work in this field, focusing on the alpha shape theory as it provides a unifying mathematical framework that enable the analytical calculations of the surface area and volume of a macromolecule represented as a union of balls, the detection of pockets and cavities in the molecule, and the quantification of contacts between the atomic balls. We have shown that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity. We conclude with a brief description of new challenges for the alpha shape theory in modern structural biology.
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Affiliation(s)
- Jie Li
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, United States
| | - Paul Mach
- Graduate Group of Applied Mathematics, University of California, Davis, 1, Shields Ave, Davis, CA, 95616, United States
| | - Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, 1, Shields Ave, Davis, CA, 95616, United States
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21
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Lukina MV, Popov AV, Koval VV, Vorobjev YN, Fedorova OS, Zharkov DO. DNA damage processing by human 8-oxoguanine-DNA glycosylase mutants with the occluded active site. J Biol Chem 2013; 288:28936-47. [PMID: 23955443 DOI: 10.1074/jbc.m113.487322] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
8-Oxoguanine-DNA glycosylase (OGG1) removes premutagenic lesion 8-oxoguanine (8-oxo-G) from DNA and then nicks the nascent abasic (apurinic/apyrimidinic) site by β-elimination. Although the structure of OGG1 bound to damaged DNA is known, the dynamic aspects of 8-oxo-G recognition are not well understood. To comprehend the mechanisms of substrate recognition and processing, we have constructed OGG1 mutants with the active site occluded by replacement of Cys-253, which forms a wall of the base-binding pocket, with bulky leucine or isoleucine. The conformational dynamics of OGG1 mutants were characterized by single-turnover kinetics and stopped-flow kinetics with fluorescent detection. Additionally, the conformational mobility of wild type and the mutant OGG1 substrate complex was assessed using molecular dynamics simulations. Although pocket occlusion distorted the active site and greatly decreased the catalytic activity of OGG1, it did not fully prevent processing of 8-oxo-G and apurinic/apyrimidinic sites. Both mutants were notably stimulated in the presence of free 8-bromoguanine, indicating that this base can bind to the distorted OGG1 and facilitate β-elimination. The results agree with the concept of enzyme plasticity, suggesting that the active site of OGG1 is flexible enough to compensate partially for distortions caused by mutation.
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Affiliation(s)
- Maria V Lukina
- From the Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090 and
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22
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Hospital A, Gelpi JL. High-throughput molecular dynamics simulations: toward a dynamic view of macromolecular structure. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1142] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Smith N, Campbell B, Li L, Li C, Alexov E. Protein Nano-Object Integrator (ProNOI) for generating atomic style objects for molecular modeling. BMC STRUCTURAL BIOLOGY 2012; 12:31. [PMID: 23217202 PMCID: PMC3532097 DOI: 10.1186/1472-6807-12-31] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 11/28/2012] [Indexed: 11/10/2022]
Abstract
Background With the progress of nanotechnology, one frequently has to model biological macromolecules simultaneously with nano-objects. However, the atomic structures of the nano objects are typically not available or they are solid state entities. Because of that, the researchers have to investigate such nano systems by generating models of the nano objects in a manner that the existing software be able to carry the simulations. In addition, it should allow generating composite objects with complex shape by combining basic geometrical figures and embedding biological macromolecules within the system. Results Here we report the Protein Nano-Object Integrator (ProNOI) which allows for generating atomic-style geometrical objects with user desired shape and dimensions. Unlimited number of objects can be created and combined with biological macromolecules in Protein Data Bank (PDB) format file. Once the objects are generated, the users can use sliders to manipulate their shape, dimension and absolute position. In addition, the software offers the option to charge the objects with either specified surface or volumetric charge density and to model them with user-desired dielectric constants. According to the user preference, the biological macromolecule atoms can be assigned charges and radii according to four different force fields: Amber, Charmm, OPLS and PARSE. The biological macromolecules and the atomic-style objects are exported as a position, charge and radius (PQR) file, or if a default dielectric constant distribution is not selected, it is exported as a position, charge, radius and epsilon (PQRE) file. As illustration of the capabilities of the ProNOI, we created a composite object in a shape of a robot, aptly named the Clemson Robot, whose parts are charged with various volumetric charge densities and holds the barnase-barstar protein complex in its hand. Conclusions The Protein Nano-Object Integrator (ProNOI) is a convenient tool for generating atomic-style nano shapes in conjunction with biological macromolecule(s). Charges and radii on the macromolecule atoms and the atoms in the shapes are assigned according to the user’s preferences allowing various scenarios of modeling. The default output file is in PQR (PQRE) format which is readable by almost any software available in biophysical field. It can be downloaded from: http://compbio.clemson.edu/downloadDir/ProNO_integrator.tar.gz
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Affiliation(s)
- Nicholas Smith
- Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
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Popov AV, Vorobjev YN, Zharkov DO. MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface. J Comput Chem 2012; 34:319-25. [DOI: 10.1002/jcc.23135] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/30/2012] [Accepted: 09/05/2012] [Indexed: 11/07/2022]
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Abstract
Coarse-grained (CG) models have proven to be very effective tools in the study of phenomena or systems that involve large time- and length-scales. By decreasing the degrees of freedom in the system and using softer interactions than seen in atomistic models, larger timesteps can be used and much longer simulation times can be studied. CG simulations are widely used to study systems of biological importance that are beyond the reach of atomistic simulation, necessitating a computationally efficient and accurate CG model for water. In this review, we discuss the methods used for developing CG water models and the relative advantages and disadvantages of the resulting models. In general, CG water models differ with regards to how many waters each CG group or bead represents, whether analytical or tabular potentials have been used to describe the interactions, and how the model incorporates electrostatic interactions. Finally, how the models are parameterized depends on their application, so, while some are fitted to experimental properties such as surface tension and density, others are fitted to radial distribution functions extracted from atomistic simulations.
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Affiliation(s)
| | - Clare McCabe
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville TN 37235-1604
- Department of Chemistry, Vanderbilt University, Nashville TN 37235-1604
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Kuznetsov NA, Vorobjev YN, Krasnoperov LN, Fedorova OS. Thermodynamics of the multi-stage DNA lesion recognition and repair by formamidopyrimidine-DNA glycosylase using pyrrolocytosine fluorescence--stopped-flow pre-steady-state kinetics. Nucleic Acids Res 2012; 40:7384-92. [PMID: 22584623 PMCID: PMC3424566 DOI: 10.1093/nar/gks423] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Formamidopyrimidine-DNA glycosylase, Fpg protein from Escherichia coli, initiates base excision repair in DNA by removing a wide variety of oxidized lesions. In this study, we perform thermodynamic analysis of the multi-stage interaction of Fpg with specific DNA-substrates containing 7,8-dihydro-8-oxoguanosine (oxoG), or tetrahydrofuran (THF, an uncleavable abasic site analog) and non-specific (G) DNA-ligand based on stopped-flow kinetic data. Pyrrolocytosine, highly fluorescent analog of the natural nucleobase cytosine, is used to record multi-stage DNA lesion recognition and repair kinetics over a temperature range (10–30°C). The kinetic data were used to obtain the standard Gibbs energy, enthalpy and entropy of the specific stages using van’t Hoff approach. The data suggest that not only enthalpy-driven exothermic oxoG recognition, but also the desolvation-accompanied entropy-driven enzyme-substrate complex adjustment into the catalytically active state play equally important roles in the overall process.
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Affiliation(s)
- Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2234-43. [PMID: 22554469 DOI: 10.1016/j.bbamem.2012.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/11/2012] [Accepted: 04/12/2012] [Indexed: 01/08/2023]
Abstract
A limited class of aquaporins has been described to form regular arrays and junctions in membranes. The biological significance of these structures, however, remains uncertain. Here we analyze the underlying physical principles with the help of a computational procedure that takes into account protein-protein as well as protein-membrane interactions. Experimentally observed array/junction structures are systematically (dis)assembled and major driving forces identified. Aquaporin 4 was found to be markedly different from the non-junction forming aquaporin 1. The environmental stabilization resulting from embedding into the biomembrane was identified as the main driving force. This highlights the role of protein-membrane interactions in aquaporin 4. Analysis of the type presented here can help to decipher the biological role of membrane arrays and junctions formed by aquaporin.
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