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Truong DT, Ho K, Pham DQH, Chwastyk M, Nguyen-Minh T, Nguyen MT. Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics. Sci Rep 2024; 14:10475. [PMID: 38714683 PMCID: PMC11076533 DOI: 10.1038/s41598-024-59899-3] [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: 02/11/2024] [Accepted: 04/16/2024] [Indexed: 05/10/2024] Open
Abstract
To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Thai Nguyen-Minh
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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2
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Li H, Hardy CD, Reidl CT, Jing Q, Xue F, Cinelli M, Silverman RB, Poulos TL. Crystallographic and Computational Insights into Isoform-Selective Dynamics in Nitric Oxide Synthase. Biochemistry 2024; 63:788-796. [PMID: 38417024 PMCID: PMC10956423 DOI: 10.1021/acs.biochem.3c00601] [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] [Received: 10/31/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/01/2024]
Abstract
In our efforts to develop inhibitors selective for neuronal nitric oxide synthase (nNOS) over endothelial nitric oxide synthase (eNOS), we found that nNOS can undergo conformational changes in response to inhibitor binding that does not readily occur in eNOS. One change involves movement of a conserved tyrosine, which hydrogen bonds to one of the heme propionates, but in the presence of an inhibitor, changes conformation, enabling part of the inhibitor to hydrogen bond with the heme propionate. This movement does not occur as readily in eNOS and may account for the reason why these inhibitors bind more tightly to nNOS. A second structural change occurs upon the binding of a second inhibitor molecule to nNOS, displacing the pterin cofactor. Binding of this second site inhibitor requires structural changes at the dimer interface, which also occurs more readily in nNOS than in eNOS. Here, we used a combination of crystallography, mutagenesis, and computational methods to better understand the structural basis for these differences in NOS inhibitor binding. Computational results show that a conserved tyrosine near the primary inhibitor binding site is anchored more tightly in eNOS than in nNOS, allowing for less flexibility of this residue. We also find that the inefficiency of eNOS to bind a second inhibitor molecule is likely due to the tighter dimer interface in eNOS compared with nNOS. This study provides a better understanding of how subtle structural differences in NOS isoforms can result in substantial dynamic differences that can be exploited in the development of isoform-selective inhibitors.
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Affiliation(s)
- Huiying Li
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United
States
| | - Christine D. Hardy
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United
States
| | - Cory T. Reidl
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Qing Jing
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Fengtian Xue
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Maris Cinelli
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Richard B. Silverman
- Department
of Chemistry, Department of Molecular Biosciences, Chemistry of Life
Processes Institute, Center for Developmental Therapeutics, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
- Department
of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
| | - Thomas L. Poulos
- Departments
of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and
Chemistry, University of California, Irvine, California 92697-3900, United
States
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3
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Malewschik T, Carey LM, de Serrano V, Ghiladi RA. Bridging the functional gap between reactivity and inhibition in dehaloperoxidase B from Amphitrite ornata: Mechanistic and structural studies with 2,4- and 2,6-dihalophenols. J Inorg Biochem 2022; 236:111944. [PMID: 35969974 DOI: 10.1016/j.jinorgbio.2022.111944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 06/29/2022] [Accepted: 07/20/2022] [Indexed: 12/15/2022]
Abstract
The multifunctional catalytic globin dehaloperoxidase (DHP) from the marine worm Amphitrite ornata was shown to catalyze the H2O2-dependent oxidation of 2,4- and 2,6-dihalophenols (DXP; X = F, Cl, Br). Product identification by LC-MS revealed multiple monomeric products with varying degrees of oxidation and/or dehalogenation, as well as oligomers with n up to 6. Mechanistic and 18O-labeling studies demonstrated sequential dihalophenol oxidation via peroxidase and peroxygenase activities. Binding studies established that 2,4-DXP (X = Cl, Br) have the highest affinities of any known DHP substrate. X-ray crystallography identified different binding positions for 2,4- and 2,6-DXP substrates in the hydrophobic distal pocket of DHP. Correlation between the number of halogens and the substrate binding orientation revealed a halogen-dependent binding motif for mono- (4-halophenol), di- (2,4- and 2,6-dihalophenol) and trihalophenols (2,4,6-trihalopenol). Taken together, the findings here on dihalophenol reactivity with DHP advance our understanding of how these compounds bridge the inhibitory and oxidative functions of their mono- and trihalophenol counterparts, respectively, and provide further insight into the protein structure-function paradigm relevant to multifunctional catalytic globins in comparison to their monofunctional analogs.
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Affiliation(s)
- Talita Malewschik
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Leiah M Carey
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States.
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4
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Wang X, Ham S, Zhou W, Qiao R. Adsorption of rhodamine 6G and choline on gold electrodes: a molecular dynamics study. NANOTECHNOLOGY 2022; 34:025501. [PMID: 36195059 DOI: 10.1088/1361-6528/ac973b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The adsorption of analyte molecules on nano-optoelectrodes (e.g. a combined nanoantenna and nanoelectrode device) significantly affects the signal characteristics in surface-enhanced Raman scattering (SERS) measurements. Understanding how different molecules adsorb on electrodes and their electrical potential modulation helps interpret SERS measurements better. We use molecular dynamics simulations to investigate the adsorption of prototypical analyte molecules (rhodamine 6G and choline) on gold electrodes with negative, neutral, and positive surface charges. We show that both molecules can readily adsorb on gold surfaces at all surface charge densities studied. Nevertheless, the configurations of the adsorbed molecules can differ for different surface charge densities, and adsorption can also change a molecule's conformation. Rhodamine 6G molecules adsorb more strongly than choline molecules, and the adsorption of both molecules is affected by electrode charge in 0.25 M NaCl solutions. The mechanisms of these observations are elucidated, and their implications for voltage-modulated SERS measurements are discussed.
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Affiliation(s)
- Xin Wang
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA 24061, United States of America
| | - Seokgyun Ham
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA 24061, United States of America
| | - Wei Zhou
- Department of Electrical and Computer Engineering Virginia Tech, Blacksburg, VA 24061, United States of America
| | - Rui Qiao
- Department of Mechanical Engineering, Virginia Tech, Blacksburg, VA 24061, United States of America
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5
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Uncovering the Molecular Basis for the Better Gefitinib Sensitivity of EGFR with Complex Mutations over Single Rare Mutation: Insights from Molecular Simulations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123844. [PMID: 35744964 PMCID: PMC9230809 DOI: 10.3390/molecules27123844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 01/21/2023]
Abstract
Epidermal growth factor receptor (EGFR) is an intensively focused target for anti-tumor compounds used in non-small cell lung cancer (NSCLC) therapy. Compared to the classical activating mutations, there are still many uncommon EGFR mutations associated with poorer responses to EGFR inhibitors. A detailed understanding of the molecular basis for multiple EGFR mutants exhibiting diverse responses to inhibitors is of critical importance for related drug development. Herein, we explored the molecular determinants contributing to the distinct responses of EGFR with a single rare mutation (G719S) or combined mutations (G719S/L858R and G719S/l861Q) to Gefitinib (IRE). Our results indicated that interactions, formed within the tetrad of residues S768 (in the αC-helix), D770 (in the αC-β4 loop), Y827 (in the αE-helix), and R831 (in the catalytic loop), play an important role in the stability of αC-helix and the maintenance of K745–E762 salt bridge in the absence of IRE, which are weakened in the EGFRG719S system and enhanced in the EGFRG719S/L858R system upon IRE binding. Besides, the introduced hydrogen bonds by the co-occurring mutation partner also contribute to the stability of αC-helix. The work done for inhibitor dissociation suggests that IRE exhibits a stronger binding affinity to EGFRG719S/L858R mutant. Together, these findings provide a deeper understanding of minor mutations, which is essential for drug development targeting EGFR with less common mutations.
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6
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Hsueh SCC, Nijland M, Peng X, Hilton B, Plotkin SS. First Principles Calculation of Protein-Protein Dimer Affinities of ALS-Associated SOD1 Mutants. Front Mol Biosci 2022; 9:845013. [PMID: 35402516 PMCID: PMC8988244 DOI: 10.3389/fmolb.2022.845013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/08/2022] [Indexed: 01/03/2023] Open
Abstract
Cu,Zn superoxide dismutase (SOD1) is a 32 kDa homodimer that converts toxic oxygen radicals in neurons to less harmful species. The dimerization of SOD1 is essential to the stability of the protein. Monomerization increases the likelihood of SOD1 misfolding into conformations associated with aggregation, cellular toxicity, and neuronal death in familial amyotrophic lateral sclerosis (fALS). The ubiquity of disease-associated mutations throughout the primary sequence of SOD1 suggests an important role of physicochemical processes, including monomerization of SOD1, in the pathology of the disease. Herein, we use a first-principles statistical mechanics method to systematically calculate the free energy of dimer binding for SOD1 using molecular dynamics, which involves sequentially computing conformational, orientational, and separation distance contributions to the binding free energy. We consider the effects of two ALS-associated mutations in SOD1 protein on dimer stability, A4V and D101N, as well as the role of metal binding and disulfide bond formation. We find that the penalty for dimer formation arising from the conformational entropy of disordered loops in SOD1 is significantly larger than that for other protein–protein interactions previously considered. In the case of the disulfide-reduced protein, this leads to a bound complex whose formation is energetically disfavored. Somewhat surprisingly, the loop free energy penalty upon dimerization is still significant for the holoprotein, despite the increased structural order induced by the bound metal cations. This resulted in a surprisingly modest increase in dimer binding free energy of only about 1.5 kcal/mol upon metalation of the protein, suggesting that the most significant stabilizing effects of metalation are on folding stability rather than dimer binding stability. The mutant A4V has an unstable dimer due to weakened monomer-monomer interactions, which are manifested in the calculation by a separation free energy surface with a lower barrier. The mutant D101N has a stable dimer partially due to an unusually rigid β-barrel in the free monomer. D101N also exhibits anticooperativity in loop folding upon dimerization. These computational calculations are, to our knowledge, the most quantitatively accurate calculations of dimer binding stability in SOD1 to date.
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Affiliation(s)
- Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada
| | - Mark Nijland
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.,Laboratory of Organic Chemistry, Wageningen University and Research, Wageningen, Netherlands.,Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Wageningen, Netherlands
| | - Xubiao Peng
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.,Center for Quantum Technology Research, School of Physics, Beijing Institute of Technology, Beijing, China
| | - Benjamin Hilton
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.,Imperial College London, London, United Kingdom
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, BC, Canada.,Genome Science and Technology Program, University of British Columbia, Vancouver, BC, Canada
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7
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Amaya JA, Lamb DC, Kelly SL, Caffrey P, Murarka VC, Poulos TL. Structural analysis of P450 AmphL from Streptomyces nodosus provides insights into substrate selectivity of polyene macrolide antibiotic biosynthetic P450s. J Biol Chem 2022; 298:101746. [PMID: 35189143 PMCID: PMC8960966 DOI: 10.1016/j.jbc.2022.101746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 01/03/2023] Open
Abstract
AmphL is a cytochrome P450 enzyme that catalyzes the C8 oxidation of 8-deoxyamphotericin B to the polyene macrolide antibiotic, amphotericin B. To understand this substrate selectivity, we solved the crystal structure of AmphL to a resolution of 2.0 Å in complex with amphotericin B and performed molecular dynamics (MD) simulations. A detailed comparison with the closely related P450, PimD, which catalyzes the epoxidation of 4,5-desepoxypimaricin to the macrolide antibiotic, pimaricin, reveals key catalytic structural features responsible for stereo- and regio-selective oxidation. Both P450s have a similar access channel that runs parallel to the active site I helix over the surface of the heme. Molecular dynamics simulations of substrate binding reveal PimD can “pull” substrates further into the P450 access channel owing to additional electrostatic interactions between the protein and the carboxyl group attached to the hemiketal ring of 4,5-desepoxypimaricin. This substrate interaction is absent in AmphL although the additional substrate -OH groups in 8-deoxyamphotericin B help to correctly position the substrate for C8 oxidation. Simulations of the oxy-complex indicates that these -OH groups may also participate in a proton relay network required for O2 activation as has been suggested for two other macrolide P450s, PimD and P450eryF. These findings provide experimentally testable models that can potentially contribute to a new generation of novel macrolide antibiotics with enhanced antifungal and/or antiprotozoal efficacy.
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Affiliation(s)
- Jose A Amaya
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California, USA
| | - David C Lamb
- Faculty of Health, Medicine and Life Sciences, Swansea University, Swansea, UK
| | - Steven L Kelly
- Faculty of Health, Medicine and Life Sciences, Swansea University, Swansea, UK
| | - Patrick Caffrey
- School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Vidhi C Murarka
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California, USA
| | - Thomas L Poulos
- Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry, University of California, Irvine, California, USA.
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8
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Li M, Xu Y, Guo J. Insights into the negative regulation of EGFR upon the binding of an allosteric inhibitor. Chem Biol Drug Des 2022; 99:650-661. [DOI: 10.1111/cbdd.14033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/29/2021] [Accepted: 01/29/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Miaomiao Li
- College of Life Sciences Nanjing Agricultural University Nanjing 210095 China
| | - Yan Xu
- College of Life Sciences Nanjing Agricultural University Nanjing 210095 China
| | - Jingjing Guo
- College of Life Sciences Nanjing Agricultural University Nanjing 210095 China
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9
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Awang T, Pongprayoon P. The penetration of human defensin 5 (HD5) through bacterial outer membrane: simulation studies. J Mol Model 2021; 27:291. [PMID: 34546425 DOI: 10.1007/s00894-021-04915-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/13/2021] [Indexed: 11/24/2022]
Abstract
Human α-defensin 5 (HD5) is one of cationic antimicrobial peptides which plays a crucial role in an innate immune system in human body. HD5 shows the killing activity against a broad spectrum of pathogenic bacteria by making a pore in a bacterial membrane and penetrating into a cytosol. Nonetheless, its pore-forming mechanisms remain unclear. Thus, in this work, the constant-velocity steered molecular dynamics (SMD) simulation was used to simulate the permeation of a dimeric HD5 into a gram-negative lipopolysaccharide (LPS) membrane model. Arginine-rich HD5 is found to strongly interact with a LPS surface. Upon arrival, arginines on HD5 interact with lipid A head groups (a top part of LPS) and then drag these charged moieties down into a hydrophobic core resulting in the formation of water-filled pore. Although all arginines are found to interact with a membrane, Arg13 and Arg32 appear to play a dominant role in the HD5 adsorption on a gram-negative membrane. Furthermore, one chain of a dimeric HD5 is required for HD5 adhesion. The interactions of arginine-lipid A head groups play a major role in adhering a cationic HD5 on a membrane surface and retarding a HD5 passage in the meantime.
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Affiliation(s)
- Tadsanee Awang
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand. .,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, 10900, Thailand.
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10
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Thompson MK, Shay MR, de Serrano V, Dumarieh R, Ghiladi RA, Franzen S. A new inhibition mechanism in the multifunctional catalytic hemoglobin dehaloperoxidase as revealed by the DHP A(V59W) mutant: A spectroscopic and crystallographic study. J PORPHYR PHTHALOCYA 2021. [DOI: 10.1142/s1088424621500826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As multifunctional catalytic hemoglobins, dehaloperoxidase isoenzymes A and B (DHP A and B) are among the most versatile hemoproteins in terms of activities displayed. The ability of DHP to bind over twenty different substrates in the distal pocket might appear to resemble the promiscuousness of monooxygenase enzymes, yet there are identifiable substrate-specific interactions that can steer the type of oxidation (O-atom vs. electron transfer) that occurs inside the DHP distal pocket. Here, we have investigated the DHP A(V59W) mutant in order to probe the limits of conformational flexibility in the distal pocket as it relates to the genesis of this substrate-dependent activity differentiation. The X-ray crystal structure of the metaquo DHP A(V59W) mutant (PDB 3K3U) and the V59W mutant in complex with fluoride [denoted as DHP A(V59W-F)] (PDB 7MNH) show significant mobility of the tryptophan in the distal pocket, with two parallel conformations having W59-N[Formula: see text] H-bonded to a heme-bound ligand (H2O or F[Formula: see text], and another conformation [observed only in DHP A(V59W-F)] that brings W59 sufficiently close to the heme as to preclude axial ligand binding. UV-vis and resonance Raman spectroscopic studies show that DHP A(V59W) is 5-coordinate high spin (5cHS) at pH 5 and 6-coordinate high spin (6cHS) at pH 7, whereas DHP A(V59W-F) is 6cHS from pH 5 to 7. Enzyme assays confirm robust peroxidase activity at pH 5, but complete loss of activity at pH 7. We find no evidence that tryptophan plays a role in the oxidation mechanism ([Formula: see text]. radical formation). Instead, the data reveal a new mechanism of DHP inhibition, namely a shift towards a non-reactive form by OH[Formula: see text] ligation to the heme-Fe that is strongly stabilized (presumably through H-bonding interactions) by the presence of W59 in the distal cavity.
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Affiliation(s)
- Matthew K. Thompson
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Madeline R. Shay
- Department of Chemistry & Biochemistry, University of Alabama, 250 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Rania Dumarieh
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Reza A. Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA
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11
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Chen LY. Thermodynamic Integration in 3n Dimensions without Biases or Alchemy for Protein Interactions. FRONTIERS IN PHYSICS 2020; 8:202. [PMID: 32542181 PMCID: PMC7295167 DOI: 10.3389/fphy.2020.00202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thermodynamic integration (TI), a powerful formalism for computing Gibbs free energy, has been implemented for many biophysical processes with alchemical schemes that require delicate human efforts to choose/design biasing potentials for sampling the desired biophysical events and to remove their artifactitious consequences afterwards. Theoretically, an alchemical scheme is exact but practically, an unsophisticated implementation of this exact formula can cause error amplifications. Small relative errors in the input parameters can be amplified many times in their propagation into the computed free energy [due to subtraction of similar numbers such as (105 ± 5)‒(100 ± 5) = 5 ± 7]. In this paper, we present an unsophisticated implementation of TI in 3n dimensions (3nD) (n=1,2,3…) for the potential of mean force along a 3nD path connecting one state in the bound state ensemble to one state in the unbound state ensemble. Fluctuations in these 3nD are integrated in the bound and unbound state ensembles but not along the 3nD path. Using TI3nD, we computed the standard binding free energies of three protein complexes: trometamol in Salmonella effector SpvD (n=1), biotin-avidin (n=2), and Colicin E9 endonuclease with cognate immunity protein Im9 (n=3). We employed three different protocols in three independent computations of E9-Im9 to show TI3nD's robustness. We also computed the hydration energies of ten biologically relevant compounds (n=1 for water, acetamide, urea, glycerol, trometamol, ammonium and n=2 for erythritol, 1,3-propanediol, xylitol, biotin). Each of the 15 computations is accomplishable within one (for hydration) to ten (for E9-Im9) days on an inexpensive GPU workstation. The computed results all agree with the available experimental data.
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Affiliation(s)
- Liao Y Chen
- Department of Physics, University of Texas at San Antonio, San Antonio, Texas 78249 U.S.A
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12
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Maleki R, Afrouzi HH, Hosseini M, Toghraie D, Piranfar A, Rostami S. pH-sensitive loading/releasing of doxorubicin using single-walled carbon nanotube and multi-walled carbon nanotube: A molecular dynamics study. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 186:105210. [PMID: 31759297 DOI: 10.1016/j.cmpb.2019.105210] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Doxorubicin is one of the drugs used to treat cancer, and many studies have been conducted to control its release. In this study, carbon nanotubes have been proposed as a doxorubicin carrier, and the effect of carboxyl functional group on the controlled release of doxorubicin has been studied. METHODS This study has been done by molecular dynamics simulation and was based on changing the pH as a mechanism controller. RESULTS This work is intended to test the efficacy of this drug carrier for the release of doxorubicin. A comparison was also made between single-walled and double-walled carbon nanotubes to answer the question of which one can be a better carrier for doxorubicin. The study of DOXORUBICIN adsorption and release showed that the DOXORUBICIN adsorption on single-walled carbon nanotube and multi-walled carbon nanotube in neutral pH was stronger than it was in acidic pH, which could be due to the electrostatic interactions between the carboxyl group of nanotubes and DOXORUBICIN. Based on this and according to the investigation of hydrogen bonds, diffusion coefficients, and other results it was clear that the drug release in acidic pH was appropriate for body conditions. Since cancer tissues pH is acidic, this shows the suitability of carbon nanotube in drug delivery and DOXORUBICIN release in cancer tissues. In addition, it was shown that the blood pH (pH = 7) is suitable for DOXORUBICIN loading on the carbon nanotube and carbon nanotube-DOXORUBICIN linkage remained stable at this pH; accordingly, the carbon nanotube could deliver DOXORUBICIN in blood quite well and release it in cancerous tissues. This suggests the carbon nanotubes as a promising drug carrier in the cancer therapy which can be also investigated in experiments. CONCLUSION It was revealed that the bonds between multi-walled carbon nanotube and DOXORUBICIN was stronger and this complex had a slower release in the cancer tissues compared to the single-walled carbon nanotube; this can be regarded as an advantage over the single-walled carbon nanotube in the DOXORUBICIN delivery and release.
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Affiliation(s)
- Reza Maleki
- Department of Chemical Engineering, Shiraz University, Shiraz, Iran
| | | | - Mirollah Hosseini
- Department of Mechanical Engineering, Islamic Azad University, Qaemshahr Branch, Qaemshahr, Mazandaran, Iran
| | - Davood Toghraie
- Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran
| | - Anahita Piranfar
- Biomechanic Department, Biomedical Engineering Faculty, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Sara Rostami
- Laboratory of Magnetism and Magnetic Materials, Advanced Institute of Materials Science, Ton Duc Thang University, Ho Chi Minh City, Vietnam; Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
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13
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You W, Tang Z, Chang CEA. Potential Mean Force from Umbrella Sampling Simulations: What Can We Learn and What Is Missed? J Chem Theory Comput 2019; 15:2433-2443. [PMID: 30811931 PMCID: PMC6456367 DOI: 10.1021/acs.jctc.8b01142] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Changes in free energy provide valuable information for molecular recognition, including both ligand-receptor binding thermodynamics and kinetics. Umbrella sampling (US), a widely used free energy calculation method, has long been used to explore the dissociation process of ligand-receptor systems and compute binding free energy. In existing publications, the binding free energy computed from the potential of mean force (PMF) with US simulation mostly yielded "ball park" values with experimental data. However, the computed PMF values are highly influenced by factors such as initial conformations and/or trajectories provided, the reaction coordinate, and sampling of conformational space in each US window. These critical factors have rarely been carefully studied. Here we used US to study the guest aspirin and 1-butanol dissociation processes of β-cyclodextrin (β-CD) and an inhibitor SB2 dissociation from a p38α mitogen-activated protein kinase (MAPK) complex. For β-CD, we used three different β-CD conformations to generate the dissociation path with US windows. For p38α, we generated the dissociation pathway by using accelerated molecular dynamics followed by conformational relaxing with short conventional MD, steered MD, and manual pulling. We found that, even for small β-CD complexes, different β-CD conformations altered the height of the PMF, but the pattern of PMF was not affected if the MD sampling in each US window was well-converged. Because changing the macrocyclic ring conformation needs to rotate dihedral angles in the ring, a bound ligand largely restrains the motion of cyclodextrin. Therefore, once a guest is in the binding site, cyclodextrin cannot freely change its initial conformation, resulting in different absolute heights of the PMF, which cannot be overcome by running excessively long MD simulations for each US window. Moreover, if the US simulations were not converged, the important barrier and minimum were missed. For ligand-protein systems, our studies also suggest that the dissociation trajectories modeled by an enhanced sampling method must maintain a natural molecular movement to avoid biased PMF plots when using US simulations.
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Affiliation(s)
- Wanli You
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Zhiye Tang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California, Riverside, California 92521, United States
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14
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Do PC, Lee EH, Le L. Steered Molecular Dynamics Simulation in Rational Drug Design. J Chem Inf Model 2018; 58:1473-1482. [DOI: 10.1021/acs.jcim.8b00261] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Phuc-Chau Do
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Eric H. Lee
- Department of Medicine and Division of Hematology and Oncology, Loma Linda University Medical Center, Loma Linda, California 92350, United States
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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15
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Dynamics of dehaloperoxidase-hemoglobin A derived from NMR relaxation spectroscopy and molecular dynamics simulation. J Inorg Biochem 2018; 181:65-73. [DOI: 10.1016/j.jinorgbio.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 12/11/2017] [Accepted: 01/07/2018] [Indexed: 11/18/2022]
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16
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Gao Q, Lu C, Wang XW, Zhang JW, Song Y, Xue YL. Molecular dynamics simulation and steered molecular dynamics simulation on irisin dimers. J Mol Model 2018; 24:95. [PMID: 29549444 DOI: 10.1007/s00894-018-3609-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/30/2018] [Indexed: 11/26/2022]
Abstract
Irisin is found closely associated with promoting the browning of beige fat cells in white adipose tissue. The crystal structure reveals that irisin forms a continuous inter-subunit β-sheet dimer. Here, molecular dynamics (MD) simulation and steered molecular dynamics (SMD) simulation were performed to investigate the dissociation process and the intricate interactions between the two irisin monomers. In the process of MD, the interactions between the monomers were roughly analyzed through the average numbers of both hydrophobic contacts and H-bonds. Then, SMD was performed to investigate the accurate interaction energy between the monomers. By the analysis of dissociation energy, the van der Waals (vdW) force was identified as the major energy to maintain the dimer structure, which also verified the results of MD simulation. Meanwhile, 11 essential residues were discovered by the magnitude of rupture force during dissociation. Among them, residues Arg75, Glu79, Ile77, Ala88, and Trp90 were reported in a previous study using the method of mutagenesis and size exclusion chromatography, and several new important residues (Arg72, Leu74, Phe76, Gln78, Val80, and Asp91) were also identified. Interestingly, the new important residues that we discovered and the important residues that were reported are located in the opposite side of the β-sheet of the dimer.
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Affiliation(s)
- Qi Gao
- College of Light Industry, Liaoning University, Shenyang, 110036, China
- Liaoning Administrative College, Shenyang, 110161, China
| | - Chao Lu
- College of Light Industry, Liaoning University, Shenyang, 110036, China
| | - Xiao-Wen Wang
- College of Light Industry, Liaoning University, Shenyang, 110036, China
| | - Jun-Wei Zhang
- College of Light Industry, Liaoning University, Shenyang, 110036, China
| | - Youtao Song
- School of Environmental Science, Liaoning University, Shenyang, 110036, China
| | - You-Lin Xue
- College of Light Industry, Liaoning University, Shenyang, 110036, China.
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17
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Li Y, Liao M, Zhou J. Catechol-cation adhesion on silica surfaces: molecular dynamics simulations. Phys Chem Chem Phys 2018; 19:29222-29231. [PMID: 29067370 DOI: 10.1039/c7cp05284g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Understanding the interaction mechanism between catechol-cation and inorganic surfaces is vital for controlling the interfacial adhesion behavior. In this work, molecular dynamics simulations are employed to study the adhesion of siderophore analogues (Tren-Lys-Cam, Tren-Arg-Cam and Tren-His-Cam) on silica surfaces with different degrees of ionization and the effects of cationic amino acids and ionic strength on adhesion are discussed. Simulation results indicate that adhesion of catechol-cation onto the ionized silica surface is dominated by electrostatic interactions. At different degrees of ionization, the rank of the adhesions of three siderophore analogues on silica is different. Further analysis shows that the amino acid terminus has a large influence on the adhesion process, especially histidine adhesion on negatively charged surfaces. Tren-Lys-Cam (TLC) has a larger adhesion free energy than Tren-Arg-Cam (TAC) at a higher degree of ionization (18%); both the bulkier structure and delocalized charge of Arg decreased the cation's electrostatic interaction with the charged silica. In addition, the adhesion free energy on ionized silica surfaces decreased with increasing ionic strength of aqueous solutions. A linear correlation between the potential of mean force obtained from umbrella sampling and the rupture force via steered molecular dynamics simulations for siderophore analogue adhesion on silica surfaces is also found. This work may provide some guidance for developing the next generation underwater adhesives.
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Affiliation(s)
- Yingtu Li
- School of Chemistry and Chemical Engineering, Guangdong Provincial Key Lab for Green Chemical Product Technology, South China University of Technology, Guangzhou, 510640, P. R. China.
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18
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Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics. Biochem Biophys Res Commun 2016; 483:203-208. [PMID: 28034750 DOI: 10.1016/j.bbrc.2016.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 12/24/2016] [Indexed: 12/25/2022]
Abstract
Computing the ligand-protein binding affinity (or the Gibbs free energy) with chemical accuracy has long been a challenge for which many methods/approaches have been developed and refined with various successful applications. False positives and, even more harmful, false negatives have been and still are a common occurrence in practical applications. Inevitable in all approaches are the errors in the force field parameters we obtain from quantum mechanical computation and/or empirical fittings for the intra- and inter-molecular interactions. These errors propagate to the final results of the computed binding affinities even if we were able to perfectly implement the statistical mechanics of all the processes relevant to a given problem. And they are actually amplified to various degrees even in the mature, sophisticated computational approaches. In particular, the free energy perturbation (alchemical) approaches amplify the errors in the force field parameters because they rely on extracting the small differences between similarly large numbers. In this paper, we develop a hybrid steered molecular dynamics (hSMD) approach to the difficult binding problems of a ligand buried deep inside a protein. Sampling the transition along a physical (not alchemical) dissociation path of opening up the binding cavity---pulling out the ligand---closing back the cavity, we can avoid the problem of error amplifications by not relying on small differences between similar numbers. We tested this new form of hSMD on retinol inside cellular retinol-binding protein 1 and three cases of a ligand (a benzylacetate, a 2-nitrothiophene, and a benzene) inside a T4 lysozyme L99A/M102Q(H) double mutant. In all cases, we obtained binding free energies in close agreement with the experimentally measured values. This indicates that the force field parameters we employed are accurate and that hSMD (a brute force, unsophisticated approach) is free from the problem of error amplification suffered by many sophisticated approaches in the literature.
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