51
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You W, Chang CEA. Role of Molecular Interactions and Protein Rearrangement in the Dissociation Kinetics of p38α MAP Kinase Type-I/II/III Inhibitors. J Chem Inf Model 2018; 58:968-981. [PMID: 29620886 PMCID: PMC5975198 DOI: 10.1021/acs.jcim.7b00640] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the governing factors of fast or slow inhibitor binding/unbinding assists in developing drugs with preferred kinetic properties. For inhibitors with the same binding affinity targeting different binding sites of the same protein, the kinetic behavior can profoundly differ. In this study, we investigated unbinding kinetics and mechanisms of fast (type-I) and slow (type-II/III) binders of p38α mitogen-activated protein kinase, where the crystal structures showed that type-I and type-II/III inhibitors bind to pockets with different conformations of the Asp-Phe-Gly (DFG) motif. The work used methods that combine conventional molecular dynamics (MD), accelerated molecular dynamics (AMD) simulations, and the newly developed pathway search guided by internal motions (PSIM) method to find dissociation pathways. The study focuses on revealing key interactions and molecular rearrangements that hinder ligand dissociation by using umbrella sampling and post-MD processing to examine changes in free energy during ligand unbinding. As anticipated, the initial dissociation steps all require breaking interactions that appeared in crystal structures of the bound complexes. Interestingly, for type-I inhibitors such as SB2, p38α keeps barrier-free conformational fluctuation in the ligand-bound complex and during ligand dissociation. In contrast, with a type-II/III inhibitor such as BIRB796, with the rearrangements of p38α in its bound state, ligand unbinding features energetically unfavorable protein-ligand concerted movement. Our results also show that the type-II/III inhibitors preferred dissociation pathways through the allosteric channel, which is consistent with an existing publication. The study suggests that the level of required protein rearrangement is one major determining factor of drug binding kinetics in p38α systems, providing useful information for development of inhibitors.
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Affiliation(s)
- Wanli You
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
| | - Chia-en A. Chang
- Department of Chemistry, University of California at Riverside, Riverside, California 92521, United States
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52
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Tu T, Li Y, Luo Y, Wang Z, Wang Y, Luo H, Yao B. A key residue for the substrate affinity enhancement of a thermophilic endo-polygalacturonase revealed by computational design. Appl Microbiol Biotechnol 2018; 102:4457-4466. [DOI: 10.1007/s00253-018-8948-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/07/2018] [Accepted: 03/14/2018] [Indexed: 12/30/2022]
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53
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Ding JN, Zhang YJ, Zhong H, Ao CC, Han JG. A simulation investigation on interaction mechanism between Ebola nucleoprotein and VP35 peptide. J Biomol Struct Dyn 2018; 36:1009-1028. [DOI: 10.1080/07391102.2017.1307143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Jing-Na Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
- Department of Clinical Medicine, Anqing Medical College, Anqing 246052, People’s Republic of China
| | - Yan-Jun Zhang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Hui Zhong
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Cheng-Cheng Ao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
| | - Ju-Guang Han
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, People’s Republic of China
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54
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Zhao F, Jin W, Ma L, Zhang JY, Wang JL, Zhang JH, Song YB. Investigation of the selectivity of one type of small-molecule inhibitor for three Na v channel isoforms based on the method of computer simulation. J Biomol Struct Dyn 2018; 37:702-713. [PMID: 29448911 DOI: 10.1080/07391102.2018.1438921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Voltage-gated sodium (Nav) channels play a pivotal role for the changes in membrane potential and belong to large membrane proteins that compose four voltage sensor domains (VSD1-4). In this study, we describe the binding mode and selectivity of one of the aryl sulfonamide sodium channel inhibitors, PF-04856264, for the VSD4s in Nav1.4, Nav1.5 and Nav1.7, respectively, through molecular dynamics simulation and enhanced post-dynamics analyses. Our results show that there are three binding site regions (BSR1-3) in the combination of the ligand and receptors, of which BSR1 and BSR3 contribute to the selectivity and affinity of the ligand to the receptor. What's more, the 39th residue (Y39 in VSD4hNav1.4/ VSD4hNav1.7 and A39 in VSD4hNav1.5) and N42 in BSR1, the 84th residue (L84 in VSD4hNav1.4, T84 in VSD4hNav1.5, and M84 in VSD4hNav1.7) in BSR2 and the conserved positive charged residues in BSR3 have major contributions to the interaction between the ligand and receptor. Further analysis reveals that if the 39th residue has a benzene ring structure, the connection of BSR1 and the ligand would be much stronger through π-stacking interaction. On the other hand, the strength and number of the hydrogen bonds formed by the ligand and the conserved arginines on S4 determine the contribution of BSR3 to the total free binding energy. We anticipate this study pave the way for the design of more effective and safe treatment for pain that selectively target Nav1.7.
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Affiliation(s)
- Fan Zhao
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
| | - Wei Jin
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
| | - Lin Ma
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
| | - Jian-Ye Zhang
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
| | - Jin-Long Wang
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
| | - Jing-Hai Zhang
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
| | - Yong-Bo Song
- a School of Life Science and Bio-pharmaceutics , Shenyang Pharmaceutical University , 103 Wenhua Road, Shenyang 110016 , China
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55
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Fu W, Chen L, Wang Z, Kang Y, Wu C, Xia Q, Liu Z, Zhou J, Liang G, Cai Y. Theoretical studies on FGFR isoform selectivity of FGFR1/FGFR4 inhibitors by molecular dynamics simulations and free energy calculations. Phys Chem Chem Phys 2018; 19:3649-3659. [PMID: 28094372 DOI: 10.1039/c6cp07964d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The activation and overexpression of fibroblast growth factor receptors (FGFRs) are highly correlated with a variety of cancers. Most small molecule inhibitors of FGFRs selectively target FGFR1-3, but not FGFR4. Hence, designing highly selective inhibitors towards FGFR4 remains a great challenge because FGFR4 and FGFR1 have a high sequence identity. Recently, two small molecule inhibitors of FGFRs, ponatinib and AZD4547, have attracted huge attention. Ponatinib, a type II inhibitor, has high affinity towards FGFR1/4 isoforms, but AZD4547, a type I inhibitor of FGFR1, displays much reduced inhibition toward FGFR4. In this study, conventional molecular dynamics (MD) simulations, molecular mechanics/generalized Born surface area (MM/GBSA) free energy calculations and umbrella sampling (US) simulations were carried out to reveal the principle of the binding preference of ponatinib and AZD4547 towards FGFR4/FGFR1. The results provided by MM/GBSA illustrate that ponatinib has similar binding affinities to FGFR4 and FGFR1, while AZD4547 has much stronger binding affinity to FGFR1 than to FGFR4. A comparison of the individual energy terms suggests that the selectivity of AZD4547 towards FGFR1 versus FGFR4 is primarily controlled by the variation of the van der Waals interactions. The US simulations reveal that the PMF profile of FGFR1/AZD4547 has more peaks and valleys compared with that of FGFR4/AZD4547, suggesting that the dissociation process of AZD4547 from FGFR1 are easily trapped into local minima. Moreover, it is observed that FGFR1/AZD4547 has much higher PMF depth than FGFR4/AZD4547, implying that it is more difficult for AZD4547 to escape from FGFR1 than from FGFR4. The physical principles provided by this study extend our understanding of the binding mechanisms and provide valuable guidance for the rational design of FGFR isoform selective inhibitors.
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Affiliation(s)
- Weitao Fu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Lingfeng Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Zhe Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Yanting Kang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China. and Epidemiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Chao Wu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Qinqin Xia
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Zhiguo Liu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Jianmin Zhou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Yuepiao Cai
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
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56
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Kuang G, Wang X, Halldin C, Nordberg A, Långström B, Ågren H, Tu Y. Theoretical study of the binding profile of an allosteric modulator NS-1738 with a chimera structure of the α7 nicotinic acetylcholine receptor. Phys Chem Chem Phys 2018; 18:28003-28009. [PMID: 27711412 DOI: 10.1039/c6cp02278b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Potentiation of the function of the α7 nicotinic acetylcholine receptor (α7-nAChR) is believed to provide a possible way for the treatment of cholinergic system dysfunctions such as Alzheimer's disease and schizophrenia. Positive allosteric modulators (PAMs) are able to augment the peak current response of the endogenous agonist of α7-nAChR by binding to some allosteric sites. In this study, the binding profile of a potent type I PAM, NS-1738, with a chimera structure (termed α7-AChBP) constructed from the extracellular domain of α7-nAChR and an acetylcholine binding protein was investigated with molecular docking, molecular dynamics simulation, and free energy calculation methods. We found that NS-1738 could bind to three allosteric sites of α7-AChBP, namely, the top pocket, the vestibule pocket and the agonist sub-pocket. NS-1738 has moderate binding affinities (-6.76 to -9.15 kcal mol-1) at each allosteric site. The urea group is critical for binding and can form hydrogen-bond interactions with the protein. The bulky trifluoromethyl group also has a great impact on the binding modes and binding affinities. We believe that our study provides valuable insight into the binding profiles of type I PAMs with α7-nAChR and is helpful for the development of novel PAMs.
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Affiliation(s)
- Guanglin Kuang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91, Stockholm, Sweden.
| | - Xu Wang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91, Stockholm, Sweden.
| | - Christer Halldin
- Karolinska Institutet, Department of Clinical Neuroscience, Centre for Psychiatric Research, 171 76, Stockholm, Sweden
| | - Agneta Nordberg
- Department of Neurobiology, Care Sciences and Society, Center of Alzheimer Research, Translational Alzheimer Neurobiology, Karolinska University Hospital, Huddinge, S-141 86, Stockholm, Sweden
| | - Bengt Långström
- Department of Chemistry, Uppsala University, 751 23 Uppsala, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91, Stockholm, Sweden.
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Center, S-106 91, Stockholm, Sweden.
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57
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2- OMe -lysophosphatidylcholine analogues are GPR119 ligands and activate insulin secretion from βTC-3 pancreatic cells: Evaluation of structure-dependent biological activity. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1863:91-103. [DOI: 10.1016/j.bbalip.2017.10.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 10/19/2017] [Accepted: 10/22/2017] [Indexed: 01/08/2023]
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58
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Zhou Y, Hussain M, Kuang G, Zhang J, Tu Y. Mechanistic insights into peptide and ligand binding of the ATAD2-bromodomain via atomistic simulations disclosing a role of induced fit and conformational selection. Phys Chem Chem Phys 2018; 20:23222-23232. [DOI: 10.1039/c8cp03860k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Atomistic simulations of the ATAD2-bromodomain disclose a role of induced fit and conformational selection upon ligand and peptide binding.
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Affiliation(s)
- Yang Zhou
- Department of Theoretical Chemistry and Biology
- KTH Royal Institute of Technology
- AlbaNova University Center
- Stockholm
- Sweden
| | - Muzammal Hussain
- Guangdong Provincial Key Laboratory of Biocomputing
- Institute of Chemical Biology
- Guangzhou Institutes of Biomedicine and Health
- Chinese Academy of Sciences
- Guangzhou 510530
| | - Guanglin Kuang
- Department of Theoretical Chemistry and Biology
- KTH Royal Institute of Technology
- AlbaNova University Center
- Stockholm
- Sweden
| | - Jiancun Zhang
- Guangdong Provincial Key Laboratory of Biocomputing
- Institute of Chemical Biology
- Guangzhou Institutes of Biomedicine and Health
- Chinese Academy of Sciences
- Guangzhou 510530
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology
- KTH Royal Institute of Technology
- AlbaNova University Center
- Stockholm
- Sweden
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59
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Watts CR, Gregory A, Frisbie C, Lovas S. Effects of force fields on the conformational and dynamic properties of amyloid β(1-40) dimer explored by replica exchange molecular dynamics simulations. Proteins 2017; 86:279-300. [PMID: 29235155 DOI: 10.1002/prot.25439] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/10/2017] [Indexed: 12/14/2022]
Abstract
The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1-40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER-ff99sb-ILDN, AMBER-ff99sb*-ILDN, AMBER-ff99sb-NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER-ff99sb-ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α-helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER-ff99sb-NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER-ff99sb-NMR force field, the others tended to under estimate the expected amount of β-sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER-ff99sb-NMR, reproduce a theoretically expected β-sheet-turn-β-sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C-terminal hydrophobic cores from residues 17-21 and 30-36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.
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Affiliation(s)
- Charles R Watts
- Department of Neurosurgery, Mayo Clinic, College of Medicine, Rochester, Minnesota.,Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Andrew Gregory
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin
| | - Cole Frisbie
- Department of Neurosurgery, Mayo Clinic Health System, La Crosse, Wisconsin.,Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
| | - Sándor Lovas
- Department of Biomedical Sciences, Creighton University, Omaha, Nebraska
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60
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Adamidou T, Arvaniti KO, Glykos NM. Folding Simulations of a Nuclear Receptor Box-Containing Peptide Demonstrate the Structural Persistence of the LxxLL Motif Even in the Absence of Its Cognate Receptor. J Phys Chem B 2017; 122:106-116. [DOI: 10.1021/acs.jpcb.7b10292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Triantafyllia Adamidou
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
| | - Konstantina-Olympia Arvaniti
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
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61
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Jin R, Chen Q, Yao S, Bai E, Fu W, Wang L, Wang J, Du X, Wei T, Xu H, Jiang C, Qiu P, Wu J, Li W, Liang G. Synthesis and anti-tumor activity of EF24 analogues as IKKβ inhibitors. Eur J Med Chem 2017; 144:218-228. [PMID: 29351887 DOI: 10.1016/j.ejmech.2017.11.077] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/16/2022]
Abstract
EF24 is an IKKβ inhibitor (IC50: 72 μM) containing various anti-tumor activities. In this study, a series of EF24 analogs targeting IKKβ were designed and synthesized. Several IKKβ inhibitors with better activities than EF24 were screened out and B3 showed best IKKβ inhibitory (IC50: 6.6 μM). Molecular docking and dynamic simulation experiments further confirmed this inhibitory effect. B3 obviously suppressed the viability of Hela229, A549, SGC-7901 and MGC-803 cells. Then, in SGC-7901 and MGC-803 cells, B3 blocked the NF-κB signal pathway by inhibiting IKKβ phosphorylation, and followed arrested the cell cycle at G2/M phase by suppressing the Cyclin B1 and Cdc2 p34 expression, induced the cell apoptosis by down-regulating Bcl-2 protein and up-regulating cleaved-caspase3. Moreover, B3 significantly reduced tumor growth and suppressed the IKKβ-NF-κB signal pathway in SGC-7901 xenograft model. In total, this study present a potential IKKβ inhibitor as anti-tumor precursor.
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Affiliation(s)
- Rong Jin
- Department of Digestive Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qiuxiang Chen
- Department of Ultrasound, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Song Yao
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Encheng Bai
- Department of Digestive Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Weitao Fu
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Ledan Wang
- Department of Gynecology and Obstetrics, The 2nd Affiliated Hospital of the Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Jiabing Wang
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xiaojing Du
- Department of Digestive Diseases, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China; Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Tao Wei
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Haineng Xu
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Wenzhou Biomedical Innovation Center, Wenzhou University and Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Chengxi Jiang
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Wenzhou Biomedical Innovation Center, Wenzhou University and Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Peihong Qiu
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jianzhang Wu
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Wenzhou Biomedical Innovation Center, Wenzhou University and Wenzhou Medical University, Wenzhou, Zhejiang 325000, China.
| | - Wulan Li
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; College of Information Science and Computer Engineering, The First Clinical Medical College, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China.
| | - Guang Liang
- Chemical Biology Research Center, College of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; Wenzhou Biomedical Innovation Center, Wenzhou University and Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
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62
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Sasmal S, Lincoff J, Head-Gordon T. Effect of a Paramagnetic Spin Label on the Intrinsically Disordered Peptide Ensemble of Amyloid-β. Biophys J 2017; 113:1002-1011. [PMID: 28877484 DOI: 10.1016/j.bpj.2017.06.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/16/2017] [Accepted: 06/30/2017] [Indexed: 10/18/2022] Open
Abstract
Paramagnetic relaxation enhancement is an NMR technique that has yielded important insight into the structure of folded proteins, although the perturbation introduced by the large spin probe might be thought to diminish its usefulness when applied to characterizing the structural ensembles of intrinsically disordered proteins (IDPs). We compare the computationally generated structural ensembles of the IDP amyloid-β42 (Aβ42) to an alternative sequence in which a nitroxide spin label attached to cysteine has been introduced at its N-terminus. Based on this internally consistent computational comparison, we find that the spin label does not perturb the signature population of the β-hairpin formed by residues 16-21 and 29-36 that is dominant in the Aβ42 reference ensemble. However, the presence of the tag induces a strong population shift in a subset of the original Aβ42 structural sub-populations, including a sevenfold enhancement of the β-hairpin formed by residues 27-31 and 33-38. Through back-calculation of NMR observables from the computational structural ensembles, we show that the structural differences between the labeled and unlabeled peptide would be evident in local residual dipolar couplings, and possibly differences in homonuclear 1H-1H nuclear Overhauser effects (NOEs) and heteronuclear 1H-15N NOEs if the paramagnetic contribution to the longitudinal relaxation does not suppress the NOE intensities in the real experiment. This work shows that molecular simulation provides a complementary approach to resolving the potential structural perturbations introduced by reporter tags that can aid in the interpretation of paramagnetic relaxation enhancement, double electron-electron resonance, and fluorescence resonance energy transfer experiments applied to IDPs.
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Affiliation(s)
- Sukanya Sasmal
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
| | - James Lincoff
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California
| | - Teresa Head-Gordon
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California; Department of Chemistry, University of California, Berkeley, Berkeley, California; Department of Bioengineering, University of California, Berkeley, Berkeley, California; Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California.
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63
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Chu Y, Tu T, Penttinen L, Xue X, Wang X, Yi Z, Gong L, Rouvinen J, Luo H, Hakulinen N, Yao B, Su X. Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose. J Biol Chem 2017; 292:19315-19327. [PMID: 28974575 PMCID: PMC5702671 DOI: 10.1074/jbc.m117.807768] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/20/2017] [Indexed: 11/06/2022] Open
Abstract
Bifunctional glycoside hydrolases have potential for cost-savings in enzymatic decomposition of plant cell wall polysaccharides for biofuels and bio-based chemicals. The N-terminal GH10 domain of a bifunctional multimodular enzyme CbXyn10C/Cel48B from Caldicellulosiruptor bescii is an enzyme able to degrade xylan and cellulose simultaneously. However, the molecular mechanism underlying its substrate promiscuity has not been elucidated. Herein, we discovered that the binding cleft of CbXyn10C would have at least six sugar-binding subsites by using isothermal titration calorimetry analysis of the inactive E140Q/E248Q mutant with xylo- and cello-oligosaccharides. This was confirmed by determining the catalytic efficiency of the wild-type enzyme on these oligosaccharides. The free form and complex structures of CbXyn10C with xylose- or glucose-configured oligosaccharide ligands were further obtained by crystallographic analysis and molecular modeling and docking. CbXyn10C was found to have a typical (β/α)8-TIM barrel fold and "salad-bowl" shape of GH10 enzymes. In complex structures with xylo-oligosaccharides, seven sugar-binding subsites were found, and many residues responsible for substrate interactions were identified. Site-directed mutagenesis indicated that 6 and 10 amino acid residues were key residues for xylan and cellulose hydrolysis, respectively. The most important residues are centered on subsites -2 and -1 near the cleavage site, whereas residues playing moderate roles could be located at more distal regions of the binding cleft. Manipulating the residues interacting with substrates in the distal regions directly or indirectly improved the activity of CbXyn10C on xylan and cellulose. Most of the key residues for cellulase activity are conserved across GH10 xylanases. Revisiting randomly selected GH10 enzymes revealed unreported cellulase activity, indicating that the dual function may be a more common phenomenon than has been expected.
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Affiliation(s)
- Yindi Chu
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Tao Tu
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Leena Penttinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Xianli Xue
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuolin Yi
- the Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China, and
| | - Li Gong
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- the Key Laboratory of Molecular Animal Nutrition and Feed Sciences, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Juha Rouvinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland
| | - Huiying Luo
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nina Hakulinen
- the Department of Chemistry, University of Eastern Finland, Joensuu Campus, Joensuu FIN-80101, Finland,
| | - Bin Yao
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China,
| | - Xiaoyun Su
- From the Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China,
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64
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Łopieńska-Biernat E, Molcan T, Paukszto Ł, Jastrzębski JP, Myszczyński K. Modelling studies determing the mode of action of anthelmintics inhibiting in vitro trehalose-6-phosphate phosphatase (TPP) of Anisakis simplex s.l. Exp Parasitol 2017; 184:46-56. [PMID: 29170085 DOI: 10.1016/j.exppara.2017.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/20/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
Abstract
The trehalose-6-phosphate phosphatase (TPP) enzyme is involved in the synthesis of trehalose, the main sugar in the energy metabolism of nematodes. TPP is a member of the HAD-like hydrolase superfamily and shows a robust and specific phosphatase activity for the substrate trehalose-6-phosphate. The presence of conserved active sites of TPP in closely related nematodes and its absence in humans makes it a promising target for antiparasitic drugs. In the present study, homology modeling, molecular docking and MD simulation techniques were used to explore the structure and dynamics of TPP. In the active site, a magnesium ion is stabilized by 3 coordinate bonds formed by D189, D191 and D400. The key amino acids involved in ligand binding by the enzyme are C198, Y201,T357, D191 and Y197. This study relied on docking to select potential inhibitors of TPP which were tested in vitro for sensitivity to anthelmintic drugs such as levamisole and ivermectin targeting Anisakis simplex. The higher toxicity of LEV than IVM was demonstrated after 96 h, 30% of larvae were motile in cultures with 100 μg/ml of LEV and 1000 μg/ml of IVM. We identified drug combination of LEV-IVM against in vitro A. simplex as agonistic effect (CI = 1.1). Levamisole appeared to be a more effective drug which inhibited enzyme activity after 48 h and expression of mRNA after 96 h at a concentration of 10 μg/ml. This preliminary study predicted the structure of TPP, and the results of an in vitro experiment involving A. simplex will contribute to the development of effective inhibitors with potential antiparasitic activity in the future.
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Affiliation(s)
- Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland.
| | - Tomasz Molcan
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
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65
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Ahmed M, Barakat K. When theory meets experiment: the PD-1 challenge. J Mol Model 2017; 23:308. [PMID: 29019005 DOI: 10.1007/s00894-017-3482-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/24/2017] [Indexed: 12/18/2022]
Abstract
Applying atomistic computational modeling to drug discovery has proven to be a hugely successful approach, allowing drug-receptor interactions to be predicted and drugs to be optimized for potency, selectivity, and safety. However, when it comes to predicting protein-protein interactions and to rationally designing regulators of these interactions, computational tools often fail. Here, we report one of the rare instances where state-of-the-art computer simulations, guided by experiment, were able to correctly predict one of the most sophisticated protein-protein interactions. We revisit our previous discovery of the complex of human PD-1 with the ligand PD-L1 and compare our earlier findings with the recently published crystal structure of the same complex. Side-by-side comparison of the model of the complex with its crystal structure reveals outstanding agreement and suggests that our protein-protein prediction workflow could be applied to similar problems.
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Affiliation(s)
- Marawan Ahmed
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Khaled Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada. .,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada. .,Li Ka Shing Applied Virology Institute, University of Alberta, Edmonton, Alberta, Canada.
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66
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Zhang D, Lazim R, Mun Yip Y. Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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67
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68
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Structural Behavior of the Peptaibol Harzianin HK VI in a DMPC Bilayer: Insights from MD Simulations. Biophys J 2017. [PMID: 28636916 DOI: 10.1016/j.bpj.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Microsecond molecular dynamics simulations of harzianin HK VI (HZ) interacting with a dimyristoylphosphatidylcholine bilayer were performed at the condition of low peptide-to-lipid ratio. Two orientations of HZ molecule in the bilayer were found and characterized. In the orientation perpendicular to the bilayer surface, HZ induces a local thinning of the bilayer. When inserted into the bilayer parallel to its surface, HZ is located nearly completely within the hydrophobic region of the bilayer. A combination of solid-state NMR and circular dichroism experiments found the latter orientation to be dominant. An extended sampling simulation provided qualitative results and showed the same orientation to be a global minimum of free energy. The secondary structure of HZ was characterized, and it was found to be located in the 310-helical family. The specific challenges of computer simulation of nonpolar peptides are discussed briefly.
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69
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Discovery of a ROCK inhibitor, FPND, which prevents cerebral hemorrhage through maintaining vascular integrity by interference with VE-cadherin. Cell Death Discov 2017; 3:17051. [PMID: 28845297 PMCID: PMC5563523 DOI: 10.1038/cddiscovery.2017.51] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 06/15/2017] [Accepted: 06/16/2017] [Indexed: 02/07/2023] Open
Abstract
Hemorrhagic stroke occurs when a weakened vessel ruptures and bleeds into the surrounding brain, leading to high rates of death and disability worldwide. A series of complex pathophysiological cascades contribute to the risk of hemorrhagic stroke, and no therapies have proven effective to prevent hemorrhagic stroke. Stabilization of vascular integrity has been considered as a potential therapeutic target for hemorrhagic stroke. ROCKs, which belong to the serine/threonine protein kinase family and participate in the organization of actin cytoskeleton, have become attractive targets for the treatment of strokes. In this study, in vitro enzyme-based assays revealed that a new compound (FPND) with a novel scaffold identified by docking-based virtual screening could inhibit ROCK1 specifically at low micromolar concentration. Molecular modeling showed that FPND preferentially interacted with ROCK1, and the difference between the binding affinity of FPND toward ROCK1 and ROCK2 primarily resulted from non-polar contributions. Furthermore, FPND significantly prevented statin-induced cerebral hemorrhage in a zebrafish model. In addition, in vitro studies using the xCELLigence RTCA system, immunofluorescence and western blotting revealed that FPND prevented statin-induced cerebral hemorrhage by enhancing endothelial cell–cell junctions through inhibiting the ROCK-mediated VE-cadherin signaling pathway. As indicated by the extremely low toxicity of FPND against mice, it is safe and can potentially prevent vascular integrity loss-related diseases, such as hemorrhagic stroke.
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70
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Siqueira AS, Lima ARJ, de Souza RC, Santos AS, Vianez Júnior JLDSG, Gonçalves EC. In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties. Mol Biol Rep 2017. [PMID: 28756560 DOI: 10.1007/s11033-017-4116-1/figures/3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
Scytovirin is a lectin isolated from the cyanobacterium Scytonema varium that has shown activity against HIV, SARS coronavirus and Zaire Ebola virus. Its 95 amino acids are divided into two structural domains (SD), the first spanning amino acids 1-48 (SD1) and the second 49-95 (SD2). Interestingly, the domains are nearly identical but differ in their affinities for carbohydrates. With the aim of enhancing understanding of the binding properties of scytovirin, we performed molecular dynamics (MD) simulations of scytovirin complexed with Man4. We set up three systems: (i) Man4 bound to both domains (SD1 + SD2) using the full-length protein; (ii) Man4 bound to an incomplete protein, containing only SD1 and (iii) Man4 bound to an incomplete protein containing only SD2. Contrary to other reports, binding free energy results suggest that Man4 can bind simultaneously to SD1 and SD2 binding regions, but SD1 individually has the best values of energy and the best affinity for Man4. Decomposition of the binding free energy showed that the residues that interact with Man4 were different in the three systems, suggesting that the binding mechanism of Man4 varies between full-length protein, SD1 and SD2. The results presented here may help to formulate strategies to use scytovirin and promote mutagenesis studies to improve the antiviral activity of scytovirin.
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Affiliation(s)
- Andrei Santos Siqueira
- Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil.
| | - Alex Ranieri Jerônimo Lima
- Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil
| | - Rafael Conceição de Souza
- Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belem, Pará, Brazil
| | - Alberdan Silva Santos
- Laboratórios de Investigação Sistemática em Biotecnologia e Biodiversidade Molecular - Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belem, Pará, Brazil
| | | | - Evonnildo Costa Gonçalves
- Laboratório de Tecnologia Biomolecular - Instituto de Ciências Biológicas, Universidade Federal do Pará, Belem, Pará, Brazil
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71
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In silico analysis of the cyanobacterial lectin scytovirin: new insights into binding properties. Mol Biol Rep 2017; 44:353-358. [PMID: 28756560 PMCID: PMC7088960 DOI: 10.1007/s11033-017-4116-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 07/25/2017] [Indexed: 11/17/2022]
Abstract
Scytovirin is a lectin isolated from the cyanobacterium Scytonema varium that has shown activity against HIV, SARS coronavirus and Zaire Ebola virus. Its 95 amino acids are divided into two structural domains (SD), the first spanning amino acids 1–48 (SD1) and the second 49–95 (SD2). Interestingly, the domains are nearly identical but differ in their affinities for carbohydrates. With the aim of enhancing understanding of the binding properties of scytovirin, we performed molecular dynamics (MD) simulations of scytovirin complexed with Man4. We set up three systems: (i) Man4 bound to both domains (SD1 + SD2) using the full-length protein; (ii) Man4 bound to an incomplete protein, containing only SD1 and (iii) Man4 bound to an incomplete protein containing only SD2. Contrary to other reports, binding free energy results suggest that Man4 can bind simultaneously to SD1 and SD2 binding regions, but SD1 individually has the best values of energy and the best affinity for Man4. Decomposition of the binding free energy showed that the residues that interact with Man4 were different in the three systems, suggesting that the binding mechanism of Man4 varies between full-length protein, SD1 and SD2. The results presented here may help to formulate strategies to use scytovirin and promote mutagenesis studies to improve the antiviral activity of scytovirin.
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72
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Koes DR, Vries JK. Evaluating amber force fields using computed NMR chemical shifts. Proteins 2017; 85:1944-1956. [PMID: 28688107 DOI: 10.1002/prot.25350] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/23/2017] [Accepted: 07/06/2017] [Indexed: 11/07/2022]
Abstract
NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical shifts generated from ab initio quantum calculations. This approach has potential utility for evaluating the force fields that underlie these simulations. Imperfections in force fields generate flawed atomic coordinates. Chemical shifts obtained from flawed coordinates have errors that can be traced back to these imperfections. We use this approach to evaluate a series of AMBER force fields that have been refined over the course of two decades (ff94, ff96, ff99SB, ff14SB, ff14ipq, and ff15ipq). For each force field a series of MD simulations are carried out for eight model proteins. The calculated chemical shifts for the 1 H, 15 N, and 13 Ca atoms are compared with experimental values. Initial evaluations are based on root mean squared (RMS) errors at the protein level. These results are further refined based on secondary structure and the types of atoms involved in nonbonded interactions. The best chemical shift for identifying force field differences is the shift associated with peptide protons. Examination of the model proteins on a residue by residue basis reveals that force field performance is highly dependent on residue position. Examination of the time course of nonbonded interactions at these sites provides explanations for chemical shift differences at the atomic coordinate level. Results show that the newer ff14ipq and ff15ipq force fields developed with the implicitly polarized charge method perform better than the older force fields.
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Affiliation(s)
- David R Koes
- Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260
| | - John K Vries
- Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260
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73
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Czeleń P. Inhibition mechanism of CDK-2 and GSK-3β by a sulfamoylphenyl derivative of indoline-a molecular dynamics study. J Mol Model 2017; 23:230. [PMID: 28726150 PMCID: PMC5517586 DOI: 10.1007/s00894-017-3395-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 06/25/2017] [Indexed: 11/22/2022]
Abstract
A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of such enzyme inhibition as analyzed by an indoline sulfamylophenyl derivative (CHEMBL410072). Previous work has shown that such compounds exhibit selective properties towards their biological targets. This study used a combined procedure involving docking and molecular dynamics simulations, which allowed identification of interactions responsible for stabilization of complexes, and analysis of the dynamic stability of the systems obtained. The initial data obtained during the molecular docking stage show that the ligand molecule exhibits a similar affinity towards both active sites, which was confirmed by quantification of identified interactions and energy values. However, the data do not cover dynamic aspects of the considered systems. Molecular dynamics simulations realized for both complexes indicate significant dissimilarities in dynamics properties of both side chains of the considered ligands, especially in the case of the part containing the sulfamide group. Such increased mobility of the analyzed systems disrupts the stability of binding in the stabilized complex with GSK-3β protein, which finally affects also the binding affinity of the ligand molecule towards this enzyme.
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Affiliation(s)
- Przemysław Czeleń
- Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpinskiego 5, 85-096, Bydgoszcz, Poland.
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74
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Moreira C, Ramos MJ, Fernandes PA. Clarifying the Catalytic Mechanism of Human Glutamine Synthetase: A QM/MM Study. J Phys Chem B 2017; 121:6313-6320. [DOI: 10.1021/acs.jpcb.7b02543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Cátia Moreira
- UCIBIO, REQUIMTE,
Departamento
de Química e Bioquímica, s/n, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto (Portugal)
| | - Maria J. Ramos
- UCIBIO, REQUIMTE,
Departamento
de Química e Bioquímica, s/n, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto (Portugal)
| | - Pedro A. Fernandes
- UCIBIO, REQUIMTE,
Departamento
de Química e Bioquímica, s/n, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto (Portugal)
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75
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Rhinehardt KL, Vance SA, Mohan RV, Sandros M, Srinivas G. Molecular modeling and SPRi investigations of interleukin 6 (IL6) protein and DNA aptamers. J Biomol Struct Dyn 2017; 36:1934-1947. [PMID: 28592206 DOI: 10.1080/07391102.2017.1338619] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Interleukin 6 (IL6), an inflammatory response protein has major implications in immune-related inflammatory diseases. Identification of aptamers for the IL6 protein aids in diagnostic, therapeutic, and theranostic applications. Three different DNA aptamers and their interactions with IL6 protein were extensively investigated in a phosphate buffed saline (PBS) solution. Molecular-level modeling through molecular dynamics provided insights of structural, conformational changes and specific binding domains of these protein-aptamer complexes. Multiple simulations reveal consistent binding region for all protein-aptamer complexes. Conformational changes coupled with quantitative analysis of center of mass (COM) distance, radius of gyration (Rg), and number of intermolecular hydrogen bonds in each IL6 protein-aptamer complex was used to determine their binding performance strength and obtain molecular configurations with strong binding. A similarity comparison of the molecular configurations with strong binding from molecular-level modeling concurred with Surface Plasmon Resonance imaging (SPRi) for these three aptamer complexes, thus corroborating molecular modeling analysis findings. Insights from the natural progression of IL6 protein-aptamer binding modeled in this work has identified key features such as the orientation and location of the aptamer in the binding event. These key features are not readily feasible from wet lab experiments and impact the efficacy of the aptamers in diagnostic and theranostic applications.
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Affiliation(s)
- Kristen L Rhinehardt
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Stephen A Vance
- b Department of Nanoscience , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Ram V Mohan
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Marinella Sandros
- b Department of Nanoscience , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
| | - Goundla Srinivas
- a Department of Nanoengineering , Joint School of Nanoscience and Nanoengineering (JSNN), North Carolina A & T State University , 2907 East Gate City Blvd., Greensboro , NC 27401 , USA
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76
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Sandoval-Perez A, Pluhackova K, Böckmann RA. Critical Comparison of Biomembrane Force Fields: Protein-Lipid Interactions at the Membrane Interface. J Chem Theory Comput 2017; 13:2310-2321. [PMID: 28388089 DOI: 10.1021/acs.jctc.7b00001] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e.g. of soluble proteins or lipid bilayers. Less strictly, due to the added complexity and missing experimental data to compare to, force fields have hardly been tested on the properties of mixed systems, e.g. on protein-lipid systems. Their selection and combination for mixed systems is further complicated by the partially differing parametrization strategies. Additionally, the presence of other compounds in the system may shift the subtle balance of force field parameters. Here, we assessed the protein-lipid interactions as described in the four atomistic force fields GROMOS54a7, CHARMM36 and the two force field combinations Amber14sb/Slipids and Amber14sb/Lipid14. Four observables were compared, focusing on the membrane-water interface: the conservation of the secondary structure of transmembrane proteins, the positioning of transmembrane peptides relative to the lipid bilayer, the insertion depth of side chains of unfolded peptides absorbed at the membrane interface, and the ability to reproduce experimental insertion energies of Wimley-White peptides at the membrane interface. Significant differences between the force fields were observed that affect e.g. membrane insertion depths and tilting of transmembrane peptides.
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Affiliation(s)
- Angelica Sandoval-Perez
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrassre 5, 91058 Erlangen, Germany
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77
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Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution. Sci Rep 2017; 7:44651. [PMID: 28300210 PMCID: PMC5353640 DOI: 10.1038/srep44651] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/09/2017] [Indexed: 01/02/2023] Open
Abstract
In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression.
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Abstract
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and molecular biology that requires a new paradigm to connect structural disorder to function. Molecular dynamics simulations and statistical thermodynamics potentially offer ideal tools for atomic-level characterizations and thermodynamic descriptions of this fascinating class of proteins that will complement experimental studies. However, IDPs display sensitivity to inaccuracies in the underlying molecular mechanics force fields. Thus, achieving an accurate structural characterization of IDPs via simulations is a challenge. It is also daunting to perform a configuration-space integration over heterogeneous structural ensembles sampled by IDPs to extract, in particular, protein configurational entropy. In this review, we summarize recent efforts devoted to the development of force fields and the critical evaluations of their performance when applied to IDPs. We also survey recent advances in computational methods for protein configurational entropy that aim to provide a thermodynamic link between structural disorder and protein activity.
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Affiliation(s)
- Song-Ho Chong
- Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;
| | - Prathit Chatterjee
- Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;
| | - Sihyun Ham
- Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;
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79
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Wang Y, Qian Y, Fang Q, Zhong P, Li W, Wang L, Fu W, Zhang Y, Xu Z, Li X, Liang G. Saturated palmitic acid induces myocardial inflammatory injuries through direct binding to TLR4 accessory protein MD2. Nat Commun 2017; 8:13997. [PMID: 28045026 PMCID: PMC5216130 DOI: 10.1038/ncomms13997] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 11/17/2016] [Indexed: 12/11/2022] Open
Abstract
Obesity increases the risk for a number of diseases including cardiovascular diseases and type 2 diabetes. Excess saturated fatty acids (SFAs) in obesity play a significant role in cardiovascular diseases by activating innate immunity responses. However, the mechanisms by which SFAs activate the innate immune system are not fully known. Here we report that palmitic acid (PA), the most abundant circulating SFA, induces myocardial inflammatory injury through the Toll-like receptor 4 (TLR4) accessory protein MD2 in mouse and cell culture experimental models. Md2 knockout mice are protected against PA- and high-fat diet-induced myocardial injury. Studies of cell surface binding, cell-free protein–protein interactions and molecular docking simulations indicate that PA directly binds to MD2, supporting a mechanism by which PA activates TLR4 and downstream inflammatory responses. We conclude that PA is a crucial contributor to obesity-associated myocardial injury, which is likely regulated via its direct binding to MD2. The free fatty acid-mediated inflammatory activities are regulated through TLR4. Here the authors show that palmitic acid binds to MD2, initiating complex formation with TLR4, recruitment of MyD88, and subsequent activation of pro-inflammatory molecules, and that MD2 blockade protects against diet-induced cardiac dysfunction.
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Affiliation(s)
- Yi Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yuanyuan Qian
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Qilu Fang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Peng Zhong
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Weixin Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Lintao Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Weitao Fu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yali Zhang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Zheng Xu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Xiaokun Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
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80
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Kuang G, Zhou Y, Zou R, Halldin C, Nordberg A, Långström B, Ågren H, Tu Y. Characterization of the binding mode of the PET tracer [18F]ASEM to a chimera structure of the α7 nicotinic acetylcholine receptor. RSC Adv 2017. [DOI: 10.1039/c7ra00496f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The binding free energy profile of the radio-ligand [18F]ASEM with the α7 nicotinic acetylcholine receptor was revealed by metadynamic simulations.
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Affiliation(s)
- Guanglin Kuang
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology (KTH)
- AlbaNova University Center
- Stockholm
| | - Yang Zhou
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology (KTH)
- AlbaNova University Center
- Stockholm
| | - Rongfeng Zou
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology (KTH)
- AlbaNova University Center
- Stockholm
| | - Christer Halldin
- Karolinska Institutet
- Department of Clinical Neuroscience
- Centre for Psychiatric Research
- Stockholm
- Sweden
| | - Agneta Nordberg
- Department of Neurobiology, Care Sciences and Society
- Center of Alzheimer Research, Translational Alzheimer Neurobiology
- Karolinska University Hospital
- Stockholm
- Sweden
| | - Bengt Långström
- Department of Chemistry
- Uppsala University
- 751 23 Uppsala
- Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology (KTH)
- AlbaNova University Center
- Stockholm
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology (KTH)
- AlbaNova University Center
- Stockholm
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81
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Abstract
Accurate chemical shifts for the atoms in molecular mechanics (MD) trajectories can be obtained from quantum mechanical (QM) calculations that depend solely on the coordinates of the atoms in the localized regions surrounding atoms of interest. If these coordinates are correct and the sample size is adequate, the ensemble average of these chemical shifts should be equal to the chemical shifts obtained from NMR spectroscopy. If this is not the case, the coordinates must be incorrect. We have utilized this fact to quantify the errors associated with the backbone atoms in MD simulations of proteins. A library of regional conformers containing 169,499 members was constructed from 6 model proteins. The chemical shifts associated with the backbone atoms in each of these conformers was obtained from QM calculations using density functional theory at the B3LYP level with a 6-311+G(2d,p) basis set. Chemical shifts were assigned to each backbone atom in each MD simulation frame using a template matching approach. The ensemble average of these chemical shifts was compared to chemical shifts from NMR spectroscopy. A large systematic error was identified that affected the 1H atoms of the peptide bonds involved in hydrogen bonding with water molecules or peptide backbone atoms. This error was highly sensitive to changes in electrostatic parameters. Smaller errors affecting the 13Ca and 15N atoms were also detected. We believe these errors could be useful as metrics for comparing the force-fields and parameter sets used in MD simulation because they are directly tied to errors in atomic coordinates.
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82
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Tu T, Li Y, Su X, Meng K, Ma R, Wang Y, Yao B, Lin Z, Luo H. Probing the role of cation-π interaction in the thermotolerance and catalytic performance of endo-polygalacturonases. Sci Rep 2016; 6:38413. [PMID: 27929074 PMCID: PMC5143973 DOI: 10.1038/srep38413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
Understanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparent Tms increased by 0.6-3.9 °C) and catalytic efficiency (by up to 32-fold). Chromatogram analysis of the hydrolysis products indicated that a larger amount of shorter sugars were released from the polygalacturonic acid by these three mutants than by the wild-type. MD analysis of the enzyme-substrate complexes illustrated that the mutants with introduced cation-π interaction have modified conformations of catalytic crevice, which provide an enviable environment for the catalytic process. Moreover, the lower plasticity of T3 loop 2 at the edge of the subsite tunnel appears to recruit the reducing ends of oligogalacturonide into the active site tunnel and initiates new hydrolysis reactions. This study demonstrates the importance of cation-π interaction in protein conformation and provides a realistic strategy to enhance the thermotolerance and catalytic performance of endo-polygalacturonases.
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Affiliation(s)
- Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yeqing Li
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhemin Lin
- Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Beijing 100081, P. R. China
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83
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Serafeim AP, Salamanos G, Patapati KK, Glykos NM. Sensitivity of Folding Molecular Dynamics Simulations to Even Minor Force Field Changes. J Chem Inf Model 2016; 56:2035-2041. [PMID: 27681090 DOI: 10.1021/acs.jcim.6b00493] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We examine the sensitivity of folding molecular dynamics simulations on the choice between three variants of the same force field (the AMBER99SB force field and its ILDN, NMR-ILDN, and STAR-ILDN variants). Using two different peptide systems (a marginally stable helical peptide and a β-hairpin) and a grand total of more than 20 μs of simulation time we show that even relatively minor force field changes can lead to appreciable differences in the peptide folding behavior.
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Affiliation(s)
- Athanasia-Panagiota Serafeim
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
| | - Georgios Salamanos
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
| | - Kalliopi K Patapati
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace , University campus, 68100 Alexandroupolis, Greece
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84
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Öztürk MA, Pachov GV, Wade RC, Cojocaru V. Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome. Nucleic Acids Res 2016; 44:6599-613. [PMID: 27270081 PMCID: PMC5001602 DOI: 10.1093/nar/gkw514] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/06/2016] [Accepted: 05/30/2016] [Indexed: 01/25/2023] Open
Abstract
Linker histones are essential for DNA compaction in chromatin. They bind to nucleosomes in a 1:1 ratio forming chromatosomes. Alternative configurations have been proposed in which the globular domain of the linker histone H5 (gH5) is positioned either on- or off-dyad between the nucleosomal and linker DNAs. However, the dynamic pathways of chromatosome assembly remain elusive. Here, we studied the conformational plasticity of gH5 in unbound and off-dyad nucleosome-bound forms with classical and accelerated molecular dynamics simulations. We find that the unbound gH5 converts between open and closed conformations, preferring the closed form. However, the open gH5 contributes to a more rigid chromatosome and restricts the motion of the nearby linker DNA through hydrophobic interactions with thymidines. Moreover, the closed gH5 opens and reorients in accelerated simulations of the chromatosome. Brownian dynamics simulations of chromatosome assembly, accounting for a range of amplitudes of nucleosome opening and different nucleosome DNA sequences, support the existence of both on- and off-dyad binding modes of gH5 and reveal alternative, sequence and conformation-dependent chromatosome configurations. Taken together, these findings suggest that the conformational dynamics of linker histones and nucleosomes facilitate alternative chromatosome configurations through an interplay between induced fit and conformational selection.
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Affiliation(s)
- Mehmet Ali Öztürk
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg 69118, Germany The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), Heidelberg University, Heidelberg 69120, Germany
| | - Georgi V Pachov
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg 69118, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg 69118, Germany Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Heidelberg 69120, Germany Interdisciplinary Center for Scientific Computing (IWR), Heidelberg 69120, Germany
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cellular and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster 48149, Germany Center for Multiscale Theory and Computation, Westfälische Wilhelms University, Münster 48149, Germany
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85
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Molecular dynamics study on inhibition mechanism of CDK-2 and GSK-3β by CHEMBL272026 molecule. Struct Chem 2016. [DOI: 10.1007/s11224-016-0803-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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86
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Li S, Andrews CT, Frembgen-Kesner T, Miller MS, Siemonsma SL, Collingsworth TD, Rockafellow IT, Ngo NA, Campbell BA, Brown RF, Guo C, Schrodt M, Liu YT, Elcock AH. Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field. J Chem Theory Comput 2016; 11:1315-29. [PMID: 26579777 DOI: 10.1021/ct5010966] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Understanding the intrinsic conformational preferences of amino acids and the extent to which they are modulated by neighboring residues is a key issue for developing predictive models of protein folding and stability. Here we present the results of 441 independent explicit-solvent MD simulations of all possible two-residue peptides that contain the 20 standard amino acids with histidine modeled in both its neutral and protonated states. (3)J(HNHα) coupling constants and δ(Hα) chemical shifts calculated from the MD simulations correlate quite well with recently published experimental measurements for a corresponding set of two-residue peptides. Neighboring residue effects (NREs) on the average (3)J(HNHα) and δ(Hα) values of adjacent residues are also reasonably well reproduced, with the large NREs exerted experimentally by aromatic residues, in particular, being accurately captured. NREs on the secondary structure preferences of adjacent amino acids have been computed and compared with corresponding effects observed in a coil library and the average β-turn preferences of all amino acid types have been determined. Finally, the intrinsic conformational preferences of histidine, and its NREs on the conformational preferences of adjacent residues, are both shown to be strongly affected by the protonation state of the imidazole ring.
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Affiliation(s)
- Shuxiang Li
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | | | - Mark S Miller
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Stephen L Siemonsma
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | | | - Isaac T Rockafellow
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Nguyet Anh Ngo
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Brady A Campbell
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Reid F Brown
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Chengxuan Guo
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Michael Schrodt
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Yu-Tsan Liu
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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87
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Wray R, Iscla I, Gao Y, Li H, Wang J, Blount P. Dihydrostreptomycin Directly Binds to, Modulates, and Passes through the MscL Channel Pore. PLoS Biol 2016; 14:e1002473. [PMID: 27280286 PMCID: PMC4900634 DOI: 10.1371/journal.pbio.1002473] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 05/04/2016] [Indexed: 12/23/2022] Open
Abstract
The primary mechanism of action of the antibiotic dihydrostreptomycin is binding to and modifying the function of the bacterial ribosome, thus leading to decreased and aberrant translation of proteins; however, the routes by which it enters the bacterial cell are largely unknown. The mechanosensitive channel of large conductance, MscL, is found in the vast majority of bacterial species, where it serves as an emergency release valve rescuing the cell from sudden decreases in external osmolarity. While it is known that MscL expression increases the potency of dihydrostreptomycin, it has remained unclear if this effect is due to a direct interaction. Here, we use a combination of genetic screening, MD simulations, and biochemical and mutational approaches to determine if dihydrostreptomycin directly interacts with MscL. Our data strongly suggest that dihydrostreptomycin binds to a specific site on MscL and modifies its conformation, thus allowing the passage of K+ and glutamate out of, and dihydrostreptomycin into, the cell.
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Affiliation(s)
- Robin Wray
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Irene Iscla
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ya Gao
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hua Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, China
| | - Junmei Wang
- Green Center for Systems Biology and Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Paul Blount
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
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88
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Lee JY, Kinch LN, Borek DM, Wang J, Wang J, Urbatsch IL, Xie XS, Grishin NV, Cohen JC, Otwinowski Z, Hobbs HH, Rosenbaum DM. Crystal structure of the human sterol transporter ABCG5/ABCG8. Nature 2016; 533:561-4. [PMID: 27144356 PMCID: PMC4964963 DOI: 10.1038/nature17666] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 03/15/2016] [Indexed: 02/08/2023]
Abstract
ATP binding cassette (ABC) transporters play critical roles in maintaining sterol balance in higher eukaryotes. The ABCG5/ABCG8 heterodimer (G5G8) mediates excretion of neutral sterols in liver and intestines. Mutations disrupting G5G8 cause sitosterolaemia, a disorder characterized by sterol accumulation and premature atherosclerosis. Here we use crystallization in lipid bilayers to determine the X-ray structure of human G5G8 in a nucleotide-free state at 3.9 Å resolution, generating the first atomic model of an ABC sterol transporter. The structure reveals a new transmembrane fold that is present in a large and functionally diverse superfamily of ABC transporters. The transmembrane domains are coupled to the nucleotide-binding sites by networks of interactions that differ between the active and inactive ATPases, reflecting the catalytic asymmetry of the transporter. The G5G8 structure provides a mechanistic framework for understanding sterol transport and the disruptive effects of mutations causing sitosterolaemia.
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Affiliation(s)
- Jyh-Yeuan Lee
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Lisa N Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Dominika M Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jin Wang
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Junmei Wang
- Cecil &Ida Green Center for Molecular, Computational and Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ina L Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas 79430, USA
| | - Xiao-Song Xie
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Nikolai V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jonathan C Cohen
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Helen H Hobbs
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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89
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Mohanty P, Bhatnagar S. Structural basis of focal adhesion targeting domain-mediated signaling in cardiac hypertrophy. J Recept Signal Transduct Res 2016; 37:38-50. [DOI: 10.3109/10799893.2016.1155067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Pallavi Mohanty
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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90
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Díaz N, Suárez D. Role of the Protonation State on the Structure and Dynamics of Albumin. J Chem Theory Comput 2016; 12:1972-88. [DOI: 10.1021/acs.jctc.5b01001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Natalia Díaz
- C/Julián
Clavería
8. Dpto. de Química Física y Analítica, Universidad de Oviedo, Oviedo, 33006 Asturias, Spain
| | - Dimas Suárez
- C/Julián
Clavería
8. Dpto. de Química Física y Analítica, Universidad de Oviedo, Oviedo, 33006 Asturias, Spain
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91
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Fu W, Chen L, Wang Z, Zhao C, Chen G, Liu X, Dai Y, Cai Y, Li C, Zhou J, Liang G. Determination of the binding mode for anti-inflammatory natural product xanthohumol with myeloid differentiation protein 2. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:455-63. [PMID: 26869767 PMCID: PMC4737557 DOI: 10.2147/dddt.s98466] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
It is recognized that myeloid differentiation protein 2 (MD-2), a coreceptor of toll-like receptor 4 (TLR4) for innate immunity, plays an essential role in activation of the lipopolysaccharide signaling pathway. MD-2 is known as a neoteric and suitable therapeutical target. Therefore, there is great interest in the development of a potent MD-2 inhibitor for anti-inflammatory therapeutics. Several studies have reported that xanthohumol (XN), an anti-inflammatory natural product from hops and beer, can block the TLR4 signaling by binding to MD-2 directly. However, the interaction between MD-2 and XN remains unknown. Herein, our work aims at characterizing interactions between MD-2 and XN. Using a combination of experimental and theoretical modeling analysis, we found that XN can embed into the hydrophobic pocket of MD-2 and form two stable hydrogen bonds with residues ARG-90 and TYR-102 of MD-2. Moreover, we confirmed that ARG-90 and TYR-102 were two necessary residues during the recognition process of XN binding to MD-2. Results from this study identified the atomic interactions between the MD-2 and XN, which will contribute to future structural design of novel MD-2-targeting molecules for the treatment of inflammatory diseases.
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Affiliation(s)
- Weitao Fu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Lingfeng Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Zhe Wang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Chengwei Zhao
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Gaozhi Chen
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Xing Liu
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Yuanrong Dai
- Department of Respiratory Medicine, the Second Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, People's Republic of China
| | - Yuepiao Cai
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Chenglong Li
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China; Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Ohio State University, Columbus, OH, USA
| | - Jianmin Zhou
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
| | - Guang Liang
- Chemical Biology Research Center, School of Pharmaceutical Sciences, Wenzhou, Zhejiang, People's Republic of China
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92
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Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J 2016; 108:1153-64. [PMID: 25762327 DOI: 10.1016/j.bpj.2014.12.047] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 12/23/2014] [Accepted: 12/29/2014] [Indexed: 11/24/2022] Open
Abstract
Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular generalized Born (GB) implicit-solvent model, as implemented in the AMBER package. We systematically investigate small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size. The speedups in conformational sampling for GB relative to PME simulations, are highly system- and problem-dependent. Where the simulation temperatures for PME and GB are the same, the corresponding speedups are approximately onefold (small conformational changes), between ∼1- and ∼100-fold (large changes), and approximately sevenfold (mixed case). The effects of temperature on speedup and free-energy landscapes, which may differ substantially between the solvent models, are discussed in detail for the case of miniprotein folding. In addition to speeding up conformational sampling, due to algorithmic differences, the implicit solvent model can be computationally faster for small systems or slower for large systems, depending on the number of solute and solvent atoms. For the conformational changes considered here, the combined speedups are approximately twofold, ∼1- to 60-fold, and ∼50-fold, respectively, in the low solvent viscosity regime afforded by the implicit solvent. For all the systems studied, 1) conformational sampling speedup increases as Langevin collision frequency (effective viscosity) decreases; and 2) conformational sampling speedup is mainly due to reduction in solvent viscosity rather than possible differences in free-energy landscapes between the solvent models.
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Affiliation(s)
| | | | - Ross C Walker
- San Diego Supercomputer Center and Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California
| | - Alexey V Onufriev
- Department of Computer Science, Virginia Tech, Blacksburg, Virginia; Department of Physics, Virginia Tech, Blacksburg, Virginia.
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93
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Pham GH, Rana ASJB, Korkmaz EN, Trang VH, Cui Q, Strieter ER. Comparison of native and non-native ubiquitin oligomers reveals analogous structures and reactivities. Protein Sci 2016; 25:456-71. [PMID: 26506216 DOI: 10.1002/pro.2834] [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: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 12/11/2022]
Abstract
Ubiquitin (Ub) chains regulate a wide range of biological processes, and Ub chain connectivity is a critical determinant of the many regulatory roles that this post-translational modification plays in cells. To understand how distinct Ub chains orchestrate different biochemical events, we and other investigators have developed enzymatic and non-enzymatic methods to synthesize Ub chains of well-defined length and connectivity. A number of chemical approaches have been used to generate Ub oligomers connected by non-native linkages; however, few studies have examined the extent to which non-native linkages recapitulate the structural and functional properties associated with native isopeptide bonds. Here, we compare the structure and function of Ub dimers bearing native and non-native linkages. Using small-angle X-ray scattering (SAXS) analysis, we show that scattering profiles for the two types of dimers are similar. Moreover, using an experimental structural library and atomistic simulations to fit the experimental SAXS profiles, we find that the two types of Ub dimers can be matched to analogous structures. An important application of non-native Ub oligomers is to probe the activity and selectivity of deubiquitinases. Through steady-state kinetic analyses, we demonstrate that different families of deubiquitinases hydrolyze native and non-native isopeptide linkages with comparable efficiency and selectivity. Considering the significant challenges associated with building topologically diverse native Ub chains, our results illustrate that chains harboring non-native linkages can serve as surrogate substrates for explorations of Ub function.
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Affiliation(s)
- Grace H Pham
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Ambar S J B Rana
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - E Nihal Korkmaz
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Vivian H Trang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Eric R Strieter
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706
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94
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Kaminský J, Jensen F. Conformational Interconversions of Amino Acid Derivatives. J Chem Theory Comput 2016; 12:694-705. [PMID: 26691979 DOI: 10.1021/acs.jctc.5b00911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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95
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Estácio SG, Martiniano HFMC, Faísca PFN. Thermal unfolding simulations of NBD1 domain variants reveal structural motifs associated with the impaired folding of F508del-CFTR. MOLECULAR BIOSYSTEMS 2016; 12:2834-48. [DOI: 10.1039/c6mb00193a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The deletion of phenylalanine 508 reshapes the conformational space of the NBD1 domain that populates unique intermediate states that provide insights into the molecular events that underlie the impaired folding of F508del-NBD1.
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Affiliation(s)
- Sílvia G. Estácio
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Hugo F. M. C. Martiniano
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - Patrícia F. N. Faísca
- BioISI – Biosystems & Integrative Sciences Institute
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
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96
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Li DW, Brüschweiler R. Protocol To Make Protein NMR Structures Amenable to Stable Long Time Scale Molecular Dynamics Simulations. J Chem Theory Comput 2015; 10:1781-7. [PMID: 26580385 DOI: 10.1021/ct4010646] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A robust protocol for the treatment of NMR protein structures is presented that makes them amenable to long time scale molecular dynamics (MD) simulations that are stable. The protocol embeds an NMR structure in a native low energy region of the recently developed ff99SB_φψ(g24;CS) molecular mechanics force field. Extended MD trajectories that start from these structures show good consistency with proton-proton nuclear Overhauser effect data, and they reproduce NMR chemical shift data better than the original NMR structures as is demonstrated for four protein systems. Moreover, for all proteins studied here the simulations spontaneously approach the X-ray crystal structures, thereby improving the effective resolution of the initial structural models.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrument Center and Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center and Department of Chemistry and Biochemistry, The Ohio State University , Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry and National High Magnetic Field Laboratory, Florida State University , Tallahassee, Florida 32306, United States
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97
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Baltzis AS, Glykos NM. Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data. Protein Sci 2015; 25:587-96. [PMID: 26609791 DOI: 10.1002/pro.2850] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/22/2015] [Accepted: 11/15/2015] [Indexed: 12/31/2022]
Abstract
The villin headpiece helical subdomain (HP36) is one of the best known model systems for computational studies of fast-folding all-α miniproteins. HP21 is a peptide fragment-derived from HP36-comprising only the first and second helices of the full domain. Experimental studies showed that although HP21 is mostly unfolded in solution, it does maintain some persistent native-like structure as indicated by the analysis of NMR-derived chemical shifts. Here we compare the experimental data for HP21 with the results obtained from a 15-μs long folding molecular dynamics simulation performed in explicit water and with full electrostatics. We find that the simulation is in good agreement with the experiment and faithfully reproduces the major experimental findings, namely that (a) HP21 is disordered in solution with <10% of the trajectory corresponding to transiently stable structures, (b) the most highly populated conformer is a native-like structure with an RMSD from the corresponding portion of the HP36 crystal structure of <1 Å, (c) the simulation-derived chemical shifts-over the whole length of the trajectory-are in reasonable agreement with the experiment giving reduced χ(2) values of 1.6, 1.4, and 0.8 for the Δδ(13) C(α) , Δδ(13) CO, and Δδ(13) C(β) secondary shifts, respectively (becoming 0.8, 0.7, and 0.3 when only the major peptide conformer is considered), and finally, (d) the secondary structure propensity scores are in very good agreement with the experiment and clearly indicate the higher stability of the first helix. We conclude that folding molecular dynamics simulations can be a useful tool for the structural characterization of even marginally stable peptides.
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Affiliation(s)
- Athanasios S Baltzis
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece
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98
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Chen J. Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born Models. J Chem Theory Comput 2015; 6:2790-803. [PMID: 26616080 DOI: 10.1021/ct100251y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The generalized Born (GB) theory is a prime choice for implicit treatment of solvent that provides a favorable balance between efficiency and accuracy for reliable simulation of protein conformational equilibria. In GB, the dielectric boundary is a key physical property that needs to be properly described. While it is widely accepted that the molecular surface (MS) should provide the most physical description, most existing GB models are based on van der Waals (vdW)-like surfaces for computational simplicity and efficiency. A simple and effective approximation to molecular volume is explored here using atom-centered dielectric functions within the context of a generalized Born model with simple switching (GBSW). The new model, termed GBSW/MS2, is as efficient as the original vdW-like-surface-based GBSW model, but is able to reproduce the Born radii calculated from the "exact" Poisson-Boltzmann theory with a correlation of 0.95. More importantly, examination of the potentials of mean force of hydrogen-bonding and charge-charge interactions demonstrates that GBSW/MS2 correctly captures the first desolvation peaks, a key signature of true MS. Physical parameters including atomic input radii and peptide backbone torsion were subsequently optimized on the basis of solvation free energies of model compounds, potentials of mean force of their interactions, and conformational equilibria of a set of helical and β-hairpin model peptides. The resulting GBSW/MS2 protein force field reasonably recapitulates the structures and stabilities of these model peptides. Several remaining limitations and possible future developments are also discussed.
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Affiliation(s)
- Jianhan Chen
- Department of Biochemistry, Kansas State University, Manhattan, Kansas 66506
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99
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Kumar A, Campitelli P, Thorpe MF, Ozkan SB. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins 2015; 83:2279-92. [PMID: 26476100 DOI: 10.1002/prot.24947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/11/2015] [Accepted: 09/29/2015] [Indexed: 12/26/2022]
Abstract
The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled.
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Affiliation(s)
- Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - M F Thorpe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona.,Rudolf Peierls Center for Theoretical Physics, University of Oxford, Oxford, OX1 3NP, United Kingdom
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
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100
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Meral D, Toal S, Schweitzer-Stenner R, Urbanc B. Water-Centered Interpretation of Intrinsic pPII Propensities of Amino Acid Residues: In Vitro-Driven Molecular Dynamics Study. J Phys Chem B 2015; 119:13237-51. [PMID: 26418575 DOI: 10.1021/acs.jpcb.5b06281] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amino acid residues of unfolded peptides in water sample only a few basins in the Ramachandran plot, including prominent polyproline II-like (pPII) conformations. Dynamics of guest residues, X, in GXG peptides in water were recently reported to be dominated by pPII and β-strand-like (β) conformations, resulting in an enthalpy-entropy compensation at ∼300 K. Using molecular dynamics (MD) in explicit solvent, we here examine pPII and β conformational ensembles of 15 guest residues in GXG peptides, quantify local orientation of water around their side chains through novel water orientation plots, and study their hydration and hydrogen bonding properties. We show that pPII and β ensembles are characterized by distinct water orientations: pPII ensembles are associated with an increased population of water oriented in parallel to the side chain surface whereas β ensembles exhibit more heterogeneous water orientations. The backbone hydration is significantly higher in pPII than in β ensembles. Importantly, pPII to β hydration differences and the solvent accessible surface area of Cβ hydrogens both correlate with experimental pPII propensities. We propose that pPII conformations are stabilized by a local, hydrogen-bonded clathrate-like water structure and that residue-specific intrinsic pPII propensities reflect distinct abilities of side chains to template this water structure.
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Affiliation(s)
- Derya Meral
- Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | - Siobhan Toal
- Department of Chemistry, Drexel University , Philadelphia, Pennsylvania 19104, United States
| | | | - Brigita Urbanc
- Department of Physics, Drexel University , Philadelphia, Pennsylvania 19104, United States.,Faculty of Mathematics and Physics, University of Ljubljana , 1000 Ljubljana, Slovenia
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