1
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Wu K, Li D, Xiu P, Ji B, Diao J. O-GlcNAcylation inhibits the oligomerization of alpha-synuclein by declining intermolecular hydrogen bonds through a steric effect. Phys Biol 2020; 18:016002. [DOI: 10.1088/1478-3975/abb6dc] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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2
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Gardner JM, Abrams CF. Energetics of Flap Opening in HIV-1 Protease: String Method Calculations. J Phys Chem B 2019; 123:9584-9591. [PMID: 31640343 PMCID: PMC7375464 DOI: 10.1021/acs.jpcb.9b08348] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
HIV-1 protease (PR) is the viral protein responsible for virion maturation, and its mechanisms of action remain incompletely understood. PR is dimeric and contains two flexible, symmetry-related flaps, which act as a gate to inhibit access to the binding pocket and hold the polypeptide substrate in the binding pocket once bound. Wide flap opening, a conformational change assumed to be necessary for substrate binding, is a rare event in the closed and bound form. In this study, we use molecular dynamics (MD) simulations and advanced MD techniques including temperature acceleration and string method in collective variables to study the conformational changes associated with substrate unbinding of both wild-type and F99Y mutant PR. The F99Y mutation is shown via MD to decouple the closing of previously unrecognized distal pockets from substrate unbinding. To determine whether or not the F99Y mutation affects the energetic cost of wide flap opening, we use string method in collective variables to determine the minimum free-energy mechanism for wide flap opening in concert with distal pocket closing. The results indicate that the major energetic cost in flap opening is disengagement of the two flap-tip Ile50 residues from each other and is not affected by the F99Y mutation.
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Affiliation(s)
- Jasmine M Gardner
- Dept. of Chemical and Biological Engineering , Drexel University , 3141 Chestnut Street , Philadelphia , Pennsylvania 19104 , United States
- Department of Chemistry - BMC , Uppsala University , Box 576, 751 23 Uppsala , Sweden
| | - Cameron F Abrams
- Dept. of Chemical and Biological Engineering , Drexel University , 3141 Chestnut Street , Philadelphia , Pennsylvania 19104 , United States
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3
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Li D, Ji B. Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2019. [DOI: 10.1016/j.medntd.2019.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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4
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Jia X, Hu X, Wang W, Du C. Non-covalent loading of ionic liquid-functionalized nanoparticles for bovine serum albumin: experiments and theoretical analysis. RSC Adv 2019; 9:19114-19120. [PMID: 35516866 PMCID: PMC9065314 DOI: 10.1039/c9ra02265a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/03/2019] [Indexed: 11/26/2022] Open
Abstract
Biomacromolecule-based nanomaterials have attracted much attention due to their excellent function in sensing, catalysis, medicine, biology and recognition. In this work, a silane-coupling ionic liquid, 1-(3-trimethoxysilylpropyl)-3-methylimidazolium chloride ([TMIM]Cl), was synthesized and applied to prepare ionic liquid-functionalized nanoparticles (SiO2@IL) using surface grafting technology. By employing multiple non-covalent interactions, including electrostatic interactions, hydrogen bonding and π–π stacking, the obtained functional nanoparticles were able to bind bovine serum albumin (BSA) with strong binding affinity, which has been illustrated through experiments and theoretical calculations. Moreover, the stability of SiO2@IL further demonstrated that it is promising in applications for biomacromolecule immobilization. Non-covalent binding between nanosilica and bovine serum albumin has been illustrated by experiments and theoretical calculations.![]()
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Affiliation(s)
- Xingang Jia
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- P. R China
- College of Chemistry and Chemical Engineering
| | - Xiaoling Hu
- School of Natural and Applied Science
- Northwestern Polytechnical University
- Xi'an 710072
- P. R China
| | - Wenzhen Wang
- College of Chemistry and Chemical Engineering
- Xi'an Shiyou University
- Xi'an 710065
- P. R. China
| | - Chunbao Du
- College of Chemistry and Chemical Engineering
- Xi'an Shiyou University
- Xi'an 710065
- P. R. China
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5
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Du C, Hu X, Cheng Y, Gao J, Zhang YW, Su K, Li Z, Zhang N, Chang N, Zeng K. Synergetically understanding the interaction between nano/microspheres and peptide for controllable drug loading via experimental and theoretical approaches. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2018; 83:169-176. [DOI: 10.1016/j.msec.2017.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 12/28/2022]
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6
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Bu B, Tong X, Li D, Hu Y, He W, Zhao C, Hu R, Li X, Shao Y, Liu C, Zhao Q, Ji B, Diao J. N-Terminal Acetylation Preserves α-Synuclein from Oligomerization by Blocking Intermolecular Hydrogen Bonds. ACS Chem Neurosci 2017; 8:2145-2151. [PMID: 28741930 DOI: 10.1021/acschemneuro.7b00250] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The abnormal aggregation of α-synuclein (α-Syn) is closely associated with Parkinson's disease. Different post-translational modifications of α-Syn have been identified and contribute distinctly in α-Syn aggregation and cytotoxicity. Recently, α-Syn was reported to be N-terminally acetylated in cells, yet the functional implication of this modification, especially in α-Syn oligomerization, remains unclear. By using a solid-state nanopore system, we found that N-terminal acetylation can significantly decrease α-Syn oligomerization. Replica-exchange molecular dynamics simulations further revealed that addition of an acetyl group at the N-terminus disrupts intermolecular hydrogen bonds, which slows down the initial α-Syn oligomerization. Our finding highlights the essential role of N-terminal acetylation of α-Syn in preserving its native conformation against pathological aggregation.
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Affiliation(s)
- Bing Bu
- Biomechanics
and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
| | - Xin Tong
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Dechang Li
- Biomechanics
and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
| | - Yachong Hu
- Department
of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States
- Key
Laboratory of Biomedical Information Engineering of the Ministry of
Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Wangxiao He
- Key
Laboratory of Biomedical Information Engineering of the Ministry of
Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Chunyu Zhao
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rui Hu
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Xiaoqing Li
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Yongping Shao
- Key
Laboratory of Biomedical Information Engineering of the Ministry of
Education, School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Cong Liu
- Interdisciplinary
Research Center on Biology and Chemistry, Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qing Zhao
- State
Key Laboratory for Mesoscopic Physics and Electron Microscopy Laboratory,
School of Physics, Peking University, Beijing 100871, China
| | - Baohua Ji
- Biomechanics
and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, China
| | - Jiajie Diao
- Department
of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States
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7
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Liu Z, Gao J, Zhang G, Cheng Y, Zhang YW. From two-dimensional nano-sheets to roll-up structures: expanding the family of nanoscroll. NANOTECHNOLOGY 2017; 28:385704. [PMID: 28653657 DOI: 10.1088/1361-6528/aa7bf8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The carbon nanoscroll (CNS), a spiral structure rolled up from a flat graphene sheet, has attracted significant attention due to its large surface area and broad electrochemical window. Despite the rapid emergence of many new two-dimensional (2D) materials, studies on nanoscrolls beyond CNS, however, remain limited. In this work, we combine first-principles calculations and theoretical analyses to determine the stable configuration of nanoscrolls constructed from several 2D materials, including graphene, h-BN, MoS2, graphyne, phosphorene, and graphene oxide. Our study shows that the inner radius of these nanoscrolls ranges from 0.36-2.3 nm, significantly expanding that of CNS (about 1.2 nm). In addition, it is shown that the difference between the inner and outer pressures of nanoscrolls can be used to tune their core sizes. Furthermore, the effect of interlayer friction is found to be significant and may play a dominant role in determining the core sizes. The present study not only expands the nanoscroll family, but also enriches the understanding of nanoscrolls in terms of the effects of pressure and friction, thus widening the application range of nanoscrolls as nano-actuators, ion/water channels, nano-sensors, and hydrogen/energy storage devices, etc.
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Affiliation(s)
- Zhigang Liu
- Institute of High Performance Computing, A*STAR, Singapore 138632
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8
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Bu B, Tian Z, Li D, Ji B. High Transmembrane Voltage Raised by Close Contact Initiates Fusion Pore. Front Mol Neurosci 2016; 9:136. [PMID: 28018169 PMCID: PMC5145871 DOI: 10.3389/fnmol.2016.00136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2016] [Indexed: 12/21/2022] Open
Abstract
Membrane fusion lies at the heart of neuronal communication but the detailed mechanism of a critical step, fusion pore initiation, remains poorly understood. Here, through atomistic molecular dynamics simulations, a transient pore formation induced by a close contact of two apposed bilayers is firstly reported. Such a close contact gives rise to a high local transmembrane voltage that induces the transient pore formation. Through simulations on two apposed bilayers fixed at a series of given distances, the process in which two bilayers approaching to each other under the pulling force from fusion proteins for membrane fusion was mimicked. Of note, this close contact induced fusion pore formation is contrasted with previous reported electroporation under ad hoc applied external electric field or ionic charge in-balance. We show that the transmembrane voltage increases with the decrease of the distance between the bilayers. Below a critical distance, depending on the lipid composition, the local transmembrane voltage can be sufficiently high to induce the transient pores. The size of these pores is approximately 1~2 nm in diameter, which is large enough to allow passing of neurotransmitters. A resealing of the membrane pores resulting from the neutralization of the transmembrane voltage by ions through the pores was then observed. We also found that the membrane tension can either prolong the lifetime of transient pores or cause them to dilate for full collapse. This result provides a possible mechanism for fusion pore formation and regulation of pathway of fusion process.
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Affiliation(s)
- Bing Bu
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology Beijing, China
| | - Zhiqi Tian
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, Center for Mitochondrial Biology and Medicine, School of Life Science and Technology, Xi'an Jiaotong University Xi'an, China
| | - Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology Beijing, China
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology Beijing, China
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9
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Li D, Liu MS, Ji B. Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case. Biophys J 2016; 109:647-60. [PMID: 26244746 DOI: 10.1016/j.bpj.2015.06.059] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 06/19/2015] [Accepted: 06/29/2015] [Indexed: 12/22/2022] Open
Abstract
Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems.
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Affiliation(s)
- Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing, China.
| | - Ming S Liu
- CSIRO - Digital Productivity Flagship, Clayton South, Victoria, Australia; Monash Institute of Medical Research, Clayton, Victoria, Australia.
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing, China.
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10
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Liu Z, Casey TM, Blackburn ME, Huang X, Pham L, de Vera IMS, Carter JD, Kear-Scott JL, Veloro AM, Galiano L, Fanucci GE. Pulsed EPR characterization of HIV-1 protease conformational sampling and inhibitor-induced population shifts. Phys Chem Chem Phys 2016; 18:5819-31. [PMID: 26489725 PMCID: PMC4758878 DOI: 10.1039/c5cp04556h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The conformational landscape of HIV-1 protease (PR) can be experimentally characterized by pulsed-EPR double electron-electron resonance (DEER). For this characterization, nitroxide spin labels are attached to an engineered cysteine residue in the flap region of HIV-1 PR. DEER distance measurements from spin-labels contained within each flap of the homodimer provide a detailed description of the conformational sampling of apo-enzyme as well as induced conformational shifts as a function of inhibitor binding. The distance distribution profiles are further interpreted in terms of a conformational ensemble scheme that consists of four unique states termed "curled/tucked", "closed", "semi-open" and "wide-open" conformations. Reported here are the DEER results for a drug-resistant variant clinical isolate sequence, V6, in the presence of FDA approved protease inhibitors (PIs) as well as a non-hydrolyzable substrate mimic, CaP2. Results are interpreted in the context of the current understanding of the relationship between conformational sampling, drug resistance, and kinetic efficiency of HIV-1PR as derived from previous DEER and kinetic data for a series of HIV-1PR constructs that contain drug-pressure selected mutations or natural polymorphisms. Specifically, these collective results support the notion that inhibitor-induced closure of the flaps correlates with inhibitor efficiency and drug resistance. This body of work also suggests DEER as a tool for studying conformational sampling in flexible enzymes as it relates to function.
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Affiliation(s)
- Zhanglong Liu
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Thomas M Casey
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Mandy E Blackburn
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Xi Huang
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Linh Pham
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Ian Mitchelle S de Vera
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jeffrey D Carter
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Jamie L Kear-Scott
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Angelo M Veloro
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Luis Galiano
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, PO BOX 117200, Gainesville, FL 32611-7200, USA.
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11
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Sengupta B, Yadav R, Sen P. Startling temperature effect on proteins when confined: single molecular level behaviour of human serum albumin in a reverse micelle. Phys Chem Chem Phys 2016; 18:14350-8. [DOI: 10.1039/c6cp00452k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The present work reports the effect of confinement, and temperature therein, on the conformational fluctuation dynamics of domain-I of human serum albumin (HSA) by fluorescence correlation spectroscopy (FCS).
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Affiliation(s)
- Bhaswati Sengupta
- Department of Chemistry, Indian Institute of Technology Kanpur
- Kanpur
- India
| | - Rajeev Yadav
- Department of Chemistry, Indian Institute of Technology Kanpur
- Kanpur
- India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur
- Kanpur
- India
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12
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Cheng Y, Koh LD, Li D, Ji B, Zhang Y, Yeo J, Guan G, Han MY, Zhang YW. Peptide-Graphene Interactions Enhance the Mechanical Properties of Silk Fibroin. ACS APPLIED MATERIALS & INTERFACES 2015; 7:21787-96. [PMID: 26364925 DOI: 10.1021/acsami.5b05615] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Studies reveal that biomolecules can form intriguing molecular structures with fascinating functionalities upon interaction with graphene. Then, interesting questions arise. How does silk fibroin interact with graphene? Does such interaction lead to an enhancement in its mechanical properties? In this study, using large-scale molecular dynamics simulations, we first examine the interaction of graphene with several typical peptide structures of silk fibroin extracted from different domains of silk fibroin, including pure amorphous (P1), pure crystalline (P2), a segment from N-terminal (P3), and a combined amorphous and crystalline segment (P4), aiming to reveal their structural modifications. Our study shows that graphene can have intriguing influences on the structures formed by the peptides with sequences representing different domains of silk fibroin. In general, for protein domains with stable structure and strong intramolecular interaction (e.g., β-sheets), graphene tends to compete with the intramolecular interactions and thus weaken the interchain interaction and reduce the contents of β-sheets. For the silk domains with random or less ordered secondary structures and weak intramolecular interactions, graphene tends to enhance the stability of peptide structures; in particular, it increases the contents of helical structures. Thereafter, tensile simulations were further performed on the representative peptides to investigate how such structure modifications affect their mechanical properties. It was found that the strength and resilience of the peptides are enhanced through their interaction with graphene. The present work reveals interesting insights into the interactions between silk peptides and graphene, and contributes in the efforts to enhance the mechanical properties of silk fibroin.
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Affiliation(s)
- Yuan Cheng
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
| | - Leng-Duei Koh
- Institute of Materials Research and Engineering, A*STAR , Singapore 117602, Singapore
- Department of Biomedical Engineering, National University of Singapore , Singapore 117575, Singapore
| | - Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology , Beijing 100081, China
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology , Beijing 100081, China
| | - Yingyan Zhang
- School of Computing, Engineering, and Mathematics, Western Sydney University , Locked Bag 1797, Penrith NSW 2751, Australia
| | - Jingjie Yeo
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
| | - Guijian Guan
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
- Institute of Materials Research and Engineering, A*STAR , Singapore 117602, Singapore
| | - Ming-Yong Han
- Institute of Materials Research and Engineering, A*STAR , Singapore 117602, Singapore
- Department of Biomedical Engineering, National University of Singapore , Singapore 117575, Singapore
| | - Yong-Wei Zhang
- Institute of High Performance Computing, A*STAR , Singapore 138632, Singapore
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13
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Romanowska J, Kokh DB, Fuller JC, Wade RC. Computational Approaches for Studying Drug Binding Kinetics. THERMODYNAMICS AND KINETICS OF DRUG BINDING 2015. [DOI: 10.1002/9783527673025.ch11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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14
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McGee TD, Edwards J, Roitberg AE. pH-REMD Simulations Indicate That the Catalytic Aspartates of HIV-1 Protease Exist Primarily in a Monoprotonated State. J Phys Chem B 2014; 118:12577-85. [DOI: 10.1021/jp504011c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T. Dwight McGee
- Department
of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
| | - Jesse Edwards
- Department
of Chemistry, Florida Agricultural and Mechanical University, Tallahassee, Florida 32307, United States
| | - Adrian E. Roitberg
- Department
of Chemistry, Quantum Theory Project, University of Florida, Gainesville, Florida 32611, United States
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15
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Cheng Y, Koh LD, Li D, Ji B, Han MY, Zhang YW. On the strength of β-sheet crystallites of Bombyx mori silk fibroin. J R Soc Interface 2014; 11:20140305. [PMID: 24789564 PMCID: PMC4032545 DOI: 10.1098/rsif.2014.0305] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 04/08/2014] [Indexed: 11/12/2022] Open
Abstract
Silk fibroin, a natural multi-domain protein, has attracted great attention due to its superior mechanical properties such as ultra-high strength and stretchability, biocompatibility, as well as its versatile biodegradability and processability. It is mainly composed of β-sheet crystallites and amorphous domains. Although its strength is well known to be controlled by the dissociation of protein chains from β-sheet crystallites, the way that water as the solvent affects its strength and the reason that its theoretically predicted strength is several times higher than experimental measurement remain unclear. We perform all-atom molecular dynamics simulations on a β-sheet crystallite of Bombyx mori silk. We find that water solvent reduces the number and strength of hydrogen bonds between β-chains, and thus greatly weakens the strength of silk fibroin. By dissociating protein chains at different locations from the crystallite, we also find that the pulling strength for the interior chains is several times higher than that for the surface/corner chains, with the former being consistent with the theoretically predicted value, while the latter on par with the experimental value. It is shown that the weakest rupture strength controls the failure strength of silk fibre. Hence, this work sheds light on the role of water in the strength of silk fibroin and also provides clues on the origin of the strength difference between theory and experiment.
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Affiliation(s)
- Yuan Cheng
- Institute of High Performance Computing, A*STAR, Singapore 138632, Republic of Singapore
| | - Leng-Duei Koh
- Institute of Materials Research and Engineering, A*STAR, Singapore 117602, Republic of Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore 117576, Republic of Singapore
| | - Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Baohua Ji
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, Beijing 100081, People's Republic of China
| | - Ming-Yong Han
- Institute of Materials Research and Engineering, A*STAR, Singapore 117602, Republic of Singapore
- Department of Biomedical Engineering, National University of Singapore, Singapore 117576, Republic of Singapore
| | - Yong-Wei Zhang
- Institute of High Performance Computing, A*STAR, Singapore 138632, Republic of Singapore
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16
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Brut M, Estève A, Landa G, Djafari Rouhani M. Toward in silico biomolecular manipulation through static modes: atomic scale characterization of HIV-1 protease flexibility. J Phys Chem B 2014; 118:2821-30. [PMID: 24568689 DOI: 10.1021/jp4113156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Probing biomolecular flexibility with atomic-scale resolution is a challenging task in current computational biology for fundamental understanding and prediction of biomolecular interactions and associated functions. This paper makes use of the static mode method to study HIV-1 protease considered as a model system to investigate the full biomolecular flexibility at the atomic scale, the screening of active site biomechanical properties, the blind prediction of allosteric sites, and the design of multisite strategies to target deformations of interest. Relying on this single calculation run of static modes, we demonstrate that in silico predictive design of an infinite set of complex excitation fields is reachable, thanks to the storage of the static modes in a data bank that can be used to mimic single or multiatom contact and efficiently anticipate conformational changes arising from external stimuli. All along this article, we compare our results to data previously published and propose a guideline for efficient, predictive, and custom in silico experiments.
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Affiliation(s)
- Marie Brut
- CNRS , LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
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17
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Xia J, Deng NJ, Levy RM. NMR relaxation in proteins with fast internal motions and slow conformational exchange: model-free framework and Markov state simulations. J Phys Chem B 2013; 117:6625-34. [PMID: 23638941 DOI: 10.1021/jp400797y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Calculating NMR relaxation effects for proteins with dynamics on multiple time scales generally requires very long trajectories based on conventional molecular dynamics simulations. In this report, we have built Markov state models from multiple MD trajectories and used the resulting MSM to capture the very fast internal motions of the protein within a free energy basin on a time scale up to hundreds of picoseconds and the more than 3 orders of magnitude slower conformational exchange between macrostates. To interpret the relaxation data, we derive new equations using the model-free framework which includes two slowly exchanging macrostates, each of which also exhibits fast local motions. Using simulations of HIV-1 protease as an example, we show how the populations of slowly exchanging conformational states as well as order parameters for the different states can be determined from the NMR relaxation data.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, USA
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Li D, Liu MS, Ji B, Hwang KC, Huang Y. Identifying the molecular mechanics and binding dynamics characteristics of potent inhibitors to HIV-1 protease. Chem Biol Drug Des 2012; 80:440-54. [PMID: 22621379 DOI: 10.1111/j.1747-0285.2012.01417.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) is one of the primary inhibition targets for chemotherapy of AIDS because of its critical role in the replication cycle of the HIV. In this work, a combinatory coarse-grained and atomistic simulation method was developed for dissecting molecular mechanisms and binding process of inhibitors to the active site of HIV-1 PR, in which 35 typical inhibitors were trialed. We found that the molecular size and stiffness of the inhibitors and the binding energy between the inhibitors and PR play important roles in regulating the binding process. Comparatively, the smaller and more flexible inhibitors have larger binding energy and higher binding rates; they even bind into PR without opening the flaps. In contrast, the larger and stiffer inhibitors have lower binding energy and lower binding rate, and their binding is subjected to the opening and gating of the PR flaps. Furthermore, the components of binding free energy were quantified and analyzed by their dependence on the molecular size, structures, and hydrogen bond networks of inhibitors. Our results also deduce significant dynamics descriptors for determining the quantitative structure and property relationship in potent drug ligands for HIV-1 PR inhibition.
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Affiliation(s)
- Dechang Li
- Biomechanics and Biomaterials Laboratory, Department of Applied Mechanics, Beijing Institute of Technology, China
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19
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Deng NJ, Zheng W, Gallicchio E, Levy RM. Insights into the dynamics of HIV-1 protease: a kinetic network model constructed from atomistic simulations. J Am Chem Soc 2011; 133:9387-94. [PMID: 21561098 DOI: 10.1021/ja2008032] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The conformational dynamics in the flaps of HIV-1 protease plays a crucial role in the mechanism of substrate binding. We develop a kinetic network model, constructed from detailed atomistic simulations, to determine the kinetic mechanisms of the conformational transitions in HIV-1 PR. To overcome the time scale limitation of conventional molecular dynamics (MD) simulations, our method combines replica exchange MD with transition path theory (TPT) to study the diversity and temperature dependence of the pathways connecting functionally important states of the protease. At low temperatures the large-scale flap opening is dominated by a small number of paths; at elevated temperatures the transition occurs through many structurally heterogeneous routes. The expanded conformation in the crystal structure 1TW7 is found to closely mimic a key intermediate in the flap-opening pathways at low temperature. We investigated the different transition mechanisms between the semi-open and closed forms. The calculated relaxation times reveal fast semi-open ↔ closed transitions, and infrequently the flaps fully open. The ligand binding rate predicted from this kinetic model increases by 38-fold from 285 to 309 K, which is in general agreement with experiments. To our knowledge, this is the first application of a network model constructed from atomistic simulations together with TPT to analyze conformational changes between different functional states of a natively folded protein.
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Affiliation(s)
- Nan-jie Deng
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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Li D, Ji B, Hwang KC, Huang Y. Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket. PLoS One 2011; 6:e19268. [PMID: 21559397 PMCID: PMC3084818 DOI: 10.1371/journal.pone.0019268] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/25/2011] [Indexed: 11/18/2022] Open
Abstract
To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the protease takes crucial roles in the dissociation process. We showed that the hydrogen bond network in the cyclic urea inhibitors AHA001/XK263 is less stable than that of the approved inhibitor ABT538 because of their large differences in the structures of the networks. In the cyclic urea inhibitor bound complex, the hydrogen bonds often distribute at the flap tips and the active site. In contrast, there are additional accessorial hydrogen bonds formed at the lateral sides of the flaps and the active site in the ABT538 bound complex, which take crucial roles in stabilizing the hydrogen bond network. In addition, the water molecule W301 also plays important roles in stabilizing the hydrogen bond network through its flexible movement by acting as a collision buffer and helping the rebinding of hydrogen bonds at the flap tips. Because of its high stability, the hydrogen bond network of ABT538 complex can work together with the hydrophobic clusters to resist the dissociation, resulting in much lower dissociation rate constant than those of cyclic urea inhibitor complexes. This study may provide useful guidelines for design of novel potent inhibitors with optimized interactions.
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Affiliation(s)
- Dechang Li
- School of Aerospace, Department of Engineering Mechanics, Tsinghua University, Beijing, China
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Structure-based design of carbon nanotubes as HIV-1 protease inhibitors: atomistic and coarse-grained simulations. J Mol Graph Model 2010; 29:171-7. [PMID: 20580296 DOI: 10.1016/j.jmgm.2010.05.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Revised: 05/20/2010] [Accepted: 05/20/2010] [Indexed: 11/24/2022]
Abstract
Nanoparticles such as fullerenes and carbon nanotubes have been extensively studied for biomedical applications. In this paper, we report the design of carbon nanotubes as HIV-1 protease inhibitors. Docking and molecular dynamics calculations are performed using an atomistic model to explore the optimal interaction structure and free energy between the nanotube and HIV-1 protease. A coarse-grained model is then developed based on the atomistic model, allowing us to investigate the dynamic behaviors of the protease in the bound and unbound states. The dynamic process reveals that the carbon nanotube is able to bind to the active site of the protease and prevent the active flaps from opening up, thus blocking the function of the protease. This process is strongly influenced by the size of the nanotube. The binding of carbon nanotubes to an alternative binding site other than the active site is also explored. Therefore, carbon nanotube-based inhibitors have great potential for application as HIV-1 protease inhibitors.
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