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Chen H, Guo Y, Ye S, Zhang J, Zhang H, Liu N, Zhou R, Hou T, Xia H, Kang Y, Duan M. On the Dynamic Mechanism of Long-Flexible Fatty Acid Binding to Fatty Acid Binding Protein: Resolving the Long-Standing Debate. J Chem Inf Model 2023; 63:5232-5243. [PMID: 37574904 DOI: 10.1021/acs.jcim.3c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Fatty acids (FAs) are one of the essential energy sources for physiological processes, and they play a vital role in regulating immune and inflammatory responses, promoting cell differentiation and apoptosis, and inhibiting tumor growth. These functions are carried out by FA binding proteins (FABPs) that recognize and transport FAs. Although the crystal structure of the FA-FABPs complex has long been characterized, the mechanism behind FA binding and dissociation from FABP remains unclear. This study employed conventional MD simulations and enhanced sampling technologies to investigate the atomic-scale complexes of heart fatty acid binding proteins and stearic acid (SA). The results revealed two primary pathways for the binding or dissociation of the flexible long-chain ligand, with the orientation of the SA carboxyl head during dissociation determining the chosen path. Conformational changes in the portal region of FABP during the ligand binding/unbinding were found to be trivial, and the overturn of the ″cap″ or the unfolding of the α2 helix was not required. This study resolves the long-standing debate on the binding mechanism of SA with the long-flexible tail to FABP, which significantly improves the understanding of the transport mechanism of FABPs and the development of related therapeutic agents.
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Affiliation(s)
- Haiyi Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Yue Guo
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Shengqing Ye
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital, Zhejiang University School of medicine, Hangzhou 310058, China
| | - Jintu Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Haotian Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
| | - Na Liu
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Rui Zhou
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Hongguang Xia
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, Zhejiang, China
- Department of Biochemistry & Research Center of Clinical Pharmacy of the First Affiliated Hospital, Zhejiang University School of medicine, Hangzhou 310058, China
| | - Yu Kang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Mojie Duan
- National Centre for Magnetic Resonance in Wuhan, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, Hubei, China
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Feng L, Pérez-Sánchez H, Bai Q. Studying noncovalent or covalent bond problem between smoothened and cholesterol by molecular dynamics simulation and Markov state model. Phys Chem Chem Phys 2022; 24:19564-19575. [PMID: 35942902 DOI: 10.1039/d2cp01453j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Smoothened (SMO) is an attractive therapeutic target for the treatment and prevention of several malignant tumors of the nervous system. The crystal structure of SMO shows cholesterol interacts with residue Asp95 via the noncovalent bond. However, some studies indicate that cholesterol covalently binds to residue Asp95 of SMO. To study these contradictory results, we performed molecular dynamics (MD) simulations and Markov state model (MSM) on SMO in complex with noncovalent-bound and covalent-bound cholesterol. The MD simulated results showed that the noncovalent-bound cholesterol was extremely unstable around the position of residue Asp95 of SMO, while the covalent-bound cholesterol could keep the stable connection with residue Asp95 of SMO. The free energy landscape showed that noncovalent-bound cholesterol had more deep energy wells than covalent-bound cholesterol when it dynamically interacted with the extracellular domain of SMO crystal structure. The MSM results showed the noncovalent-bound cholesterol had more dynamic configuration transformation pathways than the covalent-bound cholesterol. These results theoretically revealed cholesterol should have a covalent bond with residue Asp95 if cholesterol could be stable in the near position of residue Asp95 of SMO. Our studies not only elucidate the covalent binding contradictory issue between cholesterol and residue Asp95 of SMO, but also supply helpful information for antagonists design of SMO.
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Affiliation(s)
- Liya Feng
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, Gansu, P. R. China
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Murcia, Spain.
| | - Qifeng Bai
- Key Lab of Preclinical Study for New Drugs of Gansu Province, Institute of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, Gansu, P. R. China
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Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW. Identification of Structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. J Biol Chem 2022; 298:101676. [PMID: 35122790 PMCID: PMC8892158 DOI: 10.1016/j.jbc.2022.101676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/31/2022] Open
Abstract
Fatty acid (FA) transfer proteins extract FA from membranes and sequester them to facilitate their movement through the cytosol. Detailed structural information is available for these soluble protein–FA complexes, but the structure of the protein conformation responsible for FA exchange at the membrane is unknown. Staphylococcus aureus FakB1 is a prototypical bacterial FA transfer protein that binds palmitate within a narrow, buried tunnel. Here, we define the conformational change from a “closed” FakB1 state to an “open” state that associates with the membrane and provides a path for entry and egress of the FA. Using NMR spectroscopy, we identified a conformationally flexible dynamic region in FakB1, and X-ray crystallography of FakB1 mutants captured the conformation of the open state. In addition, molecular dynamics simulations show that the new amphipathic α-helix formed in the open state inserts below the phosphate plane of the bilayer to create a diffusion channel for the hydrophobic FA tail to access the hydrocarbon core and place the carboxyl group at the phosphate layer. The membrane binding and catalytic properties of site-directed mutants were consistent with the proposed membrane docked structure predicted by our molecular dynamics simulations. Finally, the structure of the bilayer-associated conformation of FakB1 has local similarities with mammalian FA binding proteins and provides a conceptual framework for how these proteins interact with the membrane to create a diffusion channel from the FA location in the bilayer to the protein interior.
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Affiliation(s)
- Jessica M Gullett
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Maxime G Cuypers
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R Grace
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shashank Pant
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chitra Subramanian
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Charles O Rock
- Departments of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Stephen W White
- Departments of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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Zhang Q, Zhao N, Meng X, Yu F, Yao X, Liu H. The prediction of protein-ligand unbinding for modern drug discovery. Expert Opin Drug Discov 2021; 17:191-205. [PMID: 34731059 DOI: 10.1080/17460441.2022.2002298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Drug-target thermodynamic and kinetic information have perennially important roles in drug design. The prediction of protein-ligand unbinding, which can provide important kinetic information, in experiments continues to face great challenges. Uncovering protein-ligand unbinding through molecular dynamics simulations has become efficient and inexpensive with the progress and enhancement of computing power and sampling methods. AREAS COVERED In this review, various sampling methods for protein-ligand unbinding and their basic principles are firstly briefly introduced. Then, their applications in predicting aspects of protein-ligand unbinding, including unbinding pathways, dissociation rate constants, residence time and binding affinity, are discussed. EXPERT OPINION Although various sampling methods have been successfully applied in numerous systems, they still have shortcomings and deficiencies. Most enhanced sampling methods require researchers to possess a wealth of prior knowledge of collective variables or reaction coordinates. In addition, most systems studied at present are relatively simple, and the study of complex systems in real drug research remains greatly challenging. Through the combination of machine learning and enhanced sampling methods, prediction accuracy can be further improved, and some problems encountered in complex systems also may be solved.
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Affiliation(s)
| | - Nannan Zhao
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaoxiao Meng
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Fansen Yu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
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The Observation of Ligand-Binding-Relevant Open States of Fatty Acid Binding Protein by Molecular Dynamics Simulations and a Markov State Model. Int J Mol Sci 2019; 20:ijms20143476. [PMID: 31311155 PMCID: PMC6678811 DOI: 10.3390/ijms20143476] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 12/21/2022] Open
Abstract
As a member of the fatty acids transporter family, the heart fatty acid binding proteins (HFABPs) are responsible for many important biological activities. The binding mechanism of fatty acid with FABP is critical to the understanding of FABP functions. The uncovering of binding-relevant intermediate states and interactions would greatly increase our knowledge of the binding process. In this work, all-atom molecular dynamics (MD) simulations were performed to characterize the structural properties of nativelike intermediate states. Based on multiple 6 μs MD simulations and Markov state model (MSM) analysis, several "open" intermediate states were observed. The transition rates between these states and the native closed state are in good agreement with the experimental measurements, which indicates that these intermediate states are binding relevant. As a common property in the open states, the partially unfolded α2 helix generates a larger portal and provides the driving force to facilitate ligand binding. On the other side, there are two kinds of open states for the ligand-binding HFABP: one has the partially unfolded α2 helix, and the other has the looser β-barrel with disjointing βD-βE strands. Our results provide atomic-level descriptions of the binding-relevant intermediate states and could improve our understanding of the binding mechanism.
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Tran DP, Kitao A. Dissociation Process of a MDM2/p53 Complex Investigated by Parallel Cascade Selection Molecular Dynamics and the Markov State Model. J Phys Chem B 2019; 123:2469-2478. [PMID: 30645121 DOI: 10.1021/acs.jpcb.8b10309] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Recently, we efficiently generated dissociation pathways of a protein-ligand complex without applying force bias with parallel cascade selection molecular dynamics (PaCS-MD) and showed that PaCS-MD in combination with the Markov state model (MSM) yielded a binding free energy comparable to experimental values. In this work, we applied the same procedure to a complex of MDM2 protein and the transactivation domain of p53 protein (TAD-p53), the latter of which is known to be very flexible in the unbound state. Using 30 independent MD simulations in PaCS-MD, we successfully generated 25 dissociation pathways of the complex, which showed complete or partial unfolding of the helical region of TAD-p53 during the dissociation process within an average simulation time of 154.8 ± 46.4 ns. The standard binding free energy obtained in combination with one-dimensional-, three-dimensional (3D)- or Cα-MSM was in good agreement with those determined experimentally. Using 3D-MSM based on the center of mass position of TAD-p53 relative to MDM2, the dissociation rate constant was calculated, which was comparable to those measured experimentally. Cα-MSM based on all Cα coordinates of TAD-p53 reproduced the experimentally measured standard binding free energy, and dissociation and association rate constants. We conclude that the combination of PaCS-MD and MSM offers an efficient computational procedure to calculate binding free energies and kinetic rates.
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Affiliation(s)
- Duy Phuoc Tran
- School of Life Sciences and Technology , Tokyo Institute of Technology , 2-12-1, Ookayama , Meguro-ku, Tokyo 152-8550 , Japan
| | - Akio Kitao
- School of Life Sciences and Technology , Tokyo Institute of Technology , 2-12-1, Ookayama , Meguro-ku, Tokyo 152-8550 , Japan
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Li Y, Dong Z. Effect of Clustering Algorithm on Establishing Markov State Model for Molecular Dynamics Simulations. J Chem Inf Model 2016; 56:1205-15. [DOI: 10.1021/acs.jcim.6b00181] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yan Li
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
| | - Zigang Dong
- The Hormel Institute, University of Minnesota, Austin, Minnesota 55912, United States
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