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Li Y, Yang L, Yang LQ. Effects of intrinsically disordered regions in gp120 underlying HIV neutralization phenotypes. Biochem Biophys Res Commun 2024; 709:149830. [PMID: 38547606 DOI: 10.1016/j.bbrc.2024.149830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/18/2024] [Accepted: 03/24/2024] [Indexed: 04/13/2024]
Abstract
HIV envelope protein gp120 is considered a primary molecular determinant of viral neutralization phenotype due to its critical role in viral entry and immune evasion. The intrinsically disordered regions (IDRs) in gp120 are responsible for their extensive sequence variations and significant structural rearrangements. Despite HIV neutralization phenotype and sequence/structural information of gp120 have been experimentally characterized, there remains a gap in our understanding of the correlation between the viral phenotype and IDRs in gp120. Here, we combined machine learning (ML) techniques and molecular dynamics (MD) simulations to gain data-driven and molecule-mechanism insights into relationships between viral sequence, structure, and phenotypes from the perspective of IDRs in gp120. ML models, trained only on the length and disorder score of IDRs, achieved equivalent performance to the best baseline model using amino acid sequences to discriminate HIV neutralization phenotype, indicating that the lengths or disorder of specific IDRs are strongly related to HIV neutralization phenotypes. Comparative MD analysis reveals that gp120 with extreme neutralization phenotypes in multiple conformational states, especially some IDRs, exhibit significantly distinct structural dynamics, conformational flexibility, and thermodynamic distributions. Taken together, our study provided insights into the role of IDRs in gp120 responding to HIV neutralization phenotypes, which will advance the understanding of molecular mechanisms underlying viral function associated with HIV neutralization phenotype and help develop antiviral vaccines or drugs.
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Affiliation(s)
- Yi Li
- College of Mathematics and Computer Science, Dali University, Dali, China
| | - Li Yang
- College of Mathematics and Computer Science, Dali University, Dali, China
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali, China; Key Laboratory of Bioinformatics and Computational Biology, Department of Education of Yunnan Province, Dali University, Dali, China.
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2
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Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
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3
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Li Y, Guo Y, Cheng H, Zeng X, Zhang X, Sang P, Chen B, Yang L. Deciphering gp120 sequence variation and structural dynamics in
HIV
neutralization phenotype by molecular dynamics simulations and graph machine learning. Proteins 2022; 90:1413-1424. [DOI: 10.1002/prot.26322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/21/2022] [Accepted: 02/10/2022] [Indexed: 02/04/2023]
Affiliation(s)
- Yi Li
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Yu‐Chen Guo
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Hong‐Han Cheng
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Xin Zeng
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Xiao‐Ling Zhang
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Peng Sang
- College of Agriculture and Biological Science Dali University Dali Yunnan China
| | - Ben‐Hui Chen
- College of Mathematics and Computer Science Dali University Dali Yunnan China
| | - Li‐Quan Yang
- College of Agriculture and Biological Science Dali University Dali Yunnan China
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4
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Mechanistic Origin of Different Binding Affinities of SARS-CoV and SARS-CoV-2 Spike RBDs to Human ACE2. Cells 2022; 11:cells11081274. [PMID: 35455955 PMCID: PMC9032924 DOI: 10.3390/cells11081274] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 12/04/2022] Open
Abstract
The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein (RBDCoV2) has a higher binding affinity to the human receptor angiotensin-converting enzyme 2 (ACE2) than the SARS-CoV RBD (RBDCoV). Here, we performed molecular dynamics (MD) simulations, binding free energy (BFE) calculations, and interface residue contact network (IRCN) analysis to explore the mechanistic origin of different ACE2-binding affinities of the two RBDs. The results demonstrate that, when compared to the RBDCoV2-ACE2 complex, RBDCoV-ACE2 features enhanced dynamicsand inter-protein positional movements and increased conformational entropy and conformational diversity. Although the inter-protein electrostatic attractive interactions are the primary determinant for the high ACE2-binding affinities of both RBDs, the significantly enhanced electrostatic attractive interactions between ACE2 and RBDCoV2 determine the higher ACE2-binding affinity of RBDCoV2 than of RBDCoV. Comprehensive comparative analyses of the residue BFE components and IRCNs between the two complexes reveal that it is the residue changes at the RBD interface that lead to the overall stronger inter-protein electrostatic attractive force in RBDCoV2-ACE2, which not only tightens the interface packing and suppresses the dynamics of RBDCoV2-ACE2, but also enhances the ACE2-binding affinity of RBDCoV2. Since the RBD residue changes involving gain/loss of the positively/negatively charged residues can greatly enhance the binding affinity, special attention should be paid to the SARS-CoV-2 variants carrying such mutations, particularly those near or at the binding interfaces with the potential to form hydrogen bonds and/or salt bridges with ACE2.
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Bennett AL, Henderson R. HIV-1 Envelope Conformation, Allostery, and Dynamics. Viruses 2021; 13:852. [PMID: 34067073 PMCID: PMC8150877 DOI: 10.3390/v13050852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 11/16/2022] Open
Abstract
The HIV-1 envelope glycoprotein (Env) mediates host cell fusion and is the primary target for HIV-1 vaccine design. The Env undergoes a series of functionally important conformational rearrangements upon engagement of its host cell receptor, CD4. As the sole target for broadly neutralizing antibodies, our understanding of these transitions plays a critical role in vaccine immunogen design. Here, we review available experimental data interrogating the HIV-1 Env conformation and detail computational efforts aimed at delineating the series of conformational changes connecting these rearrangements. These studies have provided a structural mapping of prefusion closed, open, and transition intermediate structures, the allosteric elements controlling rearrangements, and state-to-state transition dynamics. The combination of these investigations and innovations in molecular modeling set the stage for advanced studies examining rearrangements at greater spatial and temporal resolution.
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Affiliation(s)
| | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA;
- Department of Medicine, Duke University, Durham, NC 27710, USA
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Zhang ZB, Xia YL, Dong GH, Fu YX, Liu SQ. Exploring the Cold-Adaptation Mechanism of Serine Hydroxymethyltransferase by Comparative Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:1781. [PMID: 33670090 PMCID: PMC7916883 DOI: 10.3390/ijms22041781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Cold-adapted enzymes feature a lower thermostability and higher catalytic activity compared to their warm-active homologues, which are considered as a consequence of increased flexibility of their molecular structures. The complexity of the (thermo)stability-flexibility-activity relationship makes it difficult to define the strategies and formulate a general theory for enzyme cold adaptation. Here, the psychrophilic serine hydroxymethyltransferase (pSHMT) from Psychromonas ingrahamii and its mesophilic counterpart, mSHMT from Escherichia coli, were subjected to μs-scale multiple-replica molecular dynamics (MD) simulations to explore the cold-adaptation mechanism of the dimeric SHMT. The comparative analyses of MD trajectories reveal that pSHMT exhibits larger structural fluctuations and inter-monomer positional movements, a higher global flexibility, and considerably enhanced local flexibility involving the surface loops and active sites. The largest-amplitude motion mode of pSHMT describes the trends of inter-monomer dissociation and enlargement of the active-site cavity, whereas that of mSHMT characterizes the opposite trends. Based on the comparison of the calculated structural parameters and constructed free energy landscapes (FELs) between the two enzymes, we discuss in-depth the physicochemical principles underlying the stability-flexibility-activity relationships and conclude that (i) pSHMT adopts the global-flexibility mechanism to adapt to the cold environment and, (ii) optimizing the protein-solvent interactions and loosening the inter-monomer association are the main strategies for pSHMT to enhance its flexibility.
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Affiliation(s)
- Zhi-Bi Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
- Yunnan Key Laboratory of Stem Cell and Regenerative Medicine & Biomedical Engineering Research Center, Kunming Medical University, Kunming 650500, China
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
| | - Guang-Heng Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
| | - Yun-Xin Fu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
- Human Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China; (Z.-B.Z.); (Y.-L.X.); (G.-H.D.)
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Li Y, Deng L, Liang J, Dong GH, Xia YL, Fu YX, Liu SQ. Molecular dynamics simulations reveal distinct differences in conformational dynamics and thermodynamics between the unliganded and CD4-bound states of HIV-1 gp120. Phys Chem Chem Phys 2020; 22:5548-5560. [PMID: 32119016 DOI: 10.1039/c9cp06706j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The entry of human immunodeficiency virus type I (HIV-1) into host cells is initiated by binding to the cell-surface receptor CD4, which induces a conformational transition of the envelope (Env) glycoprotein gp120 from the closed, unliganded state to the open, CD4-bound state. Despite many available structures in these two states, detailed aspects on the dynamics and thermodynamics of gp120 remain elusive. Here, we performed microsecond-scale (μs-scale) multiple-replica molecular dynamics (MD) simulations to explore the differences in the conformational dynamics, protein motions, and thermodynamics between the unliganded and CD4-bound/complexed forms of gp120. Comparative analyses of MD trajectories reveal that CD4 binding promotes the structural deviations/changes and conformational flexibility, loosens the structural packing, and complicates the molecular motions of gp120. Comparison of the constructed free energy landscapes (FELs) reveals that the CD4-complexed gp120 has more conformational substates, larger conformational entropy, and lower thermostability than the unliganded form. Therefore, the unliganded conformation represents a structurally and energetically stable "ground state" for the full-length gp120. The observed great increase in the mobility of V1/V2 and V3 along with their more versatile movement directions in the CD4-bound gp120 compared to the unliganded form suggests that their orientations with respect to each other and to the structural core determine the differences in the conformational dynamics and thermodynamics between the two gp120 forms. The results presented here provide a basis by which to better understand the functional and immunological properties of gp120 and, furthermore, to deploy appropriate strategies for the development of anti-HIV-1 drugs or vaccines.
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Affiliation(s)
- Yi Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China. and College of Mathematics and Computer Science, Dali University, Dali 671003, China
| | - Lei Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Jing Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Guang-Heng Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Yuan-Ling Xia
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China.
| | - Yun-Xin Fu
- Human Genetics Center and Division of Biostatistics, School of Public Health, The University of Texas Health Science Center, Houston, USA.
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan & School of Life Sciences, Yunnan University, Kunming 650091, China.
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Li Y, Guo YC, Zhang XL, Deng L, Sang P, Yang LQ, Liu SQ. CD4-binding obstacles in conformational transitions and allosteric communications of HIV gp120. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183217. [PMID: 32061646 DOI: 10.1016/j.bbamem.2020.183217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 01/30/2020] [Accepted: 02/05/2020] [Indexed: 01/07/2023]
Abstract
As the only exposed viral protein at the membrane surface of HIV, envelope glycoprotein gp120 is responsible for recognizing host cells and mediating virus-cell membrane fusion. Available structures of gp120 indicate that it exhibits two distinct conformational states, called closed and open states. Although experimental data demonstrates that CD4 binding stabilizes open state of gp120, detailed structural dynamics and kinetics of gp120 during this process remain elusive. Here, two open-state gp120 simulation systems, one without any ligands (ligand-free) and the other complexed with CD4 (CD4-bound), were subjected to microsecond-scale molecular dynamics simulations following the conformational transitions and allosteric pathways of gp120 evaluated by using the Markov state model and a network-based method, respectively. Our results provide an atomic-resolution description of gp120 conformational transitions, suggesting that gp120 is intrinsically dynamic from the open state to closed state, whereas CD4 binding blocks these transitions. Consistent with experimental structures, five metastable conformations with different orientations of the V1/V2 region and V3 loop have been extracted. The binding of CD4 significantly enhances allosteric communications from the CD4-binding site to V3 loop and β20-21 hairpin, resulting in high-affinity interactions with coreceptors and activation of the conformational transitions switcher, respectively. This study will facilitate the structural understanding of the CD4-binding effects on conformational transitions and allosteric pathways of gp120.
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Affiliation(s)
- Yi Li
- College of Mathematics and Computer Science, Dali University, Dali, China
| | - Yu-Chen Guo
- College of Mathematics and Computer Science, Dali University, Dali, China
| | - Xiao-Ling Zhang
- College of Mathematics and Computer Science, Dali University, Dali, China
| | - Lei Deng
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China
| | - Peng Sang
- College of Agriculture and Biological Science, Dali University, Dali, China
| | - Li-Quan Yang
- College of Agriculture and Biological Science, Dali University, Dali, China.
| | - Shu-Qun Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, China.
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Li Y, Zhang XL, Yuan X, Hou JC, Sang P, Yang LQ. Probing intrinsic dynamics and conformational transition of HIV gp120 by molecular dynamics simulation. RSC Adv 2020; 10:30499-30507. [PMID: 35516019 PMCID: PMC9056330 DOI: 10.1039/d0ra06416e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/07/2020] [Accepted: 08/04/2020] [Indexed: 11/21/2022] Open
Abstract
The HIV envelope glycoprotein gp120 has evolved two distinct conformational states to balance viral infection and immune escape. One is a closed state resistant to most neutralization antibodies, and the other is an open state responsible for the binding of the receptor and coreceptors. Although the structures of gp120 in these two conformational states have been determined, a detailed molecular mechanism involving intrinsic dynamics and conformational transition is still elusive. In this study, μs-scale molecular dynamics simulation is performed to probe molecular dynamics and conformational transition away from the open state and approach the closed state. Our results reveal that open gp120 shows a larger structural deviation, higher conformational flexibility, and more conformational diversity than the form in the closed state, providing a structural explanation for receptor or coreceptor affinity at the open state and the neutralization resistance of closed conformation. Seven regions with greatly decreased coupled motions in the open states have been observed by dynamic cross-correlation analysis, indicating that conformational transition can be mainly attributed to the relaxation of intrinsic dynamics. Three conformations characterized by the structural orientations of the V1/V2 region and the V3 loop, suggesting gp120 is intrinsically dynamic from the open state to the closed state. Taken together, these findings shed light on the understanding of the conformational control mechanism of HIV. The HIV envelope glycoprotein gp120 has evolved two distinct conformational states to balance viral infection and immune escape.![]()
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Affiliation(s)
- Yi Li
- College of Mathematics and Computer Science
- Dali University
- Dali
- China
- Science and Education Department
| | - Xiao-Ling Zhang
- College of Mathematics and Computer Science
- Dali University
- Dali
- China
| | - Xue Yuan
- College of Mathematics and Computer Science
- Dali University
- Dali
- China
| | - Jiang-Chun Hou
- Science and Education Department
- Second People's Hospital of Yunnan Province
- Kunming
- China
| | - Peng Sang
- College of Agriculture and Biological Science
- Dali University
- Dali
- China
| | - Li-Quan Yang
- College of Agriculture and Biological Science
- Dali University
- Dali
- China
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