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Xu N, Wang Z, Xu Z, Zhang X, Jin Z, Dong X, Lin D. Experimentally verified flexible molecular docking and dynamic simulation of aptamer with intracellular proteins based on direct DNA 3D structure prediction. Int J Biol Macromol 2025; 316:144318. [PMID: 40383336 DOI: 10.1016/j.ijbiomac.2025.144318] [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: 12/23/2024] [Revised: 04/19/2025] [Accepted: 05/15/2025] [Indexed: 05/20/2025]
Abstract
Despite the rising spotlight on biotargeting aptamers, their mechanism of regulating cellular functions remained elusive due to lack of systematic method to investigate their intracellular behavior. This study systematically established a complete workflow including DNA secondary and 3D structure prediction, flexibilization, docking, experimental validation, and molecular dynamic (MD) simulation. RNAfold was demonstrated to provide more accurate ssDNA secondary structure predictions and compatibility for flexible docking. Feasibility of a novel direct prediction tool of DNA 3D structure, 3dDNA, has first been proven with similar reliability and better data stability in flexible docking compared to indirect prediction by RNAComposer. Flexible docking by AutoDock Vina exhibited higher reliability, while rigid docking was less reliable. Docking results were influenced by secondary and 3D structures, but the proteins' inherent affinity to nucleic acids was the key determinant. Aptamer bound to proteins with non-specificity (KD > 100 nM) and affinities (Rmax) exponentially correlated to flexible docking scores, necessitating further MD validation and identification of binding sites. Via the established workflow, binding sites of stem cell-recruiting aptamer Apt-19s on its known target (ALPL) was identified, Sec24B was first screened as its potential intracellular targets, providing theoretical guidance and feasible methodology for future exploration of aptamer biotargeting mechanisms.
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Affiliation(s)
- Nuoyan Xu
- Shanghai University of Medicine and Health Sciences, Shanghai 201318, PR China
| | - Zeying Wang
- Department of Prosthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, National Clinical Research Center for Oral Diseases, Beijing Key Laboratory of Digital Stomatology, Beijing 100081, PR China
| | - Zhenglin Xu
- Shanghai University of Medicine and Health Sciences, Shanghai 201318, PR China
| | - Xiaofan Zhang
- Shanghai University of Medicine and Health Sciences, Shanghai 201318, PR China
| | - Zhiyi Jin
- Shanghai University of Medicine and Health Sciences, Shanghai 201318, PR China
| | - Xian Dong
- Shanghai University of Medicine and Health Sciences, Shanghai 201318, PR China
| | - Dan Lin
- Shanghai University of Medicine and Health Sciences, Shanghai 201318, PR China; Shanghai University of Medicine and Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, PR China.
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Sahoo BR, Bekier ME, Liu Z, Kocman V, Stoddard AK, Anantharamaiah GM, Nowick J, Fierke CA, Wang Y, Ramamoorthy A. Structural Interaction of Apolipoprotein A-I Mimetic Peptide with Amyloid-β Generates Toxic Hetero-oligomers. J Mol Biol 2019; 432:1020-1034. [PMID: 31866295 DOI: 10.1016/j.jmb.2019.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/27/2019] [Accepted: 12/01/2019] [Indexed: 01/21/2023]
Abstract
Apolipoproteins are involved in pathological conditions of Alzheimer's disease (AD), and it has been reported that truncated apolipoprotein fragments and β-amyloid (Aβ) peptides coexist as neurotoxic heteromers within the plaques. Therefore, it is important to investigate these complexes at the molecular level to better understand their properties and roles in the pathology of AD. Here, we present a mechanistic insight into such heteromerization using a structurally homologue apolipoprotein fragment of apoA-I (4F) complexed with Aβ(M1-42) and characterize their toxicity. The 4F peptide slows down the aggregation kinetics of Aβ(M1-42) by constraining its structural plasticity. NMR and CD experiments identified 4F-Aβ(M1-42) heteromers comprised of unstructured Aβ(M1-42) and helical 4F. A uniform two-fold reduction in 15N/1H NMR signal intensities of Aβ(M1-42) with no observable chemical shift perturbation indicated the formation of a large complex, which was further confirmed by diffusion NMR experiments. Microsecond-scale atomistic molecular dynamics simulations showed that 4F interaction with Aβ(M1-42) is electrostatically driven and induces unfolding of Aβ(M1-42). Neurotoxicity profiling of Aβ(M1-42) complexed with 4F confirms a significant reduction in cell viability and neurite growth. Thus, the molecular architecture of heteromerization between 4F and Aβ(M1-42) discovered in this study provides evidence toward our understanding of the role of apolipoproteins or their truncated fragments in exacerbating AD pathology.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Michael E Bekier
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Zichen Liu
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Vojc Kocman
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - Andrea K Stoddard
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA
| | - G M Anantharamaiah
- Department of Medicine, University of Alabama at Birmingham Medical Center, Birmingham, AL, 35294, USA
| | - James Nowick
- Department of Chemistry, University of California-Irvine, Irvine, CA, 92697-2025, USA
| | - Carol A Fierke
- Department of Chemistry, University of Texas A&M, College Station, TX, 77843-3255, USA
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109-1085, USA
| | - Ayyalusamy Ramamoorthy
- Biophysics and Department of Chemistry, Biomedical Engineering, Macromolecular Science and Engineering, University of Michigan, Ann Arbor, MI, 48109-1055, USA.
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Rout AK, Paramanik S, Dehury B, Acharya V, Swain HS, Pradhan SK, Behera B, Pati SK, Behera BK, Das BK. Elucidating the molecular interaction of Zebrafish (Danio rerio) peptidoglycan recognition protein 2 with diaminopimelic acid and lysine type peptidoglycans using in silico approaches. J Biomol Struct Dyn 2019; 38:3687-3699. [DOI: 10.1080/07391102.2019.1666742] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Ajaya Kumar Rout
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sunanda Paramanik
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Budheswar Dehury
- Department of Chemistry, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Varsha Acharya
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Himanshu Sekhar Swain
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Sukanta Kumar Pradhan
- Department of Bioinformatics, Orissa University of Agriculture and Technology, Bhubaneswar, India
| | - Bhaskar Behera
- Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore, India
| | - Soumen Kumar Pati
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, Haringhata, India
| | - Bijay Kumar Behera
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
| | - Basanta Kumar Das
- Biotechnology Laboratory, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, India
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Abstract
Molecular docking is the major computational technique employed in the early stages of computer-aided drug discovery. The availability of free software to carry out docking simulations of protein-ligand systems has allowed for an increasing number of studies using this technique. Among the available free docking programs, we discuss the use of ArgusLab ( http://www.arguslab.com/arguslab.com/ArgusLab.html ) for protein-ligand docking simulation. This easy-to-use computational tool makes use of a genetic algorithm as a search algorithm and a fast scoring function that allows users with minimal experience in the simulations of protein-ligand simulations to carry out docking simulations. In this chapter, we present a detailed tutorial to perform docking simulations using ArgusLab.
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Affiliation(s)
- Gabriela Bitencourt-Ferreira
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil
| | - Walter Filgueira de Azevedo
- Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.
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Wang C, Greene D, Xiao L, Qi R, Luo R. Recent Developments and Applications of the MMPBSA Method. Front Mol Biosci 2018; 4:87. [PMID: 29367919 PMCID: PMC5768160 DOI: 10.3389/fmolb.2017.00087] [Citation(s) in RCA: 399] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method.
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Affiliation(s)
- Changhao Wang
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - D'Artagnan Greene
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Li Xiao
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
| | - Ruxi Qi
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, University of California, Irvine, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, United States
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, CA, United States
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Characterization of the ligand binding of PGRP-L in half-smooth tongue sole ( Cynoglossus semilaevis ) by molecular dynamics and free energy calculation. ELECTRON J BIOTECHN 2018. [DOI: 10.1016/j.ejbt.2017.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Sahoo BR, Fujiwara T. Conformational states of HAMP domains interacting with sensory rhodopsin membrane systems: an integrated all-atom and coarse-grained molecular dynamics simulation approach. MOLECULAR BIOSYSTEMS 2017; 13:193-207. [PMID: 27901172 DOI: 10.1039/c6mb00730a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1.15 M salt). Comparative analysis in the ground and intermediate state conformations reveals substantial inter-HAMP interactions in the intermediate state with uniform clockwise (+10° to +30°) and counterclockwise (-20° to -40°) rotations in the α1 helix and the α2 helix of the monomer, respectively. Low temperature and low salt environments (283 K and 0.15 M) significantly affect srII-htrII binding affinity in both states with unusual helix bending. The distinguished control cable, knob-into-holes packing and piston-like movements in HAMP helices are found in the intermediate state complex. The N-terminal htrII (159 residues) coupled with srII yields a binding energy (ΔGbind) of -309.22, -436.53 and -331.11 kJ mol-1 in the MM/PBSA calculation for the NphtrII homodimer, the NpsrII-htrII ground state conformation and the NpsrII-htrII intermediate state conformation, respectively. Only the HAMP1 domain shows a very low ΔGbind value (-21.03 kJ mol-1) for the ground state in comparison to that for the intermediate state (-54.68 kJ mol-1). The structural analysis highlights the key residues that include Y199srII, T189srII, E43htrII, T86htrII, M100htrII, E116htrII, E126htrII and S130htrII for complex stabilization and signal transduction.
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Affiliation(s)
- Bikash Ranjan Sahoo
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, 5650871, Japan.
| | - Toshimichi Fujiwara
- Laboratory of Molecular Biophysics, Institute for Protein Research, Osaka University, 5650871, Japan.
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Qi Z, Meng F, Zhang Q, Wang Z, Qiao G, Xu W, Shao R, Chen C. Structural insights into ligand binding of PGRP1 splice variants in Chinese giant salamander (Andrias davidianus) from molecular dynamics and free energy calculations. J Mol Model 2017; 23:135. [PMID: 28341996 DOI: 10.1007/s00894-017-3315-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 03/13/2017] [Indexed: 11/24/2022]
Abstract
Peptidoglycan (PGN) recognition proteins (PGRPs) are important pattern recognition receptors of the innate immune system. A number of PGRP splicing variants produced by alternative splicing of PGRP genes have been reported. However, several important aspects of interactions between PGRP splice variants and their ligands are still unclear. In the present study, three dimensional models of salamander PGRP1 (adPGRP1) and its splice variant (adPGRP1a) were constructed, and their key amino acids involved in interacting with PGNs were analyzed. The results revealed that adPGRP1a has a typical PGRPs structure containing five β-sheets and four α-helices, while adPGRP1 contained five β-sheets and only one α-helix due to the lack of 51 amino acids at its C-terminus. Molecular docking revealed that van der Waals and Coulombic interactions contributed to interactions in the protein-ligand complex. Further binding energy of adPGRP-PGNs computed by the MM-PBSA method revealed that adPGRP1a and adPGRP1 might selectively bind to different PGNs; the former might selectively bind Dap-type PGNs and the latter both types of PGNs. In addition, the binding energy of each residue of adPGRP1a and adPGRP1 was also calculated, revealing that residues involved in the interaction of protein-ligand complexes were different in adPGRP1a and adPGRP1. These results provided a first insight into the potential basis for interaction between PGRPs generated by alternative splicing and PGN derivatives.
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Affiliation(s)
- Zhitao Qi
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China. .,Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China.
| | - Fancui Meng
- Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, China
| | - Qihuan Zhang
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Zisheng Wang
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Guo Qiao
- Key Laboratory of Aquaculture and Ecology of Coastal Pool in Jiangsu Province, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Wei Xu
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China
| | - Rong Shao
- Jiangsu Key Laboratory of Biochemistry and Biotechnology of Marine Wetland, Yancheng Institute of Technology, Yancheng, 224051, Jiangsu, China.
| | - Chenglung Chen
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan, Republic of China
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