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Sperotto RA, Hrmova M, Graether SP, Timmers LFSM. Editorial: Structural bioinformatics and biophysical approaches for understanding the plant responses to biotic and abiotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:1012584. [PMID: 36161033 PMCID: PMC9507305 DOI: 10.3389/fpls.2022.1012584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Raul A. Sperotto
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Graduate Program in Plant Physiology, Federal University of Pelotas, Pelotas, Brazil
| | - Maria Hrmova
- Faculty of Sciences, Engineering and Technology, University of Adelaide, Adelaide, SA, Australia
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Steffen P. Graether
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada
| | - Luis Fernando S. M. Timmers
- Graduate Program in Biotechnology, University of Taquari Valley – Univates, Lajeado, Brazil
- Graduate Program in Medical Sciences, University of Taquari Valley – Univates, Lajeado, Brazil
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Panda G, Ray A. Comparative Structural and Dynamics Study of Free and gRNA-bound FnCas9 and SpCas9 Proteins. Comput Struct Biotechnol J 2022; 20:4172-4184. [PMID: 36016716 PMCID: PMC9389198 DOI: 10.1016/j.csbj.2022.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/25/2022] [Accepted: 07/25/2022] [Indexed: 12/04/2022] Open
Abstract
gRNA binding caused Cas9 to open up, exposing hydrophobic residues. Concerted domain movement was observed in both SpCas9 and FnCas9. gRNA binding led to decrease in helicity and increase in structural transitions. High binding affinity of FnCas9 with gRNA is mostly due to electrostatic interaction. Arginine-helix has shown a pivotal role in the binding of gRNA in FnCas9 protein.
The introduction of CRISPR/Cas9 based gene editing has greatly accelerated therapeutic genome editing. However, the off-target DNA cleavage by CRISPR/Cas9 protein hampers its clinical translation, hindering its widespread use as a programmable genome editing tool. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates of on-target DNA cleavage. Here, we have compared the dynamics of a more specific naturally occurring Cas9 from Francisella novicida (FnCas9) to the most widely used, SpCas9 protein. Long-scale atomistic MD simulation of free and gRNA bound forms of both the Cas9 proteins was performed, and their domain rearrangements and binding affinity with gRNA were compared to decipher the possible reason behind the enhanced specificity of FnCas9 protein. The greater binding affinity with gRNA, high domain electrostatics, and more volatility of FnCas9 than SpCas9 may explain its increased specificity and lower tolerance for mismatches.
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Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes. Biomolecules 2020; 10:biom10081114. [PMID: 32731448 PMCID: PMC7463671 DOI: 10.3390/biom10081114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022] Open
Abstract
Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
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BP[dG]-induced distortions to DNA polymerase and DNA duplex: A detailed mechanism of BP adducts blocking replication. Food Chem Toxicol 2020; 140:111325. [DOI: 10.1016/j.fct.2020.111325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/15/2020] [Accepted: 04/04/2020] [Indexed: 01/21/2023]
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Wan H, Li J, Chang S, Lin S, Tian Y, Tian X, Wang M, Hu J. Probing the Behaviour of Cas1-Cas2 upon Protospacer Binding in CRISPR-Cas Systems using Molecular Dynamics Simulations. Sci Rep 2019; 9:3188. [PMID: 30816277 PMCID: PMC6395717 DOI: 10.1038/s41598-019-39616-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 01/29/2019] [Indexed: 12/26/2022] Open
Abstract
Adaptation in CRISPR-Cas systems enables the generation of an immunological memory to defend against invading viruses. This process is driven by foreign DNA spacer (termed protospacer) selection and integration mediated by Cas1-Cas2 protein. Recently, different states of Cas1-Cas2, in its free form and in complex with protospacer DNAs, were solved by X-ray crystallography. In this paper, molecular dynamics (MD) simulations are employed to study crystal structures of one free and two protospacer-bound Cas1-Cas2 complexes. The simulated results indicate that the protospacer binding markedly increases the system stability, in particular when the protospacer containing the PAM-complementary sequence. The hydrogen bond and binding free energy calculations explain that PAM recognition introduces more specific interactions to increase the cleavage activity of Cas1. By using principal component analysis (PCA) and intramolecular angle calculation, this study observes two dominant slow motions associated with the binding of Ca1-Cas2 to the protospacer and potential target DNAs respectively. The comparison of DNA structural deformation further implies a cooperative conformational change of Cas1-Cas2 and protospacer for the target DNA capture. We propose that this cooperativity is the intrinsic requirement of the CRISPR integration complex formation. This study provides some new insights into the understanding of CRISPR-Cas adaptation.
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Affiliation(s)
- Hua Wan
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Jianming Li
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Shuoxin Lin
- Department of Electrical and Computer Engineering, James Clark School of Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yuanxin Tian
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China
| | - Xuhong Tian
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China
| | - Meihua Wang
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianping Hu
- College of Pharmacy and Biological Engineering, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Chengdu University, Chengdu, 610106, China.
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Xu L, Li D, Ding J, Pan L, Ding X. Insight into tetrodotoxin blockade and resistance mechanisms of Na v 1.2 sodium channel by theoretical approaches. Chem Biol Drug Des 2018; 92:1445-1457. [PMID: 29673065 DOI: 10.1111/cbdd.13310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/08/2018] [Accepted: 03/17/2018] [Indexed: 11/30/2022]
Abstract
Nav 1.2, a member of voltage-gated sodium channels (Nav s) that are responsible for the generation and propagation of action potentials along the cell membrane, and play a vital role in the process of information transmission within the nervous system and muscle contraction, is preferentially expressed in the central nervous system. As a potent and selective blocker of Nav s, tetrodotoxin (TTX) has been extensively studied in biological and chemical sciences, whereas the detailed mechanism by which it blocks nine Nav 1 channel subtypes remain elusive. Despite the high structural similarity, the TTX metabolite 4,9-anhydro-TTX is 161 times less effective toward the mammalian Nav 1.2, which puzzled us to ask a question why such a subtle structural variation results in the largely binding affinity difference. In the current work, an integrated computational strategy, including homology modeling, induced fit docking, explicit-solvent MD simulations, and free energy calculations, was employed to investigate the binding mechanism and conformational determinants of TTX analogs. Based on the computational results, the H-bond interactions between C4-OH and C9-OH of TTX and the outer ring carboxylates of the selectivity-filter residues, and the cation-π interaction between the primary amine of guanidinium of TTX and Phe385 determine the difference of their binding affinities. Moreover, the computationally simulations were carried out for the D384N and E945K mutants of hNav 1.2-TTX, and the rank of the predicted binding free energies is in accordance with the experimental data. These observations provide a valuable model to design potent and selective neurotoxins of Nav 1.2 and shed light on the blocking mechanism of TTX to sodium channels.
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Affiliation(s)
- Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, China
| | - Dayu Li
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
| | - Junjie Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
| | - Li Pan
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
| | - Xiaoqin Ding
- Beijing Institute of Pharmaceutical Chemistry, Beijing, China
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Fan JR, Zhang HX, Mu YG, Zheng QC. Studying the recognition mechanism of TcaR and ssDNA using molecular dynamic simulations. J Mol Graph Model 2018; 80:67-75. [DOI: 10.1016/j.jmgm.2017.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 10/18/2022]
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Tian Y, Yu Y, Shen Y, Wan H, Chang S, Zhang T, Wan S, Zhang J. Molecular Simulation Studies on the Binding Selectivity of Type-I Inhibitors in the Complexes with ROS1 versus ALK. J Chem Inf Model 2017; 57:977-987. [PMID: 28318251 DOI: 10.1021/acs.jcim.7b00019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
ROS1 and ALK are promising targets of anticancer drugs for non-small-cell lung cancer. Since they have 49% amide acid sequence homology in the kinases domain and 77% identity at the ATP binding area, some ALK inhibitors also showed some significant responses for ROS1 in the clinical trial, such as the type-I binding inhibitor crizotinib and PF-06463922. As a newly therapeutic target, the selective ROS1 inhibitor is relatively rare. Moreover, the molecular basis for the selectivity of ROS1 versus ALK still remains unclear. In order to disclose the binding preference toward ROS1 over ALK and to aid the design of selective ROS1 inhibitors, the specific interactions and difference of conformational changes in the dual and selective ROS1/ALK inhibitors systems were investigated by molecular dynamics (MD) simulation and principle component analysis (PCA) in our work. Afterward, binding free energies (MM/GBSA) and binding free energies decomposition analysis indicated that the dominating effect of Van der Waals interaction drives the specific binding process of the type-I inhibitor, and residues of the P-loop and the DFG motif would play an important role in selectivity. On the basis of the modeling results, the new designed compound 14c was verified as a selective ROS1 inhibitor versus ALK, and SMU-B was a dual ROS1/ALK inhibitor by the kinase inhibitory study. These results are expected to facilitate the discovery and rational design of novel and specific ROS1 inhibitors.
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Affiliation(s)
- Yuanxin Tian
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Yonghuan Yu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Yudong Shen
- College of Food Sciences, South China Agricultural University , Guangzhou, 510642, People's Republic of China
| | - Hua Wan
- College of Mathematics and Informatics, South China Agricultural University , Guangzhou, 510642, People's Republic of China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology , Changzhou, 213001, People's Republic of China
| | - Tingting Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Shanhe Wan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
| | - Jiajie Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University , Guangzhou, 510515, People's Republic of China
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Zhou Q, Sun X, Xia X, Fan Z, Luo Z, Zhao S, Shakhnovich E, Liang H. Exploring the Mutational Robustness of Nucleic Acids by Searching Genotype Neighborhoods in Sequence Space. J Phys Chem Lett 2017; 8:407-414. [PMID: 28045264 DOI: 10.1021/acs.jpclett.6b02769] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To assess the mutational robustness of nucleic acids, many genome- and protein-level studies have been performed, where nucleic acids are treated as genetic information carriers and transferrers. However, the molecular mechanisms through which mutations alter the structural, dynamic, and functional properties of nucleic acids are poorly understood. Here we performed a SELEX in silico study to investigate the fitness distribution of the l-Arm-binding aptamer genotype neighborhoods. Two novel functional genotype neighborhoods were isolated and experimentally verified to have comparable fitness as the wild-type. The experimental aptamer fitness landscape suggests the mutational robustness is strongly influenced by the local base environment and ligand-binding mode, whereas bases distant from the binding pocket provide potential evolutionary pathways to approach the global fitness maximum. Our work provides an example of successful application of SELEX in silico to optimize an aptamer and demonstrates the strong sensitivity of mutational robustness to the site of genetic variation.
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Affiliation(s)
- Qingtong Zhou
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
| | - Xianbao Sun
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Xiaole Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University , Wuxi, Jiangsu 214122, China
| | - Zhou Fan
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200031, China
- University of Chinese Academy of Sciences , Beijing 100049, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Zhaofeng Luo
- School of Life Science, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University , Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University , Shanghai 201210, China
| | - Eugene Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China , Hefei, Anhui 230026, China
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Metal binding mediated conformational change of XPA protein:a potential cytotoxic mechanism of nickel in the nucleotide excision repair. J Mol Model 2016; 22:156. [PMID: 27307058 DOI: 10.1007/s00894-016-3017-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/26/2016] [Indexed: 12/13/2022]
Abstract
Nucleotide excision repair (NER) is a pivotal life process for repairing DNA nucleotide mismatch caused by chemicals, metal ions, radiation, and other factors. As the initiation step of NER, the xeroderma pigmentosum complementation group A protein (XPA) recognizes damaged DNA molecules, and recruits the replication protein A (RPA), another important player in the NER process. The stability of the Zn(2+)-chelated Zn-finger domain of XPA center core portion (i.e., XPA98-210) is the foundation of its biological functionality, while the displacement of the Zn(2+) by toxic metal ions (such as Ni(2+), a known human carcinogen and allergen) may impair the effectiveness of NER and hence elevate the chance of carcinogenesis. In this study, we first calculated the force field parameters for the bonded model in the metal center of the XPA98-210 system, showing that the calculated results, including charges, bonds, angles etc., are congruent with previously reported results measured by spectrometry experiments and quantum chemistry computation. Then, comparative molecular dynamics simulations using these parameters revealed the changes in the conformation and motion mode of XPA98-210 Zn-finger after the substitution of Zn(2+) by Ni(2+). The results showed that Ni(2+) dramatically disrupted the relative positions of the four Cys residues in the Zn-finger structure, forcing them to collapse from a tetrahedron into an almost planar structure. Finally, we acquired the binding mode of XPA98-210 with its ligands RPA70N and DNA based on molecular docking and structural alignment. We found that XPA98-210's Zn-finger domain primarily binds to a V-shaped cleft in RPA70N, while the cationic band in its C-terminal subdomain participates in the recognition of damaged DNA. In addition, this article sheds light on the multi-component interaction pattern among XPA, DNA, and other NER-related proteins (i.e., RPA70N, RPA70A, RPA70B, RPA70C, RPA32, and RPA14) based on previously reported structural biology information. Thus, we derived a putative cytotoxic mechanism associated with the nickel ion, where the Ni(2+) disrupts the conformation of the XPA Zn-finger, directly weakening its interaction with RPA70N, and thus lowering the effectiveness of the NER process. In sum, this work not only provides a theoretical insight into the multi-protein interactions involved in the NER process and potential cytotoxic mechanism associated with Ni(2+) binding in XPA, but may also facilitate rational anti-cancer drug design based on the NER mechanism.
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Xu L, Kong R, Zhu J, Sun H, Chang S. Unraveling the conformational determinants of LARP7 and 7SK small nuclear RNA by theoretical approaches. MOLECULAR BIOSYSTEMS 2016; 12:2613-21. [DOI: 10.1039/c6mb00252h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
LARP7, a member of the La-related proteins (LARPs), shares a conserved La module comprising the La-motif (LAM) and the RNA-recognition motif (RRM1), binding exclusively to the non-coding RNA 7SK.
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Affiliation(s)
- Lei Xu
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
| | - Jingyu Zhu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Huiyong Sun
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering
- School of Electrical and Information Engineering
- Jiangsu University of Technology
- Changzhou 213001
- China
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Potential Role of the Last Half Repeat in TAL Effectors Revealed by a Molecular Simulation Study. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8036450. [PMID: 27803930 PMCID: PMC5075638 DOI: 10.1155/2016/8036450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/16/2016] [Accepted: 08/24/2016] [Indexed: 11/30/2022]
Abstract
TAL effectors (TALEs) contain a modular DNA-binding domain that is composed of tandem repeats. In all naturally occurring TALEs, the end of tandem repeats is invariantly a truncated half repeat. To investigate the potential role of the last half repeat in TALEs, we performed comparative molecular dynamics simulations for the crystal structure of DNA-bound TALE AvrBs3 lacking the last half repeat and its modeled structure having the last half repeat. The structural stability analysis indicates that the modeled system is more stable than the nonmodeled system. Based on the principle component analysis, it is found that the AvrBs3 increases its structural compactness in the presence of the last half repeat. The comparison of DNA groove parameters of the two systems implies that the last half repeat also causes the change of DNA major groove binding efficiency. The following calculation of hydrogen bond reveals that, by stabilizing the phosphate binding with DNA at the C-terminus, the last half repeat helps to adopt a compact conformation at the protein-DNA interface. It further mediates more contacts between TAL repeats and DNA nucleotide bases. Finally, we suggest that the last half repeat is required for the high-efficient recognition of DNA by TALE.
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