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Thirumal Kumar D, Udhaya Kumar S, Nishaat Laeeque AS, Apurva Abhay S, Bithia R, Magesh R, Kumar M, Zayed H, George Priya Doss C. Computational model to analyze and characterize the functional mutations of NOD2 protein causing inflammatory disorder – Blau syndrome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 120:379-408. [DOI: 10.1016/bs.apcsb.2019.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Agrahari AK, Doss GPC, Siva R, Magesh R, Zayed H. Molecular insights of the G2019S substitution in LRRK2 kinase domain associated with Parkinson's disease: A molecular dynamics simulation approach. J Theor Biol 2019; 469:163-171. [PMID: 30844370 DOI: 10.1016/j.jtbi.2019.03.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/15/2019] [Accepted: 03/01/2019] [Indexed: 12/19/2022]
Abstract
The G2019S substitution in the Leucine-rich repeat kinase 2 (LRRK2) is significantly associated with Parkinson's disease (PD). This substitution was identified in both familial and sporadic forms of PD with a higher frequency. Few computational studies have reported the impact of G2019S substitution on inhibitors of the kinase domain of LRRK2. However, no computational study deeply investigated the possible impact of the G2019S substitution on the kinase domain in its Apo conformation. Therefore, in this study, we used 200 ns molecular dynamic simulation using the GROMACS 5.1.4 package software to investigate the impact of the G2019S substitution on the structure of the kinase domain of LRRK2. Our results indicate that the G2019S substitution affects the dynamics and stability of LRRK2 by decreasing the flexibility and increasing the compactness of the kinase domain and showing its tendency to be in an active conformation for long time interval because of the high energy barrier between active and inactive conformation. This study predicts the molecular pathogenicity mechanism of the G2019S on patients with PD and provides a potential platform for developing therapeutics for patients with PD that harbor this amino acid substitution.
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Affiliation(s)
- Ashish Kumar Agrahari
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - George Priya C Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India.
| | - R Siva
- Department of Integrative Biology, School of Biosciences and Technology, VIT, Vellore, Tamil Nadu 632014, India
| | - R Magesh
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (SRIHER), Deemed to be University (DU), Porur, Chennai, 600116, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar.
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A computational model to predict the structural and functional consequences of missense mutations in O6-methylguanine DNA methyltransferase. DNA Repair (Amst) 2019; 115:351-369. [DOI: 10.1016/bs.apcsb.2018.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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Thirumal Kumar D, Eldous HG, Mahgoub ZA, George Priya Doss C, Zayed H. Computational modelling approaches as a potential platform to understand the molecular genetics association between Parkinson's and Gaucher diseases. Metab Brain Dis 2018; 33:1835-1847. [PMID: 29978341 DOI: 10.1007/s11011-018-0286-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022]
Abstract
Gaucher's disease (GD) is a genetic disorder in which glucocerebroside accumulates in cells and specific organs. It is broadly classified into type I, type II and type III. Patients with GD are at high risk of Parkinson's disease (PD), and the clinical and pathological presentation of GD patients with PD is almost identical to idiopathic PD. Several experimental models like cell culture, animal models, and transgenic mice models were used to understand the molecular mechanism behind GD and PD association; however, such mechanism remains unclear. In this context, based on literature reports, we identified the most common mutations K198T, E326K, T369M, N370S, V394L, D409H, L444P, and R496H, in the Glucosylceramidase (GBA) protein that are known to cause GD1, and represent a risk of developing PD. However, to date, no computational analyses have designed to elucidate the potential functional role of GD mutations with increased risk of PD. The present computational pipeline allows us to understand the structural and functional significance of these GBA mutations with PD. Based on the published data, the most common and severe mutations were E326K, N370S, and L444P, which further selected for our computational analysis. PredictSNP and iStable servers predicted L444P mutant to be the most deleterious and responsible for the protein destabilization, followed by the N370S mutation. Further, we used the structural analysis and molecular dynamics approach to compare the most frequent deleterious mutations (N370S and L444P) with the mild mutation E326K. The structural analysis demonstrated that the location of E326K and N370S in the alpha helix region of the protein whereas the mutant L444P was in the starting region of the beta sheet, which might explain the predicted pathogenicity level and destabilization effect of the L444P mutant. Finally, Molecular Dynamics (MD) at 50 ns showed the highest deviation and fluctuation pattern in the L444P mutant compared to the two mutants E326K and N370S and the native protein. This was consistent with more loss of intramolecular hydrogen bonds and less compaction of the radius of gyration in the L444P mutant. The proposed study is anticipated to serve as a potential platform to understand the mechanism of the association between GD and PD, and might facilitate the process of drug discovery against both GD and PD.
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Affiliation(s)
- D Thirumal Kumar
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India
| | - Hend Ghasan Eldous
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar
| | - Zainab Alaa Mahgoub
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar
| | - C George Priya Doss
- School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632014, India.
| | - Hatem Zayed
- College of Health Sciences, Department of Biomedical Sciences, Qatar University, Doha, Qatar.
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Agrahari AK, Kumar A, R S, Zayed H, C GPD. Substitution impact of highly conserved arginine residue at position 75 in GJB1 gene in association with X-linked Charcot-Marie-tooth disease: A computational study. J Theor Biol 2018; 437:305-317. [PMID: 29111421 DOI: 10.1016/j.jtbi.2017.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/23/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
Abstract
X-linked Charcot-Marie-Tooth type 1 X (CMTX1) disease is a subtype of Charcot-Marie-Tooth (CMT), which is mainly caused by mutations in the GJB1 gene. It is also known as connexin 32 (Cx32) that leads to Schwann cell abnormalities and peripheral neuropathy. CMTX1 is considered as the second most common form of CMT disease. The aim of this study is to computationally predict the potential impact of different single amino acid substitutions at position 75 of Cx32, from arginine (R) to proline (P), glutamine (Q) and tryptophan (W). This position is known to be highly conserved among the family of connexin. To understand the structural and functional changes due to these single amino acid substitutions, we employed a homology-modeling technique to build the three-dimensional structure models for the native and mutant proteins. The protein structures were further embedded into a POPC lipid bilayer, inserted into a water box, and subjected to molecular dynamics simulation for 50 ns. Our results show that the mutants R75P, R75Q and R75W display variable structural conformation and dynamic behavior compared to the native protein. Our data proves useful in predicting the potential pathogenicity of the mutant proteins and is expected to serve as a platform for drug discovery for patients with CMT.
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Affiliation(s)
| | - Amit Kumar
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy; Biosciences Sector, Center for advanced study research and development in Sardinia (CRS4), Loc. Piscina Manna, 09010 Pula, Italy
| | - Siva R
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
| | - George Priya Doss C
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
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Ali SK, Sneha P, Priyadharshini Christy J, Zayed H, George Priya Doss C. Molecular dynamics-based analyses of the structural instability and secondary structure of the fibrinogen gamma chain protein with the D356V mutation. J Biomol Struct Dyn 2016; 35:2714-2724. [PMID: 27677677 DOI: 10.1080/07391102.2016.1229634] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Mutations in the fibrinogen gamma chain (FGG) gene have been associated with various disorders, such as dysfibrinogenemia, thrombophilia, and hypofibrinogenemia. A literature survey showed that a residue exchange in fibrinogen Milano I from γ Asp to Val at position 330 impairs fibrin polymerization. The D356V (D330V) mutation located in the C-terminus was predicted to be highly deleterious and to affect the function of the protein. The pathogenicity of the altered gene and changes in protein functions were predicted using in silico methods, such as SIFT, PolyPhen 2, I-Mutant 3.0, Align GV-GD, PhD-SNP, and SNPs&GO. The secondary structure of the mutant protein was unwound by the end of the 50-ns simulation period, and a structural change in the helix-turn transition of the alpha-helical (352-356) region residues was observed. Moreover, a change in the length of the helical region was visualized in the mutant trajectory file, indicating the local transient unfolding of the protein. The obtained computational results suggest that the substitution of the neutral amino acid valine for the acidic amino acid aspartic acid at position 356 results in an unwound conformation within 50 ns, which might contribute to defective polymerization. Our analysis also provides insights into the effect of the conformational change in the D356V (D330V) mutant on protein structure and function.
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Affiliation(s)
- Shabana Kouser Ali
- a Department of Integrative Biology, School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - P Sneha
- a Department of Integrative Biology, School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - J Priyadharshini Christy
- a Department of Integrative Biology, School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
| | - Hatem Zayed
- b Biomedical Sciences Program, College of Health Sciences , Qatar University , P.O. Box 2713, Doha , Qatar
| | - C George Priya Doss
- a Department of Integrative Biology, School of Biosciences and Technology , VIT University , Vellore , Tamil Nadu 632014 , India
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Thirumal Kumar D, George Priya Doss C. Role of E542 and E545 missense mutations of PIK3CA in breast cancer: a comparative computational approach. J Biomol Struct Dyn 2016; 35:2745-2757. [DOI: 10.1080/07391102.2016.1231082] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- D. Thirumal Kumar
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
| | - C. George Priya Doss
- Department of Integrative Biology, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014, India
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Agrahari A, George Priya Doss C. Impact of I30T and I30M substitution in MPZ gene associated with Dejerine–Sottas syndrome type B (DSSB): A molecular modeling and dynamics. J Theor Biol 2015; 382:23-33. [DOI: 10.1016/j.jtbi.2015.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 06/10/2015] [Indexed: 11/28/2022]
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Chikan NA, Bukhari S, Shabir N, Amin A, Shafi S, Qadri RA, Patel TNC. Atomic Insight into the Altered O6-Methylguanine-DNA Methyltransferase Protein Architecture in Gastric Cancer. PLoS One 2015; 10:e0127741. [PMID: 26011121 PMCID: PMC4444098 DOI: 10.1371/journal.pone.0127741] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/19/2015] [Indexed: 11/22/2022] Open
Abstract
O6-methylguanine-DNA methyltransferase (MGMT) is one of the major DNA repair protein that counteracts the alkalyting agent-induced DNA damage by replacing O6-methylguanine (mutagenic lesion) back to guanine, eventually suppressing the mismatch errors and double strand crosslinks. Exonic alterations in the form of nucleotide polymorphism may result in altered protein structure that in turn can lead to the loss of function. In the present study, we focused on the population feared for high exposure to alkylating agents owing to their typical and specialized dietary habits. To this end, gastric cancer patients pooled out from the population were selected for the mutational screening of a specific error prone region of MGMT gene. We found that nearly 40% of the studied neoplastic samples harbored missense mutation at codon151 resulting into Serine to Isoleucine variation. This variation resulted in bringing about the structural disorder, subsequently ensuing into a major stoichiometric variance in recognition domain, substrate binding and selectivity loop of the active site of the MGMT protein, as observed under virtual microscope of molecular dynamics simulation (MDS). The atomic insight into MGMT protein by computational approach showed a significant change in the intra molecular hydrogen bond pattern, thus leading to the observed structural anomalies. To further examine the mutational implications on regulatory plugs of MGMT that holds the protein in a DNA-Binding position, a MDS based analysis was carried out on, all known physically interacting amino acids essentially clustered into groups based on their position and function. The results generated by physical-functional clustering of protein indicated that the identified mutation in the vicinity of the active site of MGMT protein causes the local and global destabilization of a protein by either eliminating the stabilizing salt bridges in cluster C3, C4, and C5 or by locally destabilizing the “protein stabilizing hing” mapped on C3-C4 cluster, preceding the active site.
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Affiliation(s)
- Naveed Anjum Chikan
- Division of Medical Biotechnology, School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Shoiab Bukhari
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Nadeem Shabir
- Department of Animal Biotechnology, College of Veterinary Sciences, Anand Agricultural University, Anand, Gujarat, India, 388 001
| | - Asif Amin
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Sheikh Shafi
- Department of Clinical Biochemistry, Sher-i- Kashmir Institute of Medical Sciences, Srinagar, Kashmir, 190011, India
| | - Raies Ahmad Qadri
- Departments of Biotechnology, University of Kashmir, Srinagar, Kashmir, 190006, India
| | - Trupti Navin Chandra Patel
- Division of Medical Biotechnology, School of Bioscience and Technology, VIT University, Vellore, Tamil Nadu, 632014, India
- * E-mail:
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