1
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Dans MG, Boulet C, Watson GM, Nguyen W, Dziekan JM, Evelyn C, Reaksudsan K, Mehra S, Razook Z, Geoghegan ND, Mlodzianoski MJ, Goodman CD, Ling DB, Jonsdottir TK, Tong J, Famodimu MT, Kristan M, Pollard H, Stewart LB, Brandner-Garrod L, Sutherland CJ, Delves MJ, McFadden GI, Barry AE, Crabb BS, de Koning-Ward TF, Rogers KL, Cowman AF, Tham WH, Sleebs BE, Gilson PR. Aryl amino acetamides prevent Plasmodium falciparum ring development via targeting the lipid-transfer protein PfSTART1. Nat Commun 2024; 15:5219. [PMID: 38890312 PMCID: PMC11189555 DOI: 10.1038/s41467-024-49491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
With resistance to most antimalarials increasing, it is imperative that new drugs are developed. We previously identified an aryl acetamide compound, MMV006833 (M-833), that inhibited the ring-stage development of newly invaded merozoites. Here, we select parasites resistant to M-833 and identify mutations in the START lipid transfer protein (PF3D7_0104200, PfSTART1). Introducing PfSTART1 mutations into wildtype parasites reproduces resistance to M-833 as well as to more potent analogues. PfSTART1 binding to the analogues is validated using organic solvent-based Proteome Integral Solubility Alteration (Solvent PISA) assays. Imaging of invading merozoites shows the inhibitors prevent the development of ring-stage parasites potentially by inhibiting the expansion of the encasing parasitophorous vacuole membrane. The PfSTART1-targeting compounds also block transmission to mosquitoes and with multiple stages of the parasite's lifecycle being affected, PfSTART1 represents a drug target with a new mechanism of action.
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Affiliation(s)
- Madeline G Dans
- Burnet Institute, Melbourne, VIC, 3004, Australia.
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, VIC, 3220, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Coralie Boulet
- Burnet Institute, Melbourne, VIC, 3004, Australia
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, 1206, Switzerland
| | - Gabrielle M Watson
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - William Nguyen
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jerzy M Dziekan
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Cindy Evelyn
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Kitsanapong Reaksudsan
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Somya Mehra
- Burnet Institute, Melbourne, VIC, 3004, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
| | - Zahra Razook
- Burnet Institute, Melbourne, VIC, 3004, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
| | - Niall D Geoghegan
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael J Mlodzianoski
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | | | - Thorey K Jonsdottir
- Burnet Institute, Melbourne, VIC, 3004, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Joshua Tong
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
| | - Mufuliat Toyin Famodimu
- Department of Infection Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
| | - Mojca Kristan
- Wellcome Trust Human Malaria Transmission Facility, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Harry Pollard
- Wellcome Trust Human Malaria Transmission Facility, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Lindsay B Stewart
- Wellcome Trust Human Malaria Transmission Facility, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Luke Brandner-Garrod
- Wellcome Trust Human Malaria Transmission Facility, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Colin J Sutherland
- Department of Infection Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
- Wellcome Trust Human Malaria Transmission Facility, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
| | - Michael J Delves
- Department of Infection Biology, Faculty of Infectious Diseases, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
| | - Geoffrey I McFadden
- School of Biosciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Alyssa E Barry
- Burnet Institute, Melbourne, VIC, 3004, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
| | - Brendan S Crabb
- Burnet Institute, Melbourne, VIC, 3004, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Monash University, 3800, Melbourne, VIC, Australia
| | - Tania F de Koning-Ward
- Institute of Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
| | - Kelly L Rogers
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Alan F Cowman
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Wai-Hong Tham
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Brad E Sleebs
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gilson
- Burnet Institute, Melbourne, VIC, 3004, Australia.
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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Waheed S, Ramzan K, Ahmad S, Khan MS, Wajid M, Ullah H, Umar A, Iqbal R, Ullah R, Bari A. Identification and In-Silico study of non-synonymous functional SNPs in the human SCN9A gene. PLoS One 2024; 19:e0297367. [PMID: 38394191 PMCID: PMC10889873 DOI: 10.1371/journal.pone.0297367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 02/25/2024] Open
Abstract
Single nucleotide polymorphisms are the most common form of DNA alterations at the level of a single nucleotide in the genomic sequence. Genome-wide association studies (GWAS) were carried to identify potential risk genes or genomic regions by screening for SNPs associated with disease. Recent studies have shown that SCN9A comprises the NaV1.7 subunit, Na+ channels have a gene encoding of 1988 amino acids arranged into 4 domains, all with 6 transmembrane regions, and are mainly found in dorsal root ganglion (DRG) neurons and sympathetic ganglion neurons. Multiple forms of acute hypersensitivity conditions, such as primary erythermalgia, congenital analgesia, and paroxysmal pain syndrome have been linked to polymorphisms in the SCN9A gene. Under this study, we utilized a variety of computational tools to explore out nsSNPs that are potentially damaging to heath by modifying the structure or activity of the SCN9A protein. Over 14 potentially damaging and disease-causing nsSNPs (E1889D, L1802P, F1782V, D1778N, C1370Y, V1311M, Y1248H, F1237L, M936V, I929T, V877E, D743Y, C710W, D623H) were identified by a variety of algorithms, including SNPnexus, SNAP-2, PANTHER, PhD-SNP, SNP & GO, I-Mutant, and ConSurf. Homology modeling, structure validation, and protein-ligand interactions also were performed to confirm 5 notable substitutions (L1802P, F1782V, D1778N, V1311M, and M936V). Such nsSNPs may become the center of further studies into a variety of disorders brought by SCN9A dysfunction. Using in-silico strategies for assessing SCN9A genetic variations will aid in organizing large-scale investigations and developing targeted therapeutics for disorders linked to these variations.
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Affiliation(s)
- Sana Waheed
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Kainat Ramzan
- Faculty of Life Science, Department of Biochemistry, University of Okara, Okara, Pakistan
| | - Sibtain Ahmad
- Faculty of Animal Husbandry, Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Saleem Khan
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Muhammad Wajid
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Hayat Ullah
- Department of Chemistry, University of Okara, Okara, Pakistan
| | - Ali Umar
- Faculty of Life Science, Department of Zoology, University of Okara, Okara, Pakistan
| | - Rashid Iqbal
- Faculty of Agriculture and Environment, Department of Agronomy, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Riaz Ullah
- Department of Pharmacognosy College of Pharmacy King Saud University, Riyadh, Saudi Arabia
| | - Ahmed Bari
- Department of Pharmaceutical Chemistry, College of Pharmacy King Saud University, Riyadh, Saudi Arabia
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Shinwari K, Wu Y, Rehman HM, Xiao N, Bolkov M, Tuzankina I, Chereshnev V. In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function. BMC Bioinformatics 2023; 24:251. [PMID: 37322437 DOI: 10.1186/s12859-023-05361-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 06/17/2023] Open
Abstract
Hennekam Lymphangiectasia-Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectasia, severe lymphedema and distinctive facial appearance. Up till now, no extensive studies have been conducted to elucidate the mechanism of the disease caused by various mutations. As a preliminary investigation of HKLLS3, we sorted out the most deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) that might affect the structure and function of ADAMTS3 protein by using a variety of in silico tools. A total of 919 nsSNPs in the ADAMTS3 gene were identified. 50 nsSNPs were predicted to be deleterious by multiple computational tools. 5 nsSNPs (G298R, C567Y, A370T, C567R and G374S) were found to be the most dangerous and can be associated with the disease as predicted by different bioinformatics tools. Modelling of the protein shows it can be divided into segments 1, 2 and 3, which are connected by short loops. Segment 3 mainly consists of loops without substantial secondary structures. With prediction tools and molecular dynamics simulation, some SNPs were found to significantly destabilize the protein structure and disrupt the secondary structures, especially in segment 2. The deleterious effects of mutations in segment 1 are possibly not from destabilization but from other factors such as the change in phosphorylation as suggested by post-translational modification (PTM) studies. This is the first-ever study of ADAMTS3 gene polymorphism, and the predicted nsSNPs in ADAMST3, some of which have not been reported yet in patients, will serve for diagnostic purposes and further therapeutic implications in Hennekam syndrome, contributing to better diagnosis and treatment.
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Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia.
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia.
| | - Yurong Wu
- Department of Chemistry, Hong Kong University of Science and Technology, Hong Kong, China
| | | | - Ningkun Xiao
- Department of Psychology, Ural Federal University, Yekaterinburg, Russia
| | - Mikhail Bolkov
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Irina Tuzankina
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
| | - Valery Chereshnev
- Insitutite of Immunology and Physiology, Russian Academy of Science, Yekaterinburg, Russia
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Xu D, Shao Q, Zhou C, Mahmood A, Zhang J. In Silico Analysis of nsSNPs of Human KRAS Gene and Protein Modeling Using Bioinformatic Tools. ACS OMEGA 2023; 8:13362-13370. [PMID: 37065036 PMCID: PMC10099408 DOI: 10.1021/acsomega.3c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
The KRAS gene belongs to the RAS family and codes for 188 amino acid residues of KRAS protein, with a molecular mass of 21.6 kD. Non-synonymous single-nucleotide polymorphisms (nsSNPs) have been identified within the coding region in which some are associated with different diseases. However, structural changes are not well defined yet. In this study, we first categorized SNPs in the KRAS coding area and then used computational methods to determine their impact on the protein structure and stability. In addition, the three-dimensional model of KRAS was taken from the Protein Data Bank for structural modeling. Furthermore, genomic data were extracted from a variety of sources, including the 1000 Genome Project, dbSNPs, and ENSEMBLE, and assessed through in silico methods. Based on various tools used in this study, 10 out of 48 missense SNPs with rsIDs were found deleterious. The substitution of alanine for proline at position 146 pushed several residues toward the center of the protein. Arginine instead of leucine has a minor effect on protein structure and stability. In addition, the substitution of proline for leucine at the 34th position disrupted the structure and led to a bigger size than the wild-type protein, hence interrupting the protein interaction. Using the well-intended computational approach and applying several bioinformatic tools, we characterized and identified most damaging nsSNPs and further explored the structural dynamics and stability of KRAS protein.
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Affiliation(s)
- Duoduo Xu
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
| | - Qiqi Shao
- Department
of Nursing, Central Health Center of Zeya
Town, Ouhai District, Wenzhou 325000, China
| | - Chen Zhou
- Ultrasonography
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325099, China
| | - Arif Mahmood
- Center
for Medical Genetics and Hunan Key Laboratory of Medical Genetics,
School of Life Sciences, Central South University, Changsha 410078, Hunan, China
| | - Jizhou Zhang
- Oncology
Department, Wenzhou Hospital of Traditional
Chinese Medicine Affiliated to Zhejiang Chinese Medicine University, Wenzhou 325000, China
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R HC, Kumar S U, R G, Naayanan PJ, Sathiyarajeswaren P, Devi MSS, K SS, Doss C GP. An integrated investigation of structural and pathway alteration caused by PIK3CA and TP53 mutations identified in cfDNA of metastatic breast cancer. J Cell Biochem 2023; 124:188-204. [PMID: 36563059 DOI: 10.1002/jcb.30354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/12/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
In peripheral blood, cell-free DNA (cfDNA) contains circulating tumor DNA (ctDNA), which indicates molecular abnormalities in metastatic breast tumor tissue. The sequencing of cfDNA of Metastatic Breast Cancer (MBC) patients allows assessment of therapy response and noninvasive treatment. In the proposed study, clinically significant alterations in PIK3CA and TP53 genes associated with MBC resulting in a missense substitution of His1047Arg and Arg282Trp from an next-generation sequencing-based multi-gene panel were reported in a cfDNA of a patient with MBC. To investigate the impact of the reported mutation, we used molecular docking, molecular dynamics simulation, network analysis, and pathway analysis. Molecular Docking analysis determined the distinct binding pattern revealing H1047R-ATP complex has a higher number of Hydrogen bonds (H-bonds) and binding affinity with a slight difference compared to the PIK3CA-ATP complex. Following, molecular dynamics simulation for 200 ns, of which H1047R-ATP complex resulted in the instability of PIK3CA. Similarly, for TP53 mutant R282W, the zinc-free state (apo) and zinc-bounded (holo) complexes were investigated for conformational change between apo and holo complexes, of which the holo complex mutant R282W was unstable. To validate the conformational change of PIK3CA and TP53, 80% mutation of H1047R in the kinase domain of p110α expressed ubiquitously in PIK3CA protein that alters PI3K pathway, while R282W mutation in DNA binding helix (H2) region of P53 protein inhibits the transcription factor in P53 pathway causing MBC. According to our findings, the extrinsic (hypoxia, oxidative stress, and acidosis); intrinsic factors (MYC amplification) in PIK3CA and TP53 mutations will provide potential insights for developing novel therapeutic methods for MBC therapy.
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Affiliation(s)
- Hephzibah Cathryn R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Udhaya Kumar S
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Gnanasambandan R
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | | | - M S Shree Devi
- Siddha Central Research Institute (CCRS), Chennai, Tamil Nadu, India
| | - Satish Srinivas K
- Department of Radiation Oncology, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, India
| | - George Priya Doss C
- Laboratory of Integrative Genomics, Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Exploring different computational approaches for effective diagnosis of breast cancer. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 177:141-150. [PMID: 36509230 DOI: 10.1016/j.pbiomolbio.2022.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/28/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Breast cancer has been identified as one among the top causes of female death worldwide. According to recent research, earlier detection plays an important role toward fortunate medicaments and thus, decreasing the mortality rate due to breast cancer among females. This review provides a fleeting summary involving traditional diagnostic procedures from the past and today, and also modern computational tools that have greatly aided in the identification of breast cancer. Computational techniques involving different algorithms such as Support vector machines, deep learning techniques and robotics are popular among the academicians for detection of breast cancer. They discovered that Convolutional neural network was a common option for categorization among such approaches. Deep learning techniques are evaluated using performance indicators such as accuracy, sensitivity, specificity, or measure. Furthermore, molecular docking, homology modeling and Molecular dynamics Simulation gives a road map for future discussions about developing improved early detection approaches that holds greater potential in increasing the survival rate of cancer patients. The different computational techniques can be a new dominion among researchers and combating the challenges associated with breast cancer.
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Schaefer‐Ramadan S, Aleksic J, Al‐Thani NM, Malek JA. Novel protein contact points among TP53 and minichromosome maintenance complex proteins 2, 3, and 5. Cancer Med 2022; 11:4989-5000. [PMID: 35567389 PMCID: PMC9761056 DOI: 10.1002/cam4.4805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 02/03/2023] Open
Abstract
OBJECTIVE Identify protein contact points between TP53 and minichromosome maintenance (MCM) complex proteins 2, 3, and 5 with high resolution allowing for potential novel Cancer drug design. METHODS A next-generation sequencing-based protein-protein interaction method developed in our laboratory called AVA-Seq was applied to a gold-standard human protein interaction set. Proteins including TP53, MCM2, MCM3, MCM5, HSP90AA1, PCNA, NOD1, and others were sheared and ligated into the AVA-Seq system. Protein-protein interactions were then identified in both mild and stringent selective conditions. RESULTS Known interactions among MCM2, MCM3, and MCM5 were identified with the AVA-Seq system. The interacting regions detected between these three proteins overlap with the structural data of the MCM complex, and novel domains were identified with high resolution determined by multiple overlapping fragments. Fragments of wild type TP53 were shown to interact with MCM2, MCM3, and MCM5, and details on the location of the interactions were provided. Finally, a mini-network of known and novel cancer protein interactions was provided, which could have implications for fundamental changes in multiple cancers. CONCLUSION We provide a high-resolution mini-interactome that could direct novel drug targets and implicate possible effects of specific cancer mutations.
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Affiliation(s)
| | - Jovana Aleksic
- Department of Genetic MedicineWeill Cornell Medicine in QatarDohaQatar
| | - Nayra M. Al‐Thani
- Department of Genetic MedicineWeill Cornell Medicine in QatarDohaQatar
| | - Joel A. Malek
- Department of Genetic MedicineWeill Cornell Medicine in QatarDohaQatar
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Shinwari K, Rehman HM, Liu G, Bolkov MA, Tuzankina IA, Chereshnev VA. Novel Disease-Associated Missense Single-Nucleotide Polymorphisms Variants Predication by Algorithms Tools and Molecular Dynamics Simulation of Human TCIRG1 Gene Causing Congenital Neutropenia and Osteopetrosis. Front Mol Biosci 2022; 9:879875. [PMID: 35573728 PMCID: PMC9095858 DOI: 10.3389/fmolb.2022.879875] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/04/2022] [Indexed: 12/16/2022] Open
Abstract
T Cell Immune Regulator 1, ATPase H + Transporting V0 Subunit A3 (TCIRG1 gene provides instructions for making one part, the a3 subunit, of a large protein complex known as a vacuolar H + -ATPase (V-ATPase). V-ATPases are a group of similar complexes that act as pumps to move positively charged hydrogen atoms (protons) across membranes. Single amino acid changes in highly conserved areas of the TCIRG1 protein have been linked to autosomal recessive osteopetrosis and severe congenital neutropenia. We used multiple computational approaches to classify disease-prone single nucleotide polymorphisms (SNPs) in TCIRG1. We used molecular dynamics analysis to identify the deleterious nsSNPs, build mutant protein structures, and assess the impact of mutation. Our results show that fifteen nsSNPs (rs199902030, rs200149541, rs372499913, rs267605221, rs374941368, rs375717418, rs80008675, rs149792489, rs116675104, rs121908250, rs121908251, rs121908251, rs149792489 and rs116675104) variants are likely to be highly deleterious mutations as by incorporating them into wild protein they destabilize the wild protein structure and function. They are also located in the V-ATPase I domain, which may destabilize the structure and impair TCIRG1 protein activation, as well as reduce its ATPase effectiveness. These mutants have not yet been identified in patients suffering from CN and osteopetrosis while (G405R, R444L, and D517N) reported in our study are already associated with osteopetrosis. Mutation V52L reported in our study was identified in a patient suspected for CN. Finally, these mutants can help to further understand the broad pool of illness susceptibilities associated with TCIRG1 catalytic kinase domain activation and aid in the development of an effective treatment for associated diseases.
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Affiliation(s)
- Khyber Shinwari
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- *Correspondence: Khyber Shinwari,
| | - Hafiz Muzzammel Rehman
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- Alnoorians Group of Institutes, Shad Bagh, Lahore, Pakistan
| | - Guojun Liu
- School of Life Science and Technology, Inner Mongolia University of Science and Technology, Baotou, China
| | - Mikhail A. Bolkov
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Irina A. Tuzankina
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
| | - Valery. A. Chereshnev
- Institute of Chemical Engineering, Department of Immunochemistry, Ural Federal University, Yekaterinburg, Russia
- Institute of Immunology and Physiology of the Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
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Impact of deleterious missense PRKCI variants on structural and functional dynamics of protein. Sci Rep 2022; 12:3781. [PMID: 35260606 PMCID: PMC8904829 DOI: 10.1038/s41598-022-07526-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/08/2022] [Indexed: 11/09/2022] Open
Abstract
Protein kinase C iota (PKCɩ) is a novel protein containing 596 amino acids and is also a member of atypical kinase family. The role of PKCɩ has been explored in neurodegenerative diseases, neuroblastoma, ovarian and pancreatic cancers. Single nucleotide polymorphisms (SNPs) have not been studied in PKCɩ till date. The purpose of the current study is to scrutinize the deleterious missense variants in PKCɩ and determine the effect of these variants on stability and dynamics of the protein. The structure of protein PKCɩ was predicted for the first time and post translational modifications were determined. Genetic variants of PKCɩ were retrieved from ENSEMBL and only missense variants were further analyzed because of its linkage with diseases. The pathogenicity of missense variants, effect on structure and function of protein, association with cancer and conservancy of the protein residues were determined through computational approaches. It is observed that C1 and the pseudo substrate region has the highest number of pathogenic SNPs. Variations in the kinase domain of the protein are predicted to alter overall phosphorylation of the protein. Molecular dynamic simulations predicted noteworthy change in structural and functional dynamics of the protein because of these variants. The study revealed that nine deleterious variants can possibly contribute to malfunctioning of the protein and can be associated with diseases. This can be useful in diagnostics and developing therapeutics for diseases related to these polymorphisms.
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10
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Lira SS, Ahammad I. A comprehensive in silico investigation into the nsSNPs of Drd2 gene predicts significant functional consequences in dopamine signaling and pharmacotherapy. Sci Rep 2021; 11:23212. [PMID: 34853389 PMCID: PMC8636637 DOI: 10.1038/s41598-021-02715-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/18/2021] [Indexed: 01/01/2023] Open
Abstract
DRD2 is a neuronal cell surface protein involved in brain development and function. Variations in the Drd2 gene have clinical significance since DRD2 is a pharmacotherapeutic target for treating psychiatric disorders like ADHD and schizophrenia. Despite numerous studies on the disease association of single nucleotide polymorphisms (SNPs) in the intronic regions, investigation into the coding regions is surprisingly limited. In this study, we aimed at identifying potential functionally and pharmaco-therapeutically deleterious non-synonymous SNPs of Drd2. A wide array of bioinformatics tools was used to evaluate the impact of nsSNPs on protein structure and functionality. Out of 260 nsSNPs retrieved from the dbSNP database, initially 9 were predicted as deleterious by 15 tools. Upon further assessment of their domain association, conservation profile, homology models and inter-atomic interaction, the mutant F389V was considered as the most impactful. In-depth analysis of F389V through Molecular Docking and Dynamics Simulation revealed a decline in affinity for its native agonist dopamine and an increase in affinity for the antipsychotic drug risperidone. Remarkable alterations in binding interactions and stability of the protein-ligand complex in simulated physiological conditions were also noted. These findings will improve our understanding of the consequence of nsSNPs in disease-susceptibility and therapeutic efficacy.
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Affiliation(s)
- Samia Sultana Lira
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Ishtiaque Ahammad
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka, 1349, Bangladesh.
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11
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Sun Y, Yang N, Utama FE, Udhane SS, Zhang J, Peck AR, Yanac A, Duffey K, Langenheim JF, Udhane V, Xia G, Peterson JF, Jorns JM, Nevalainen MT, Rouet R, Schofield P, Christ D, Ormandy CJ, Rosenberg AL, Chervoneva I, Tsaih SW, Flister MJ, Fuchs SY, Wagner KU, Rui H. NSG-Pro mouse model for uncovering resistance mechanisms and unique vulnerabilities in human luminal breast cancers. SCIENCE ADVANCES 2021; 7:eabc8145. [PMID: 34524841 PMCID: PMC8443188 DOI: 10.1126/sciadv.abc8145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Most breast cancer deaths are caused by estrogen receptor-α–positive (ER+) disease. Preclinical progress is hampered by a shortage of therapy-naïve ER+ tumor models that recapitulate metastatic progression and clinically relevant therapy resistance. Human prolactin (hPRL) is a risk factor for primary and metastatic ER+ breast cancer. Because mouse prolactin fails to activate hPRL receptors, we developed a prolactin-humanized Nod-SCID-IL2Rγ (NSG) mouse (NSG-Pro) with physiological hPRL levels. Here, we show that NSG-Pro mice facilitate establishment of therapy-naïve, estrogen-dependent PDX tumors that progress to lethal metastatic disease. Preclinical trials provide first-in-mouse efficacy of pharmacological hPRL suppression on residual ER+ human breast cancer metastases and document divergent biology and drug responsiveness of tumors grown in NSG-Pro versus NSG mice. Oncogenomic analyses of PDX lines in NSG-Pro mice revealed clinically relevant therapy-resistance mechanisms and unexpected, potently actionable vulnerabilities such as DNA-repair aberrations. The NSG-Pro mouse unlocks previously inaccessible precision medicine approaches for ER+ breast cancers.
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Affiliation(s)
- Yunguang Sun
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ning Yang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Fransiscus E. Utama
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Sameer S. Udhane
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Junling Zhang
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Amy R. Peck
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Alicia Yanac
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Katherine Duffey
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - John F. Langenheim
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Vindhya Udhane
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Guanjun Xia
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Jess F. Peterson
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Julie M. Jorns
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marja T. Nevalainen
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Romain Rouet
- Immunology Division, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Peter Schofield
- Immunology Division, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Daniel Christ
- Immunology Division, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Christopher J. Ormandy
- Garvan Institute of Medical Research and St. Vincent’s Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Anne L. Rosenberg
- Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Inna Chervoneva
- Department of Pharmacology, Division of Biostatistics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Shirng-Wern Tsaih
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Michael J. Flister
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Serge Y. Fuchs
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA 19104, USA
| | - Kay-Uwe Wagner
- Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, USA
| | - Hallgeir Rui
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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12
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Kushwaha PP, Singh AK, Bansal T, Yadav A, Prajapati KS, Shuaib M, Kumar S. Identification of Natural Inhibitors Against SARS-CoV-2 Drugable Targets Using Molecular Docking, Molecular Dynamics Simulation, and MM-PBSA Approach. Front Cell Infect Microbiol 2021; 11:730288. [PMID: 34458164 PMCID: PMC8387699 DOI: 10.3389/fcimb.2021.730288] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 02/05/2023] Open
Abstract
The present study explores the SARS-CoV-2 drugable target inhibition efficacy of phytochemicals from Indian medicinal plants using molecular docking, molecular dynamics (MD) simulation, and MM-PBSA analysis. A total of 130 phytochemicals were screened against SARS-CoV-2 Spike (S)-protein, RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro). Result of molecular docking showed that Isoquercetin potentially binds with the active site/protein binding site of the Spike, RdRP, and Mpro targets with a docking score of -8.22, -6.86, and -9.73 kcal/mole, respectively. Further, MS 3, 7-Hydroxyaloin B, 10-Hydroxyaloin A, showed -9.57, -7.07, -8.57 kcal/mole docking score against Spike, RdRP, and Mpro targets respectively. The MD simulation was performed to study the favorable confirmation and energetically stable complex formation ability of Isoquercetin and 10-Hydroxyaloin A phytochemicals in Mpro-unbound/ligand bound/standard inhibitor bound system. The parameters such as RMSD, RMSF, Rg, SASA, Hydrogen-bond formation, energy landscape, principal component analysis showed that the lead phytochemicals form stable and energetically stabilized complex with the target protein. Further, MM-PBSA analysis was performed to compare the Gibbs free energy of the Mpro-ligand bound and standard inhibitor bound complexes. The analysis revealed that the His-41, Cys145, Met49, and Leu27 amino acid residues were majorly responsible for the lower free energy of the complex. Drug likeness and physiochemical properties of the test compounds showed satisfactory results. Taken together, the study concludes that that the Isoquercetin and 10-Hydroxyaloin A phytochemical possess significant efficacy to bind SARS-Cov-2 Mpro active site. The study necessitates further in vitro and in vivo experimental validation of these lead phytochemicals to assess their anti-SARS-CoV-2 potential.
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Affiliation(s)
- Prem Prakash Kushwaha
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Atul Kumar Singh
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Tanya Bansal
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Akansha Yadav
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Kumari Sunita Prajapati
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Mohd Shuaib
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
| | - Shashank Kumar
- Molecular Signaling & Drug Discovery Laboratory, Department of Biochemistry, Central University of Punjab, Bathinda, India
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13
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Novel structural and functional impact of damaging single nucleotide polymorphisms (SNPs) on human SMYD2 protein using computational approaches. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100871] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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14
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Stalin A, Lin D, Josephine Princy J, Feng Y, Xiang H, Ignacimuthu S, Chen Y. Computational analysis of single nucleotide polymorphisms (SNPs) in PPAR gamma associated with obesity, diabetes and cancer. J Biomol Struct Dyn 2020; 40:1843-1857. [DOI: 10.1080/07391102.2020.1835724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Antony Stalin
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | - Ding Lin
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | | | - Yue Feng
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, China
| | - Haiping Xiang
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
| | | | - Yuan Chen
- State Key Laboratory of Subtropical Silviculture, Department of Traditional Chinese Medicine, Zhejiang A&F University, Hangzhou, China
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15
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Yazar M, Özbek P. In Silico Tools and Approaches for the Prediction of Functional and Structural Effects of Single-Nucleotide Polymorphisms on Proteins: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:23-37. [PMID: 33058752 DOI: 10.1089/omi.2020.0141] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Single-nucleotide polymorphisms (SNPs) are single-base variants that contribute to human biological variation and pathogenesis of many human diseases. Among all SNP types, nonsynonymous single-nucleotide polymorphisms (nsSNPs) can alter many structural, biochemical, and functional features of a protein such as folding characteristics, charge distribution, stability, dynamics, and interactions with other proteins/nucleotides. These modifications in the protein structure can lead nsSNPs to be closely associated with many multifactorial diseases such as cancer, diabetes, and neurodegenerative diseases. Predicting structural and functional effects of nsSNPs with experimental approaches can be time-consuming and costly; hence, computational prediction tools and algorithms are being widely and increasingly utilized in biology and medical research. This expert review examines the in silico tools and algorithms for the prediction of functional or structural effects of SNP variants, in addition to the description of the phenotypic effects of nsSNPs on protein structure, association between pathogenicity of variants, and functional or structural features of disease-associated variants. Finally, case studies investigating the functional and structural effects of nsSNPs on selected protein structures are highlighted. We conclude that creating a consistent workflow with a combination of in silico approaches or tools should be considered to increase the performance, accuracy, and precision of the biological and clinical predictions made in silico.
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Affiliation(s)
- Metin Yazar
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey.,Department of Genetics and Bioengineering, Istanbul Okan University, Tuzla, Istanbul, Turkey
| | - Pemra Özbek
- Department of Bioengineering, Marmara University, Göztepe, İstanbul, Turkey
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16
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Computational SNP Analysis and Molecular Simulation Revealed the Most Deleterious Missense Variants in the NBD1 Domain of Human ABCA1 Transporter. Int J Mol Sci 2020; 21:ijms21207606. [PMID: 33066695 PMCID: PMC7589834 DOI: 10.3390/ijms21207606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/12/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
The ATP-binding cassette transporter A1 (ABCA1) is a membrane-bound exporter protein involved in regulating serum HDL level by exporting cholesterol and phospholipids to load up in lipid-poor ApoA-I and ApoE, which allows the formation of nascent HDL. Mutations in the ABCA1 gene, when presents in both alleles, disrupt the canonical function of ABCA1, which associates with many disorders related to lipid transport. Although many studies have reported the phenotypic effects of a large number of ABCA1 variants, the pathological effect of non-synonymous polymorphisms (nsSNPs) in ABCA1 remains elusive. Therefore, aiming at exploring the structural and functional consequences of nsSNPs in ABCA1, in this study, we employed an integrated computational approach consisting of nine well-known in silico tools to identify damaging SNPs and molecular dynamics (MD) simulation to get insights into the magnitudes of the damaging effects. In silico tools revealed four nsSNPs as being most deleterious, where the two SNPs (G1050V and S1067C) are identified as the highly conserved and functional disrupting mutations located in the NBD1 domain. MD simulation suggested that both SNPs, G1050V and S1067C, changed the overall structural flexibility and dynamics of NBD1, and induced substantial alteration in the structural organization of ATP binding site. Taken together, these findings direct future studies to get more insights into the role of these variants in the loss of the ABCA1 function.
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17
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Suresh R, Subramaniam V. Molecular dynamics simulation involved in expounding the activation of adrenoceptors by sympathetic nervous system signaling. Struct Chem 2020. [DOI: 10.1007/s11224-020-01553-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Kanipakam H, Sharma K, Thinlas T, Mohammad G, Pasha MAQ. Structural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study. J Biomol Struct Dyn 2020; 39:294-309. [PMID: 31902292 DOI: 10.1080/07391102.2019.1711190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The human endothelial nitric oxide synthase (NOS3) is 28 Kbp at 7q36.1 and encodes protein comprising of 1280 amino acids. Being a major source of nitric oxide, the enzyme is crucial to the vascular homeostasis and thereby to be an important pharmaceutical target. We hence have been investigating this molecule in a high-altitude disorder namely, high-altitude pulmonary edema (HAPE). We performed a genome-wide association study (GWAS) in a case-control design of sojourners that included healthy controls and HAPE patients (n = 200) each. Four NOS3 missense SNPs i.e. rs1799983 (E298D), rs3918232 (V827M), rs3918201 (R885M) and rs3918234 (Q982L), were associated significantly with HAPE (P-value < 0.05). Furthermore, extensive in silico analyses were performed to predict the detrimental effect of the four variant types and their three most relevant co-factors namely, heme, flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) that are accountable for amendment of protein stability leading to structural de-construction. Subsequently, we validated the findings in a larger sample size of the two study groups. HAPE patients had a higher frequency of the four variants and significantly decreased levels of circulating nitric oxide (NO) (P-value < 0.001). The in silico and human subjects findings complement each other. This study explored the impact of HAPE-associated NOS3 variants with its protein structure stability and holds promise to be current and future drug targets.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hema Kanipakam
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Kavita Sharma
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Tashi Thinlas
- Department of Medicine, SNM Hospital, Leh, Ladakh, India
| | | | - M A Qadar Pasha
- Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
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19
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Islam MJ, Khan AM, Parves MR, Hossain MN, Halim MA. Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation. Sci Rep 2019; 9:16426. [PMID: 31712642 PMCID: PMC6848484 DOI: 10.1038/s41598-019-52308-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/09/2019] [Indexed: 02/08/2023] Open
Abstract
Serine-threonine kinase11 (STK11) is a tumor suppressor gene which plays a key role in regulating cell growth and apoptosis. It is widely known as a multitasking kinase and engaged in cell polarity, cell cycle arrest, chromatin remodeling, energy metabolism, and Wnt signaling. The substitutions of single amino acids in highly conserved regions of the STK11 protein are associated with Peutz-Jeghers syndrome (PJS), which is an autosomal dominant inherited disorder. The abnormal function of the STK11 protein is still not well understood. In this study, we classified disease susceptible single nucleotide polymorphisms (SNPs) in STK11 by using different computational algorithms. We identified the deleterious nsSNPs, constructed mutant protein structures, and evaluated the impact of mutation by employing molecular docking and molecular dynamics analysis. Our results show that W239R and W308C variants are likely to be highly deleterious mutations found in the catalytic kinase domain, which may destabilize structure and disrupt the activation of the STK11 protein as well as reduce its catalytic efficiency. The W239R mutant is likely to have a greater impact on destabilizing the protein structure compared to the W308C mutant. In conclusion, these mutants can help to further realize the large pool of disease susceptibilities linked with catalytic kinase domain activation of STK11 and assist to develop an effective drug for associated diseases.
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Affiliation(s)
- Md Jahirul Islam
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Khulshi- 4202, Chittagong, Bangladesh
| | - Akib Mahmud Khan
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
| | - Md Rimon Parves
- Department of Biochemistry and Biotechnology, University of Science and Technology Chittagong (USTC), Foy's Lake, Khulshi- 4202, Chittagong, Bangladesh
| | - Md Nayeem Hossain
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh
| | - Mohammad A Halim
- Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, 218 Elephant Road, Dhaka, 1205, Bangladesh.
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20
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Pandey S, Dhusia K, Katara P, Singh S, Gautam B. An in silico analysis of deleterious single nucleotide polymorphisms and molecular dynamics simulation of disease linked mutations in genes responsible for neurodegenerative disorder. J Biomol Struct Dyn 2019; 38:4259-4272. [DOI: 10.1080/07391102.2019.1682047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Sapna Pandey
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
| | - Kalyani Dhusia
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
- Department of Biomedical Engineering, Institute of Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan, USA
| | - Pramod Katara
- Centre of Bioinformatics, University of Allahabad, Allahabad, India
| | - Satendra Singh
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
| | - Budhayash Gautam
- Department of Computational Biology & Bioinformatics, Jacob Institute of Biotechnology & Bio-Engineering, Sam Higginbottom University of Agriculture, Technology and Science (SHUATS), Allahabad, India
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21
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Monteiro LLS, Franco OL, Alencar SA, Porto WF. Deciphering the structural basis for glucocorticoid resistance caused by missense mutations in the ligand binding domain of glucocorticoid receptor. J Mol Graph Model 2019; 92:216-226. [PMID: 31401440 DOI: 10.1016/j.jmgm.2019.07.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/01/2019] [Accepted: 07/31/2019] [Indexed: 11/25/2022]
Abstract
The glucocorticoid resistance hereditary condition may emerge from the occurrence of point mutations in the glucocorticoid receptor (GR), which could impair its functionality. Because the main feature of such pathology is the resistance of the hypothalamic-pituitary-adrenal axis to the hormone cortisol, we used the GR ligand binding domain three-dimensional structure to perform computational analysis for eight variants known to cause this clinical condition (I559 N, V571A, D641V, G679S, F737L, I747 M, L753F and L773P), aiming to understand, on the atom scale, how they cause glucocorticoid resistance. We observed that the mutations generated a reduced affinity to cortisol and they alter some loop conformations, which could be a consequence from changes in protein motion, which in turn could result from the reduced stability of mutant GR structures. Therefore, the analyzed mutations compromise the GR ligand binding domain structure and cortisol binding, which could characterize the glucocorticoid resistance phenotype.
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Affiliation(s)
- L L S Monteiro
- Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - O L Franco
- Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil; S-Inova Biotech, Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - S A Alencar
- Programa de Pós-Graduação Em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
| | - W F Porto
- Porto Reports, Brasília, DF, Brazil; S-Inova Biotech, Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
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22
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Chitrala KN, Nagarkatti M, Nagarkatti P, Yeguvapalli S. Analysis of the TP53 Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach. Int J Mol Sci 2019; 20:ijms20122962. [PMID: 31216622 PMCID: PMC6627686 DOI: 10.3390/ijms20122962] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk factors, estrogen levels play a crucial role. Among the estrogen receptors, estrogen receptor alpha (ERα) is known to interact with tumor suppressor protein p53 directly thereby repressing its function. Previously, we have studied the impact of deleterious breast cancer-associated non-synonymous single nucleotide polymorphisms (nsnps) rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 gene on the p53 DNA-binding core domain. In the present study, we aimed to analyze the impact of these mutations on p53–ERα interaction. To this end, we, have modelled the full-length structure of human p53 and validated its quality using PROCHECK and subjected it to energy minimization using NOMAD-Ref web server. Three-dimensional structure of ERα activation function-2 (AF-2) domain was downloaded from the protein data bank. Interactions between the modelled native and mutant (R110P, P278A, P151T) p53 with ERα was studied using ZDOCK. Machine learning predictions on the interactions were performed using Weka software. Results from the protein–protein docking showed that the atoms, residues and solvent accessibility surface area (SASA) at the interface was increased in both p53 and ERα for R110P mutation compared to the native complexes indicating that the mutation R110P has more impact on the p53–ERα interaction compared to the other two mutants. Mutations P151T and P278A, on the other hand, showed a large deviation from the native p53-ERα complex in atoms and residues at the surface. Further, results from artificial neural network analysis showed that these structural features are important for predicting the impact of these three mutations on p53–ERα interaction. Overall, these three mutations showed a large deviation in total SASA in both p53 and ERα. In conclusion, results from our study will be crucial in making the decisions for hormone-based therapies against breast cancer.
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Affiliation(s)
- Kumaraswamy Naidu Chitrala
- Department of Zoology, Sri Venkateswara University, Tirupati 517502, India.
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29208, USA.
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23
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Ren Y, Li Y, Duan X, Wang H, Wang H, Li Z. One-Step Quantitative Single Nucleotide Polymorphism (SNP) Diagnosis By Modified Loop-Mediated Isothermal Amplification (mLAMP). ChemistrySelect 2019. [DOI: 10.1002/slct.201802693] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Yiqian Ren
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Yanru Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Xinrui Duan
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
| | - Honghong Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Hui Wang
- School of Chemistry and Biological Engineering; University of Science&Technology Beijing; Beijing 100083, P.R. China
| | - Zhengping Li
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province and; School of Chemistry and Chemical Engineering; Shaanxi Normal University; 620 Xi Chang'an Street, Xi'an Shaanxi 710119, People's Republic of China
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Elevated expression of p53 in early colon polyps in a pig model of human familial adenomatous polyposis. J Appl Genet 2018; 59:485-491. [PMID: 30145695 DOI: 10.1007/s13353-018-0461-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 01/02/2023]
Abstract
Familial adenomatous polyposis (FAP) is a hereditary predisposition to formation of colon polyps that can progress to colorectal cancer (CRC). The severity of polyposis varies substantially within families bearing the same germline mutation in the adenomatous polyposis coli (APC) tumour suppressor gene. The progressive step-wise accumulation of genetic events in tumour suppressor genes and oncogenes leads to oncogenic transformation, with driver alterations in the tumour protein p53 (TP53) gene playing a key role in advanced stage CRC. We analysed groups of pigs carrying a truncating mutation in APC (APC1311/+; orthologous to human APC1309/+) to study the influence of TP53 polymorphisms and expression on the frequency of polyp formation and polyp progression in early-stage FAP. Five generations of APC1311/+ pigs were examined by colonoscopy for polyposis severity and development. A total of 19 polymorphisms were found in 5'-flanking, coding, and 3' untranslated regions of TP53. The distribution of TP53 genotypes did not differ between APC1311/+ pigs with low (LP) and high (HP) number of colon polyps. p53 mRNA expression was analysed in distally located normal mucosa samples of wild-type pigs, APC1311/+ LP and HP pigs, and also in distally located polyp samples histologically classified as low-grade (LG-IEN) and high-grade intraepithelial dysplastic (HG-IEN) from APC1311/+ pigs. p53 mRNA expression was found to be significantly elevated in HG-IEN compared to LG-IEN samples (p = 0.012), suggesting a role for p53 in the early precancerous stages of polyp development.
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Parvizpour S, Razmara J, Omidi Y. Breast cancer vaccination comes to age: impacts of bioinformatics. ACTA ACUST UNITED AC 2018; 8:223-235. [PMID: 30211082 PMCID: PMC6128970 DOI: 10.15171/bi.2018.25] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/01/2023]
Abstract
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Introduction: Breast cancer, as one of the major causes of cancer death among women, is the central focus of this study. The recent advances in the development and application of computational tools and bioinformatics in the field of immunotherapy of malignancies such as breast cancer have emerged the new dominion of immunoinformatics, and therefore, next generation of immunomedicines .
Methods: Having reviewed the most recent works on the applications of computational tools, we provide comprehensive insights into the breast cancer incidence and its leading causes as well as immunotherapy approaches and the future trends. Furthermore, we discuss the impacts of bioinformatics on different stages of vaccine design for the breast cancer, which can be used to produce much more efficient vaccines through a rationalized time- and cost-effective in silico approaches prior to conducting costly experiments.
Results: The tools can be significantly used for designing the immune system-modulating drugs and vaccines based on in silico approaches prior to in vitro and in vivo experimental evaluations. Application of immunoinformatics in the cancer immunotherapy has shown its success in the pre-clinical models. This success returns back to the impacts of several powerful computational approaches developed during the last decade.
Conclusion: Despite the invention of a number of vaccines for the cancer immunotherapy, more computational and clinical trials are required to design much more efficient vaccines against various malignancies, including breast cancer.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Pharmaceutics, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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Chen K, Duan W, Han Q, Sun X, Li W, Hu S, Wan J, Wu J, Ge Y, Liu D. Identification of the hot spot residues for pyridine derivative inhibitor CCT251455 and ATP substrate binding on monopolar spindle 1 (MPS1) kinase by molecular dynamic simulation. J Biomol Struct Dyn 2018; 37:611-622. [PMID: 29380674 DOI: 10.1080/07391102.2018.1433552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinase monopolar spindle 1 plays an important role in spindle assembly checkpoint at the onset of mitosis. Over expression of MPS1 correlated with a wide range of human tumors makes it an attractive target for finding an effective and specific inhibitor. In this work, we performed molecular dynamics simulations of protein MPS1 itself as well as protein bound systems with the inhibitor and natural substrate based on crystal structures. The reported orally bioavailable 1 h-pyrrolo [3,2-c] pyridine inhibitors of MPS1 maintained stable binding in the catalytic site, while natural substrate ATP could not stay. Comparative study of stability and flexibility of three systems reveals position shifting of β-sheet region within the catalytic site, which indicates inhibition mechanism was through stabilizing the β-sheet region. Binding free energies calculated with MM-GB/PBSA method shows different binding affinity for inhibitor and ATP. Finally, interactions between protein and inhibitor during molecular dynamic simulations were measured and counted. Residue Gly605 and Leu654 were suggested as important hot spots for stable binding of inhibitor by molecular dynamic simulation. Our results reveal an important position shifting within catalytic site for non-inhibited proteins. Together with hot spots found by molecular dynamic simulation, the results provide important information of inhibition mechanism and will be referenced for designing novel inhibitors.
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Affiliation(s)
- Kai Chen
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Wenxiu Duan
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Qianqian Han
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Xuan Sun
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Wenqian Li
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Shuangyun Hu
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Jiajia Wan
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Jiang Wu
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Yushu Ge
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
| | - Dan Liu
- a Collaborative Innovation Center of Chemistry for Life Sciences, Institute of Immunology and the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences , University of Sciences and Technology of China , Hefei , 230027 , P. R. China
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Porto WF, Marques FA, Pogue HB, de Oliveira Cardoso MT, do Vale MGR, da Silva Pires Á, Franco OL, de Alencar SA, Pogue R. Computational Investigation of Growth Hormone Receptor Trp169Arg Heterozygous Mutation in a Child With Short Stature. J Cell Biochem 2017; 118:4762-4771. [DOI: 10.1002/jcb.26144] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 05/17/2017] [Indexed: 11/07/2022]
Affiliation(s)
- William Farias Porto
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Porto ReportsBrasília – DFBrazil
| | - Felipe Albuquerque Marques
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Departamento de FarmáciaUniversidade CEUMASão‐Luis – MABrazil
- Departamento de BiomedicinaUniversidade CEUMASão‐Luis – MABrazil
| | - Huri Brito Pogue
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
| | - Maria Teresinha de Oliveira Cardoso
- Curso de MedicinaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Núcleo de Genética da Secretaria de Saúde do Distrito FederalBrasília – DFBrazil
| | | | - Állan da Silva Pires
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
| | - Octavio Luiz Franco
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- Centro de Análises Proteômicas e Bioquímicas, Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
- S‐Inova Biotech, Pós‐graduação em BiotecnologiaUniversidade Católica Dom BoscoCampo GrandeMSBrazil
| | - Sérgio Amorim de Alencar
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
| | - Robert Pogue
- Programa de Pós‐Graduação em Ciências Genômicas e BiotecnologiaUniversidade Católica de BrasíliaBrasília – DFBrazil
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Pires AS, Porto WF, Franco OL, Alencar SA. In silico analyses of deleterious missense SNPs of human apolipoprotein E3. Sci Rep 2017; 7:2509. [PMID: 28559539 PMCID: PMC5449402 DOI: 10.1038/s41598-017-01737-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/27/2017] [Indexed: 12/23/2022] Open
Abstract
ApoE3 is the major chylomicron apolipoprotein, binding in a specific liver peripheral cell receptor, allowing transport and normal catabolism of triglyceride-rich lipoprotein constituents. Point mutations in ApoE3 have been associated with Alzheimer's disease, type III hyperlipoproteinemia, atherosclerosis, telomere shortening and impaired cognitive function. Here, we evaluate the impact of missense SNPs in APOE retrieved from dbSNP through 16 computational prediction tools, and further evaluate the structural impact of convergent deleterious changes using 100 ns molecular dynamics simulations. We have found structural changes in four analyzed variants (Pro102Arg, Arg132Ser, Arg176Cys and Trp294Cys), two of them (Pro102Arg and Arg176Cys) being previously associated with human diseases. In all cases, except for Trp294Cys, there was a loss in the number of hydrogen bonds between CT and NT domains that could result in their detachment. In conclusion, data presented here could increase the knowledge of ApoE3 activity and be a starting point for the study of the impact of variations on APOE gene.
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Affiliation(s)
- Allan S Pires
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - William F Porto
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
- Porto Reports, Brasília-DF, Brazil
| | - Octavio L Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Sérgio A Alencar
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.
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Skrlj B, Kunej T. Computational identification of non-synonymous polymorphisms within regions corresponding to protein interaction sites. Comput Biol Med 2016; 79:30-35. [PMID: 27744178 DOI: 10.1016/j.compbiomed.2016.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/02/2016] [Accepted: 10/03/2016] [Indexed: 11/24/2022]
Abstract
BACKGROUND Protein-protein interactions (PPI) play an important role in function of all organisms and enable understanding of underlying metabolic processes. Computational predictions of PPIs are an important aspect in proteomics, as experimental methods may result in high degree of false positive results and are more expensive. Although there are many databases collecting predicted PPIs, exploration of genetics information underlying PPI interactions has not been investigated thoroughly. The aim of the present study was to identify genomic locations corresponding to regions involved in predicted PPIs and to collect non-synonymous polymorphisms (nsSNPs) located within those regions; which we termed PPI-SNPs. METHODS Predicted PPIs were obtained from PiSITE database (http://pisite.hgc.jp). Non-synonymous SNPs mapped on protein structural data (PDBs) were obtained from the UCSC server. Polymorphism locations on protein structures were mapped to predicted PPI regions. DAVID tool was used for pathway enrichment and gene cluster analysis (https://david.ncifcrf.gov/). RESULTS We collected 544 polymorphisms located within predicted PPI sites that map to 197 genes. We identified 9 SNPs, previously associated with diseases, but not yet associated with PPI sites. We also found examples in which polymorphisms located within predicted PPI regions are also occurring within previously experimentally validated PPIs and within experimentally determined functional domains. CONCLUSIONS Our study provides the first catalog of nsSNPs located within predicted PPIs. These prioritized SNPs present the basis for planning experimental validation of SNPs that cause gain or loss of PPIs. Our implementation is expandable, as datasets used are constantly updated.
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Affiliation(s)
- Blaz Skrlj
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, Slovenia.
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Groblje 3, Slovenia.
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Kure S, Wada R, Peng WX, Ishii H, Kitamura T, Fujii T, Inai S, Nagao T, Naito Z. A case of oncocytic papillary cystadenocarcinoma of the parotid gland—Pathological and molecular features of a rare tumor. HUMAN PATHOLOGY: CASE REPORTS 2016. [DOI: 10.1016/j.ehpc.2015.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Sousa DA, Porto WF, Silva MZ, da Silva TR, Franco OL. Influence of Cysteine and Tryptophan Substitution on DNA-Binding Activity on Maize α-Hairpinin Antimicrobial Peptide. Molecules 2016; 21:E1062. [PMID: 27529210 PMCID: PMC6273665 DOI: 10.3390/molecules21081062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/29/2016] [Accepted: 08/09/2016] [Indexed: 12/03/2022] Open
Abstract
For almost four decades, antimicrobial peptides have been studied, and new classes are being discovered. However, for therapeutic use of these molecules, issues related to the mechanism of action must be answered. In this work, the antimicrobial activity of the hairpinin MBP-1 was studied by the synthesis of two variants, one replacing cysteines and one tryptophan with alanine. Antibacterial activity was abolished in both variants. No membrane disturbance, even in concentrations higher than those required to inhibit the bacteria, was observed in SEM microscopy. The gel retardation assay showed that MBP-1 possesses a higher DNA-binding ability than variants. Finally, molecular modelling showed that the lack of cysteines resulted in structure destabilization and lack of tryptophan resulted in a less flexible peptide, with less solvent assessable surface area, both characteristics that could contribute to absence of activity. In summary, the data here reported add more information about the multiple mechanisms of action of α-hairpinins.
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Affiliation(s)
- Daniel A Sousa
- Programa de Pós Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil.
| | - William F Porto
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil.
| | - Maria Z Silva
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil.
| | - Tatiane R da Silva
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil.
| | - Octávio L Franco
- Programa de Pós Graduação em Patologia Molecular, Universidade de Brasília, Brasília, DF 70910-900, Brazil.
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF 70790-160, Brazil.
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Catolica Dom Bosco, Campo Grande, MS 79117-900, Brazil.
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A Comprehensive In Silico Analysis on the Structural and Functional Impact of SNPs in the Congenital Heart Defects Associated with NKX2-5 Gene-A Molecular Dynamic Simulation Approach. PLoS One 2016; 11:e0153999. [PMID: 27152669 PMCID: PMC4859487 DOI: 10.1371/journal.pone.0153999] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 03/21/2016] [Indexed: 11/23/2022] Open
Abstract
Congenital heart defects (CHD) presented as structural defects in the heart and blood vessels during birth contribute an important cause of childhood morbidity and mortality worldwide. Many Single nucletotide polymorphisms (SNPs) in different genes have been associated with various types of congenital heart defects. NKX 2–5 gene is one among them, which encodes a homeobox-containing transcription factor that plays a crucial role during the initial phases of heart formation and development. Mutations in this gene could cause different types of congenital heart defects, including Atrial septal defect (ASD), Atrial ventricular block (AVB), Tetralogy of fallot and ventricular septal defect. This highlights the importance of studying the impact of different SNPs found within this gene that might cause structural and functional modification of its encoded protein. In this study, we retrieved SNPs from the database (dbSNP), followed by identification of potentially deleterious Non-synonymous single nucleotide polymorphisms (nsSNPs) and prediction of their effect on proteins by computational screening using SIFT and Polyphen. Furthermore, we have carried out molecular dynamic simulation (MDS) in order to uncover the SNPs that would cause the most structural damage to the protein altering its biological function. The most important SNP that was found using our approach was rs137852685 R161P, which was predicted to cause the most damage to the structural features of the protein. Mapping nsSNPs in genes such as NKX 2–5 would provide valuable information about individuals carrying these polymorphisms, where such variations could be used as diagnostic markers.
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Porto WF, Nolasco DO, Pires ÁS, Fernandes GR, Franco OL, Alencar SA. HD5 and HBD1 variants’ solvation potential energy correlates with their antibacterial activity against Escherichia coli. Biopolymers 2016; 106:43-50. [DOI: 10.1002/bip.22763] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 10/22/2015] [Accepted: 11/02/2015] [Indexed: 11/06/2022]
Affiliation(s)
- William F. Porto
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
| | - Diego O. Nolasco
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Curso De Física; Universidade Católica De Brasília; Brasília DF Brazil
| | - Állan S. Pires
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
| | - Gabriel R. Fernandes
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
| | - Octávio L. Franco
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
- S-Inova Biotech; Pos Graduação em Biotecnologia; Universidade Catolica Dom Bosco; Campo Grande Campo Grande Brazil
| | - Sérgio A. Alencar
- Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia; Universidade Católica De Brasília; Brasília- DF Brazil
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Koulgi S, Achalere A, Sonavane U, Joshi R. Investigating DNA Binding and Conformational Variation in Temperature Sensitive p53 Cancer Mutants Using QM-MM Simulations. PLoS One 2015; 10:e0143065. [PMID: 26579714 PMCID: PMC4651507 DOI: 10.1371/journal.pone.0143065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/30/2015] [Indexed: 12/12/2022] Open
Abstract
The tp53 gene is found to be mutated in 50% of all the cancers. The p53 protein, a product of tp53 gene, is a multi-domain protein. It consists of a core DNA binding domain (DBD) which is responsible for its binding and transcription of downstream target genes. The mutations in p53 protein are responsible for creating cancerous conditions and are found to be occurring at a high frequency in the DBD region of p53. Some of these mutations are also known to be temperature sensitive (ts) in nature. They are known to exhibit partial or strong binding with DNA in the temperature range (298–306 K). Whereas, at 310 K and above they show complete loss in binding. We have analyzed the changes in binding and conformational behavior at 300 K and 310 K for three of the ts-mutants viz., V143A, R249S and R175H. QM-MM simulations have been performed on the wild type and the above mentioned ts-mutants for 30 ns each. The optimal estimate of free energy of binding for a particular number of interface hydrogen bonds was calculated using the maximum likelihood method as described by Chodera et. al (2007). This parameter has been observed to be able to mimic the binding affinity of the p53 ts-mutants at 300 K and 310 K. Thus the correlation between MM-GBSA free energy of binding and hydrogen bonds formed by the interface residues between p53 and DNA has revealed the temperature dependent nature of these mutants. The role of main chain dihedrals was obtained by performing dihedral principal component analysis (PCA). This analysis, suggests that the conformational variations in the main chain dihedrals (ϕ and ψ) of the p53 ts-mutants may have caused reduction in the overall stability of the protein. The solvent exposure of the side chains of the interface residues were found to hamper the binding of the p53 to the DNA. Solvent Accessible Surface Area (SASA) also proved to be a crucial property in distinguishing the conformers obtained at 300 K and 310 K for the three ts-mutants from the wild type at 300 K.
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Affiliation(s)
- Shruti Koulgi
- Bioinformatics Group, Center for Development of Advanced Computing (C-DAC), S.P.Pune University Campus, Pune, India
| | - Archana Achalere
- Bioinformatics Group, Center for Development of Advanced Computing (C-DAC), S.P.Pune University Campus, Pune, India
| | - Uddhavesh Sonavane
- Bioinformatics Group, Center for Development of Advanced Computing (C-DAC), S.P.Pune University Campus, Pune, India
| | - Rajendra Joshi
- Bioinformatics Group, Center for Development of Advanced Computing (C-DAC), S.P.Pune University Campus, Pune, India
- * E-mail:
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Porto WF, Franco OL, Alencar SA. Computational analyses and prediction of guanylin deleterious SNPs. Peptides 2015; 69:92-102. [PMID: 25899674 DOI: 10.1016/j.peptides.2015.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/10/2015] [Accepted: 04/12/2015] [Indexed: 01/01/2023]
Abstract
Human guanylin, coded by the GUCA2A gene, is a member of a peptide family that activates intestinal membrane guanylate cyclase, regulating electrolyte and water transport in intestinal and renal epithelia. Deregulation of guanylin peptide activity has been associated with colon adenocarcinoma, adenoma and intestinal polyps. Besides, it is known that mutations on guanylin receptors could be involved in meconium ileus. However, there are no previous works regarding the alterations driven by single nucleotide polymorphisms in guanylin peptides. A comprehensive in silico analysis of missense SNPs present in the GUCA2A gene was performed taking into account 16 prediction tools in order to select the deleterious variations for further evaluation by molecular dynamics simulations (50 ns). Molecular dynamics data suggest that the three out of five variants (Cys104Arg, Cys112Ser and Cys115Tyr) have undergone structural modifications in terms of flexibility, volume and/or solvation. In addition, two nonsense SNPs were identified, both preventing the formation of disulfide bonds and resulting in the synthesis of truncated proteins. In summary the structural analysis of missense SNPs is important to decrease the number of potential mutations to be in vitro evaluated for associating them with some genetic diseases. In addition, data reported here could lead to a better understanding of structural and functional aspects of guanylin peptides.
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Affiliation(s)
- William F Porto
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil
| | - Octávio L Franco
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil; C S-Inova, Pos-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil.
| | - Sérgio A Alencar
- Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF, Brazil.
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