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Araujo NA, Bubis J. Analysis of a Novel Peptide That Is Capable of Inhibiting the Enzymatic Activity of the Protein Kinase A Catalytic Subunit-Like Protein from Trypanosoma equiperdum. Protein J 2023; 42:709-727. [PMID: 37713008 DOI: 10.1007/s10930-023-10153-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 09/16/2023]
Abstract
A 26-residue peptide possessing the αN-helix motif of the protein kinase A (PKA) regulatory subunit-like proteins from the Trypanozoom subgenera (VAP26, sequence = VAPYFEKSEDETALILKLLTYNVLFS), was shown to inhibit the enzymatic activity of the Trypanosoma equiperdum PKA catalytic subunit-like protein, in a similar manner that the mammalian heat-stable soluble PKA inhibitor known as PKI. However, VAP26 does not contain the PKI inhibitory sequence. Bioinformatics analyzes of the αN-helix motif from various Trypanozoon PKA regulatory subunit-like proteins suggested that the sequence could form favorable peptide-protein interactions of hydrophobic nature with the PKA catalytic subunit-like protein, which possibly may represent an alternative PKA inhibitory mechanism. The sequence of the αN-helix motif of the Trypanozoon proteins was shown to be highly homologous but significantly divergent from the corresponding αN-helix motifs of their Leishmania and mammalian counterparts. This sequence divergence contrasted with the proposed secondary structure of the αN-helix motif, which appeared conserved in every analyzed regulatory subunit-like protein. In silico mutation experiments at positions I234, L238 and F244 of the αN-helix motif from the Trypanozoon proteins destabilized both the specific motif and the protein. On the contrary, mutations at positions T239 and Y240 stabilized the motif and the protein. These results suggested that the αN-helix motif from the Trypanozoon proteins probably possessed a different evolutionary path than their Leishmania and mammalian counterparts. Moreover, finding stabilizing mutations indicated that new inhibitory peptides may be designed based on the αN-helix motif from the Trypanozoon PKA regulatory subunit-like proteins.
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Affiliation(s)
- Nelson A Araujo
- Escuela de Ciencias Agroalimentarias, Animales y Ambientales, Universidad de O'Higgins, Campus Colchagua, ruta I-90, Km 3, San Fernando, Chile.
| | - José Bubis
- Unidad de Polimorfismo Genético, Genómica y Proteómica, Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas, 1015-A, Venezuela
- Unidad de Señalización Celular y Bioquímica de Parásitos, Dirección de Salud, Fundación Instituto de Estudios Avanzados IDEA, Caracas, 1015-A, Venezuela
- Departamento de Biología Celular, Universidad Simón Bolívar, Apartado 89.000, Caracas, 1081‑A, Venezuela
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Rehman A, Akram AM, Chaudhary A, Sheikh N, Hussain Z, Alsanie WF, Rehman RA, Hameed N, Saleem T, Zafar A, Absar M, Iqbal Z, Alhazmi A, Baeshen HA, Mohammedsaleh ZM, Qamer S, Sayed S, Gaber A. RUNX1 mutation and elevated FLT3 gene expression cooperates to induce inferior prognosis in cytogenetically normal acute myeloid leukemia patients. Saudi J Biol Sci 2021; 28:4845-4851. [PMID: 34466057 PMCID: PMC8381075 DOI: 10.1016/j.sjbs.2021.07.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 11/25/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a bone marrow malignancy having multiple molecular pathways driving its progress. In recent years, the main causes of AML considered all over the world are genetic variations in cancerous cells. The RUNX1 and FLT3 genes are necessary for the normal hematopoiesis and differentiation process of hematopoietic stem cells into mature blood cells, therefore they are the most common targets for point mutations resulting in AML. Methods We screened 32 CN-AML patients for FLT3-ITD (by Allele-specific PCR) and RUNX1 mutations (by Sanger sequencing). The FLT3 mRNA expression was assessed in all AML patients and its subgroups. Results Eight patients (25%) carried RUNX1 mutation (K83E) while three patients (9.37%) were found to have internal tandem duplications in FLT3 gene. The RUNX1 mutation data were correlated with clinical parameters and FLT3 gene expression profile. The RUNX1 mutations were observed to be significantly prevalent in older males. Moreover, RUNX1 and FLT3-mutated patients had lower complete remission rate, event-free survival rate, and lower overall survival rate than patients with wild-type RUNX1 and FLT3 gene. The RUNX1 and FLT3 mutant patients with up-regulated FLT3 gene expression showed even worse prognosis. Bradford Assay showed that protein concentration was down-regulated in RUNX1 and FLT3 mutants in comparison to RUNX1 and FLT3 wild-type groups. Conclusion This study constitutes the first report from Pakistan reporting significant molecular mutation analysis of RUNX1 and FLT3 genes including FLT3 expression evaluation with follow-up. This provides an insight that aforementioned mutations are markers of poor prognosis but the study with a large AML cohort will be useful to further investigate their role in disease biology of AML.
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Affiliation(s)
- Atia Rehman
- Cell and Molecular Biology Lab (CMBL), Department of Zoology, University of the Punjab, Lahore, Pakistan.,Molecular Biology Lab, University of Education, Township Campus, College Road, Lahore, Pakistan
| | - Afia Muhammad Akram
- Molecular Biology Lab, University of Education, Township Campus, College Road, Lahore, Pakistan
| | - Asma Chaudhary
- Molecular Biology Lab, University of Education, Township Campus, College Road, Lahore, Pakistan
| | - Nadeem Sheikh
- Cell and Molecular Biology Lab (CMBL), Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Zawar Hussain
- Molecular Biology Lab, University of Education, Township Campus, College Road, Lahore, Pakistan
| | - Walaa F Alsanie
- Center of Biomedical Sciences Research (CBSR), Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.,Department of Clinical Laboratories Sciences, The Faculty of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Rahat Abdul Rehman
- Department of Forensic Science, University of Health Sciences, Lahore, Pakistan
| | - Naila Hameed
- Cell and Molecular Biology Lab (CMBL), Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Tayyaba Saleem
- Cell and Molecular Biology Lab (CMBL), Department of Zoology, University of the Punjab, Lahore, Pakistan
| | - Amjad Zafar
- Department of Oncology, Mayo Hospital, Anarkali Bazar, Lahore, Pakistan
| | - Muhammad Absar
- Microbiology, Pathology & Laboratory Medicine, King Abdulaziz Hospital, Ministry of National Guard-Health Affairs, Saudi Arabia
| | - Zafar Iqbal
- Cancer and Medical Genetics, CAMS-A, King Saud Bin Abdulaziz University for Health Sciences & King Abdullah International Medical Research Centre (KAIMRC), King Abdulaziz Medical City, National Guard Health Affairs, Al Ahsa, Saudi Arabia
| | - Alaa Alhazmi
- Medical Laboratory Technology Department, Jazan University, Jazan, Saudi Arabia.,SMIRES for Consultation in Specialized Medical Laboratories, Jazan University, Jazan, Saudi Arabia
| | - Hosam Ali Baeshen
- Department of Orthodontics, Faculty of Dentistry, King Abdulaziz University, P.O. Box 80209, Jeddah 21589, Saudi Arabia
| | - Zuhair M Mohammedsaleh
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Samina Qamer
- Department of Zoology, Government College University, Faisalabad, Pakistan
| | - Samy Sayed
- Department of Science and Technology, University College-Ranyah, Taif University, B.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed Gaber
- Center of Biomedical Sciences Research (CBSR), Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia.,Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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Prabantu VM, Naveenkumar N, Srinivasan N. Influence of Disease-Causing Mutations on Protein Structural Networks. Front Mol Biosci 2021; 7:620554. [PMID: 33778000 PMCID: PMC7987782 DOI: 10.3389/fmolb.2020.620554] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/17/2020] [Indexed: 01/18/2023] Open
Abstract
The interactions between residues in a protein tertiary structure can be studied effectively using the approach of protein structure network (PSN). A PSN is a node-edge representation of the structure with nodes representing residues and interactions between residues represented by edges. In this study, we have employed weighted PSNs to understand the influence of disease-causing mutations on proteins of known 3D structures. We have used manually curated information on disease mutations from UniProtKB/Swiss-Prot and their corresponding protein structures of wildtype and disease variant from the protein data bank. The PSNs of the wildtype and disease-causing mutant are compared to analyse variation of global and local dissimilarity in the overall network and at specific sites. We study how a mutation at a given site can affect the structural network at a distant site which may be involved in the function of the protein. We have discussed specific examples of the disease cases where the protein structure undergoes limited structural divergence in their backbone but have large dissimilarity in their all atom networks and vice versa, wherein large conformational alterations are observed while retaining overall network. We analyse the effect of variation of network parameters that characterize alteration of function or stability.
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Affiliation(s)
| | - Nagarajan Naveenkumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,National Centre for Biological Sciences, TIFR, Bangalore, India.,Bharathidasan University, Tiruchirappalli, India
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Zhang T, Na JH, Li S, Chen Z, Zhang G, Pang S, Daniyan AF, Li Y, Shi L, Du YCN. Functional impact of cancer patient-associated Bcl-xL mutations. MedComm (Beijing) 2020; 1:328-337. [PMID: 34308416 PMCID: PMC8302207 DOI: 10.1002/mco2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Bcl-xL, an antiapoptotic protein, is frequently overexpressed in cancer to promote survival of tumor cells. However, we have previously shown that Bcl-xL promotes migration, invasion, and metastasis independent of its antiapoptotic function in mitochondria. The pro-metastatic function of Bcl-xL may require its translocation into the nucleus. Besides overexpression, patient-associated mutations of Bcl-xL have been identified in large-scale cancer genomics projects. Understanding the functions of these mutations will guide the development of precision medicine. Here, we selected four patient-associated Bcl-xL mutations, R132W, N136K, R165W, and A201T, to investigate their impacts on antiapoptosis, migration, and nuclear translocation. We found that all four mutation proteins could be detected in both the nucleus and cytosol. Although all four mutations disrupted the antiapoptosis function, one of these mutants, N136K, significantly improved the ability to promote cell migration. These data suggest the importance of developing novel Bcl-xL inhibitors to ablate both antiapoptotic and pro-metastatic functions of Bcl-xL in cancer.
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Affiliation(s)
- Tiantian Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Joseph HyungJoon Na
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Samantha Li
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
| | - George Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Sharon Pang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
| | - Anthony F Daniyan
- Department of Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, Maryland
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York
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P. Katare D, Malik S, J. Mani R, Ranjpour M, Jain SK. Novel mutations in transthyretin gene associated with hepatocellular carcinoma. Mol Carcinog 2017; 57:70-77. [DOI: 10.1002/mc.22732] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/08/2017] [Accepted: 09/05/2017] [Indexed: 02/04/2023]
Affiliation(s)
- Deepshikha P. Katare
- Proteomics and Translational Research Lab; Centre for Medical Biotechnology; Amity Institute of Biotechnology; Amity University; Noida Uttar Pradesh India
| | - Shabnam Malik
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| | - Ruchi J. Mani
- Proteomics and Translational Research Lab; Centre for Medical Biotechnology; Amity Institute of Biotechnology; Amity University; Noida Uttar Pradesh India
| | - Maryam Ranjpour
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
| | - Swatantra K. Jain
- Faculty of Chemical and Life Sciences; Department of Biotechnology; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
- Department of Medical Biochemistry; Hamdard Institute of Medical Sciences and Research; Hamdard University; New Delhi India
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Computational Approaches and Resources in Single Amino Acid Substitutions Analysis Toward Clinical Research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2014; 94:365-423. [DOI: 10.1016/b978-0-12-800168-4.00010-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res 2011; 39:e118. [PMID: 21727090 PMCID: PMC3177186 DOI: 10.1093/nar/gkr407] [Citation(s) in RCA: 1393] [Impact Index Per Article: 107.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The information in these patterns is derived from aligned families and sub-families of sequence homologs within and between species using combinatorial entropy formalism. The score performs well on a large set of human protein mutations in separating disease-associated variants (∼19 200), assumed to be strongly functional, from common polymorphisms (∼35 600), assumed to be weakly functional (area under the receiver operating characteristic curve of ∼0.86). In cancer, using recurrence, multiplicity and annotation for ∼10 000 mutations in the COSMIC database, the method does well in assigning higher scores to more likely functional mutations ('drivers'). To guide experimental prioritization, we report a list of about 1000 top human cancer genes frequently mutated in one or more cancer types ranked by likely functional impact; and, an additional 1000 candidate cancer genes with rare but likely functional mutations. In addition, we estimate that at least 5% of cancer-relevant mutations involve switch of function, rather than simply loss or gain of function.
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Affiliation(s)
- Boris Reva
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, NY 10065, USA
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Zhang N, Jiang Y, Zou J, Yu Q, Zhao W. Structural basis for the complete loss of GSK3beta catalytic activity due to R96 mutation investigated by molecular dynamics study. Proteins 2009; 75:671-81. [PMID: 19003984 DOI: 10.1002/prot.22279] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many Ser/Thr protein kinases, to be fully activated, are obligated to introduce a phospho-Ser/Thr in their activation loop. Presently, the similarity of activation loop between two crystal complexes, i.e. glycogen synthase kinase 3beta (GSK3beta)-AMPNP and GSK3beta-sulfate ion complex, indicates that the activation segment of GSK3beta is preformed requiring neither a phosphorylation event nor conformational changes. GSK3beta, when participated in glycogen synthesis and Wnt signaling pathways, possesses a unique feature with the preference of such substrate with a priming phosphate. Experimental mutagenesis proved that the residue arginine at amino acid 96 mutations to lysine (R96K) or alanine (R96A) selectively abolish activity on the substrates involved in glycogen synthesis signaling pathway. Based on two solved crystal structures, wild type (WT) and two mutants (R96K and R96A) GSK3beta-ATP-phospho-Serine (pSer) complexes were modeled. Molecular dynamics simulations and energy analysis were employed to investigate the effect of pSer involvement on the GSK3beta structure in WT, and the mechanisms of GSK3beta deactivation due to R96K and R96A mutations. The results indicate that the introduction of pSer to WT GSK3beta generates a slight lobe closure on GSK3beta without any remarkable changes, which may illuminate the experimental conclusion, whereas the conformations of GSK3beta and ATP undergo significant changes in two mutants. As to GSK3beta, the affected positions distribute over activation loop, alpha-helix, and glycine-rich loop. Based on coupling among the mentioned positions, the allosteric mechanisms for distorted ATP were proposed. Energy decomposition on the residues of activation loop identified the important residues Arg96 and Arg180 in anchoring the phosphate group.
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Affiliation(s)
- Na Zhang
- Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo, China
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