D. Es, Beutline Malgija, Appadurai Muthamil Iniyan, S. Vincent
Myeloid cell leukemia‐1 (MCL1), an anti‐apoptotic BCL‐2 family protein plays a major role in the control of apoptosis as the regulator of mitochondrial permeability which is deregulated in various solid and hematological malignancies. Interaction of the executioner proteins Bak/Bax with anti‐apoptotic MCL1 and its cellular composition determines the apoptotic or survival pathway. Mutations act at various levels in the apoptotic process and can contribute to disease. Single nucleotide polymorphism (SNP) in MCL1 gene was focused as they result in changes in the amino acid sequence and have been associated with tumorigenesis. This study highlighted the deleterious MCL1‐Bax stabilizing effect of the mutation V220F on MCL1 structure through computational protein–protein interaction predictions and molecular dynamics simulations. The single point mutation at V220F was selected as it is residing at the hydrophobic core region of BH3 conserved domain, the site of Bax binding. The molecular dynamics simulation studies showed increase in stability of the mutated MCL1 before and after Bax binding comparable with the native MCL1. The clusters from free energy landscape found out structural variation in folding pattern with additional helix near the BH3 domain in the mutated structure. This loop to helix structural change in the mutated complex favored stable interaction of the complex and also induced Bax conformational change. Moreover, molecular mechanics‐based binding free energy calculations confirmed increased affinity of Bax toward mutated MCL1. Residue‐wise interaction network analysis showed the individual residues in Bax binding responsible for the change in stability and interaction due to the protein mutation. In conclusion, the overall findings from the study reveal that the presence of V220F mutation on MCL1 is responsible for the structural confirmational change leading to disruption of its biological functions which might be responsible for tumorigenesis. The mutation could possibly be used as future diagnostic markers in treating cancers.
{"title":"Mutation in MCL1 predicted loop to helix structural transition stabilizes MCL1–Bax binding interaction favoring cancer cell survival","authors":"D. Es, Beutline Malgija, Appadurai Muthamil Iniyan, S. Vincent","doi":"10.1002/prot.26347","DOIUrl":"https://doi.org/10.1002/prot.26347","url":null,"abstract":"Myeloid cell leukemia‐1 (MCL1), an anti‐apoptotic BCL‐2 family protein plays a major role in the control of apoptosis as the regulator of mitochondrial permeability which is deregulated in various solid and hematological malignancies. Interaction of the executioner proteins Bak/Bax with anti‐apoptotic MCL1 and its cellular composition determines the apoptotic or survival pathway. Mutations act at various levels in the apoptotic process and can contribute to disease. Single nucleotide polymorphism (SNP) in MCL1 gene was focused as they result in changes in the amino acid sequence and have been associated with tumorigenesis. This study highlighted the deleterious MCL1‐Bax stabilizing effect of the mutation V220F on MCL1 structure through computational protein–protein interaction predictions and molecular dynamics simulations. The single point mutation at V220F was selected as it is residing at the hydrophobic core region of BH3 conserved domain, the site of Bax binding. The molecular dynamics simulation studies showed increase in stability of the mutated MCL1 before and after Bax binding comparable with the native MCL1. The clusters from free energy landscape found out structural variation in folding pattern with additional helix near the BH3 domain in the mutated structure. This loop to helix structural change in the mutated complex favored stable interaction of the complex and also induced Bax conformational change. Moreover, molecular mechanics‐based binding free energy calculations confirmed increased affinity of Bax toward mutated MCL1. Residue‐wise interaction network analysis showed the individual residues in Bax binding responsible for the change in stability and interaction due to the protein mutation. In conclusion, the overall findings from the study reveal that the presence of V220F mutation on MCL1 is responsible for the structural confirmational change leading to disruption of its biological functions which might be responsible for tumorigenesis. The mutation could possibly be used as future diagnostic markers in treating cancers.","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"59 1","pages":"1699 - 1713"},"PeriodicalIF":0.0,"publicationDate":"2022-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84786425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.26094","DOIUrl":"https://doi.org/10.1002/prot.26094","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"13 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77695984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Boosting the analysis of protein interfaces with Multiple Interface String Alignments: illustration on the spikes of coronaviruses S. Bereux, B. Delmas, F. Cazals Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions T. O'Donnell, C. H. Robert, F. Cazals The non-prion SUP35 preexists in large chaperone-containing molecular complexes Shiwha Park, Xin Wang, Wen Xi, Roy Richardson, Thomas M. Laue, Clyde L. Denis In Memoriam of Narayanaswamy Srinivasan (1962-2021) Frank Eisenhaber, Chandra Verma, Tom Blundell Substrate-Assisted Activation and Selectivity of the Bacterial RavD Effector Deubiquitinylase Eric Schulze-Niemand, Michael Naumann, Matthias Stein Scaling-up a fragment-based protein-protein interaction method using a human reference interaction set Stephanie Schaefer-Ramadan, Jovana Aleksic, Nayra M. Al-Thani, Yasmin A. Mohamoud, David E. Hill, Joel A. Malek A novel chimeric protein with enhanced cytotoxic effects on breast cancer in vitro and in vivo Fereshte Hazrati, Massoud Saidijam, Yaghoub Ahmadyousefi, Fatemeh Nouri, Hamidreza Ghadimipour, Mohammadreza Moradi, Rasool Haddadi, Meysam Soleimani A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions Ayca Circir, Gozde Koksal Bicakci, Busra Savas, Didem Naz Doken, Şevki Onur Henden, Tolga Can, Ezgi Karaca, Ayse Elif Erson-Bensan
多界面串比对促进蛋白质界面分析——以冠状病毒刺突为例S. Bereux, B. Delmas, F. Cazals三肽环闭合Stephanie Schaefer-Ramadan, Jovana Aleksic, Nayra M. Al-Thani, Yasmin a . Mohamoud, David E. Hill, Joel a . Malek体外和体内增强乳腺癌细胞毒作用的新型嵌合蛋白Fereshte Hazrati, Massoud Saidijam, Yaghoub Ahmadyousefi, Fatemeh Nouri, Hamidreza Ghadimipour, Mohammadreza Moradi, Rasool Haddadi，Ayca circirr, Gozde Koksal Bicakci, Busra Savas, Didem Naz Doken， Şevki Onur Henden, Tolga Can, Ezgi Karaca, Ayse Elif Erson-Bensan编码的C-term截断EIF2Bγ蛋白引入不利的EIF2Bγ - eif2γ相互作用
{"title":"Issue Information ‐ Forthcoming","authors":"Thomas M. Laue, Clyde L. Denis","doi":"10.1002/prot.26091","DOIUrl":"https://doi.org/10.1002/prot.26091","url":null,"abstract":"Boosting the analysis of protein interfaces with Multiple Interface String Alignments: illustration on the spikes of coronaviruses S. Bereux, B. Delmas, F. Cazals Tripeptide loop closure: a detailed study of reconstructions based on Ramachandran distributions T. O'Donnell, C. H. Robert, F. Cazals The non-prion SUP35 preexists in large chaperone-containing molecular complexes Shiwha Park, Xin Wang, Wen Xi, Roy Richardson, Thomas M. Laue, Clyde L. Denis In Memoriam of Narayanaswamy Srinivasan (1962-2021) Frank Eisenhaber, Chandra Verma, Tom Blundell Substrate-Assisted Activation and Selectivity of the Bacterial RavD Effector Deubiquitinylase Eric Schulze-Niemand, Michael Naumann, Matthias Stein Scaling-up a fragment-based protein-protein interaction method using a human reference interaction set Stephanie Schaefer-Ramadan, Jovana Aleksic, Nayra M. Al-Thani, Yasmin A. Mohamoud, David E. Hill, Joel A. Malek A novel chimeric protein with enhanced cytotoxic effects on breast cancer in vitro and in vivo Fereshte Hazrati, Massoud Saidijam, Yaghoub Ahmadyousefi, Fatemeh Nouri, Hamidreza Ghadimipour, Mohammadreza Moradi, Rasool Haddadi, Meysam Soleimani A C-term truncated EIF2Bγ protein encoded by an intronically polyadenylated isoform introduces unfavorable EIF2Bγ–EIF2γ interactions Ayca Circir, Gozde Koksal Bicakci, Busra Savas, Didem Naz Doken, Şevki Onur Henden, Tolga Can, Ezgi Karaca, Ayse Elif Erson-Bensan","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"46 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82592614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.26090","DOIUrl":"https://doi.org/10.1002/prot.26090","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"90 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80784934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The devastating, unexpected news of Prof. Narayanaswamy Srinivasan, a world-renowned pioneer in structural computational biology, genomics, and biophysics, passing away on September 3, 2021, spread among the international scientific community within hours. We mourn not only the loss of a super-engaged, creative scientist with a sharp mind but also the loss of a teacher for numerous PhD students and postdocs who made a career after their time with him and of an influential voice in the Indian academic system always defending the importance and the needs of science and its benefits for society. N. Srinivasan was an unusual man. He had the extraordinary gift to win people over, to see and to emphasize the common interest, to let his colleagues feel appreciated and convenient with him. This is not a little achievement in the generally very competitive scientific community that is overpopulated with very personal success-oriented or borderline personalities (maybe, as a side effect of the constant demand for creativity). For his wide, international circle of close friends and colleagues, he was Srini, the sanguine, friendly smiling scientist with a neverending interest in scientific discovery. For those who encountered him first at later stages of his life, he was always seen together with his lovely life companion Mini (Prof. Ramanathan Sowdhamini, currently at NCBS, Bangalore). Mini and Srini were the epitome of a scientific couple, both being impactful in their own right but most effective together. His family was very important to him. His joy did not know any bounds when, in 1996, his daughter Jayashree (currently studying biotechnology) was born. Srini was often preoccupied in being social with his friends and colleagues and playful (yes, also playing computer games or enjoying watching cricket games, sometimes, much to the annoyance of his fiancé!). He liked to share breakfast, typically starting at 8 a.m., with guests, all the time gossiping away on the lives, trials, and tribulations of acquaintances, some scientific discovery, or usually him excitedly discussing a recent discovery made in his lab. This routine had a very funny ending, which was usually around 9 a.m., when he would suddenly look at his watch with horror and with that warm smile admonish himself for leaving too late and rush off to catch the bus that would ferry him to his office at the Indian Institute of Science. Narayanaswamy Srinivasan was born on April 1, 1962 (at Government Kasturba Gandhi Hospital for Women and Children in Triplicane, Chennai/Tamil Nadu) to late Mr. K. Narayanaswamy and Ms. N. Jayalakshmi as the youngest child to a family of eight children. Maybe, being born on April Fools' Day had forever inserted the sense for humor and joke into him. As a young boy, Srinivasan was very sports-oriented and enjoyed playing cricket. His high schooling was in Rajah Muthiah Higher Secondary School (in Raja Annamalai Puram, Chennai) during the years 1976–1979. He earned hi
{"title":"In memoriam of Narayanaswamy Srinivasan (1962–2021)","authors":"F. Eisenhaber, Chandra Verma, T. Blundell","doi":"10.1002/prot.26287","DOIUrl":"https://doi.org/10.1002/prot.26287","url":null,"abstract":"The devastating, unexpected news of Prof. Narayanaswamy Srinivasan, a world-renowned pioneer in structural computational biology, genomics, and biophysics, passing away on September 3, 2021, spread among the international scientific community within hours. We mourn not only the loss of a super-engaged, creative scientist with a sharp mind but also the loss of a teacher for numerous PhD students and postdocs who made a career after their time with him and of an influential voice in the Indian academic system always defending the importance and the needs of science and its benefits for society. N. Srinivasan was an unusual man. He had the extraordinary gift to win people over, to see and to emphasize the common interest, to let his colleagues feel appreciated and convenient with him. This is not a little achievement in the generally very competitive scientific community that is overpopulated with very personal success-oriented or borderline personalities (maybe, as a side effect of the constant demand for creativity). For his wide, international circle of close friends and colleagues, he was Srini, the sanguine, friendly smiling scientist with a neverending interest in scientific discovery. For those who encountered him first at later stages of his life, he was always seen together with his lovely life companion Mini (Prof. Ramanathan Sowdhamini, currently at NCBS, Bangalore). Mini and Srini were the epitome of a scientific couple, both being impactful in their own right but most effective together. His family was very important to him. His joy did not know any bounds when, in 1996, his daughter Jayashree (currently studying biotechnology) was born. Srini was often preoccupied in being social with his friends and colleagues and playful (yes, also playing computer games or enjoying watching cricket games, sometimes, much to the annoyance of his fiancé!). He liked to share breakfast, typically starting at 8 a.m., with guests, all the time gossiping away on the lives, trials, and tribulations of acquaintances, some scientific discovery, or usually him excitedly discussing a recent discovery made in his lab. This routine had a very funny ending, which was usually around 9 a.m., when he would suddenly look at his watch with horror and with that warm smile admonish himself for leaving too late and rush off to catch the bus that would ferry him to his office at the Indian Institute of Science. Narayanaswamy Srinivasan was born on April 1, 1962 (at Government Kasturba Gandhi Hospital for Women and Children in Triplicane, Chennai/Tamil Nadu) to late Mr. K. Narayanaswamy and Ms. N. Jayalakshmi as the youngest child to a family of eight children. Maybe, being born on April Fools' Day had forever inserted the sense for humor and joke into him. As a young boy, Srinivasan was very sports-oriented and enjoyed playing cricket. His high schooling was in Rajah Muthiah Higher Secondary School (in Raja Annamalai Puram, Chennai) during the years 1976–1979. He earned hi","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78634463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25942","DOIUrl":"https://doi.org/10.1002/prot.25942","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"24 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88473031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for non-catalytic roles Anindita Paul, Seemadri Subhadarshini, Narayanaswamy Srinivasan Chemical Reactivity and Binding Interactions in RNA–Peptide Complexes Ruby Srivastava MMPL-Family Proteins in Bacteria, Protozoa, Fungi, Plants and Animals: A Bioinformatics and Structural Investigation Satish R. Malwal, Eric Oldfield In Silico Prediction of SARS-CoV-2 Main Protease Cleavage Sites Zheng Rong Yang Prokaryotic expression, evaluation, and prediction of the structure and function of the ecarin metalloproteinase domain Nasrin Mohammadi, Mojgan Bandehpour, Fattah Sotoodehnejadnematalahi, Bahram Kazemi Molecular insights into the inhibition of glutamate dehydrogenase (GDH) by the dicarboxylic acid metabolites Barsa Kanchan Jyotshna Godsora, Prem Prakash, Narayan S. Punekar, Prasenjit Bhaumik Physics-based protein structure refinement in the era of artificial intelligence Lim Heo, Giacomo Janson, Michael Feig Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas
{"title":"Issue Information ‐ Forthcoming","authors":"Seemadri Subhadarshini","doi":"10.1002/prot.25939","DOIUrl":"https://doi.org/10.1002/prot.25939","url":null,"abstract":"Pseudokinases repurpose flexibility signatures associated with the protein kinase fold for non-catalytic roles Anindita Paul, Seemadri Subhadarshini, Narayanaswamy Srinivasan Chemical Reactivity and Binding Interactions in RNA–Peptide Complexes Ruby Srivastava MMPL-Family Proteins in Bacteria, Protozoa, Fungi, Plants and Animals: A Bioinformatics and Structural Investigation Satish R. Malwal, Eric Oldfield In Silico Prediction of SARS-CoV-2 Main Protease Cleavage Sites Zheng Rong Yang Prokaryotic expression, evaluation, and prediction of the structure and function of the ecarin metalloproteinase domain Nasrin Mohammadi, Mojgan Bandehpour, Fattah Sotoodehnejadnematalahi, Bahram Kazemi Molecular insights into the inhibition of glutamate dehydrogenase (GDH) by the dicarboxylic acid metabolites Barsa Kanchan Jyotshna Godsora, Prem Prakash, Narayan S. Punekar, Prasenjit Bhaumik Physics-based protein structure refinement in the era of artificial intelligence Lim Heo, Giacomo Janson, Michael Feig Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80229138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25938","DOIUrl":"https://doi.org/10.1002/prot.25938","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"183 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77543144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25934","DOIUrl":"https://doi.org/10.1002/prot.25934","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"4 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87115720","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Issue Information ‐ Table of Content","authors":"","doi":"10.1002/prot.25930","DOIUrl":"https://doi.org/10.1002/prot.25930","url":null,"abstract":"","PeriodicalId":20789,"journal":{"name":"Proteins: Structure","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91308710","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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