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EDITORIAL
Prakash Kulkarni, Stefania Brocca, A Keith Dunker, Sonia Longhi
Until the late 1990s, we believed that protein function required a unique, well-defined 3D structure encrypted in the amino acid sequence [...].
June 19, 2023: Biomolecules
#2
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID-percentage of intrinsic disorder-of the membrane protein M, PIDM ) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PIDN ) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations...
September 23, 2022: Biomolecules
#3
REVIEW
Lolita Piersimoni, Marina Abd El Malek, Twinkle Bhatia, Julian Bender, Christin Brankatschk, Jaime Calvo Sánchez, Guy W Dayhoff, Alessio Di Ianni, Jhonny Oscar Figueroa Parra, Dailen Garcia-Martinez, Julia Hesselbarth, Janett Köppen, Luca M Lauth, Laurin Lippik, Lisa Machner, Shubhra Sachan, Lisa Schmidt, Robin Selle, Ioannis Skalidis, Oleksandr Sorokin, Daniele Ubbiali, Bruno Voigt, Alice Wedler, Alan An Jung Wei, Peter Zorn, Alan Keith Dunker, Marcel Köhn, Andrea Sinz, Vladimir N Uversky
Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry...
July 26, 2022: Cellular and Molecular Life Sciences: CMLS
#4
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. The SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9%-lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants and pangolin-CoV-2017 (5...
April 25, 2022: Biomolecules
#5
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
The shell disorder models have predicted that SARS-CoV-2 is of a specific but peculiar evolutionary nature. All coronaviruses (CoVs) closely related to SARS-CoV-2 have been found to have the hardest outer shells (M protein) among CoVs. This hard shell (low M percentage of intrinsic disorder (PID)) is associated with burrowing animals, for example, pangolins, and is believed to be responsible for the high contagiousness of SARS-CoV-2 because it will be more resistant to antimicrobial enzymes found in saliva/mucus...
February 10, 2022: Journal of Proteome Research
#6
EDITORIAL
Sarah E Bondos, A Keith Dunker, Vladimir N Uversky
For proteins, the sequence → structure → function paradigm applies primarily to enzymes, transmembrane proteins, and signaling domains. This paradigm is not universal, but rather, in addition to structured proteins, intrinsically disordered proteins and regions (IDPs and IDRs) also carry out crucial biological functions. For these proteins, the sequence → IDP/IDR ensemble → function paradigm applies primarily to signaling and regulatory proteins and regions. Often, in order to carry out function, IDPs or IDRs cooperatively interact, either intra- or inter-molecularly, with structured proteins or other IDPs or intermolecularly with nucleic acids...
August 30, 2021: Cell Communication and Signaling: CCS
#7
JOURNAL ARTICLE
Mikhail Makarov, Jingwei Meng, Vyacheslav Tretyachenko, Pavel Srb, Anna Březinová, Valerio Guido Giacobelli, Lucie Bednárová, Jiří Vondrášek, A Keith Dunker, Klára Hlouchová
The wide variety of protein structures and functions results from the diverse properties of the 20 canonical amino acids. The generally accepted hypothesis is that early protein evolution was associated with enrichment of a primordial alphabet, thereby enabling increased protein catalytic efficiencies and functional diversification. Aromatic amino acids were likely among the last additions to genetic code. The main objective of this study was to test whether enzyme catalysis can occur without the aromatic residues (aromatics) by studying the structure and function of dephospho-CoA kinase (DPCK) following aromatic residue depletion...
March 19, 2021: Protein Science
#8
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
Several related viral shell disorder (disorder of shell proteins of viruses) models were built using a disorder predictor via AI. The parent model detected the presence of high levels of disorder at the outer shell in viruses, for which vaccines are not available. Another model found correlations between inner shell disorder and viral virulence. A third model was able to positively correlate the levels of respiratory transmission of coronaviruses (CoVs). These models are linked together by the fact that they have uncovered two novel immune evading strategies employed by the various viruses...
2021: Pacific Symposium on Biocomputing
#9
JOURNAL ARTICLE
Gil Alterovitz, Wei-Lun Alterovitz, Gail H Cassell, Lixin Zhang, A Keith Dunker
AI for infectious disease modelling and therapeutics is an emerging area that leverages new computational approaches and data in this area. Genomics, proteomics, biomedical literature, social media, and other resources are proving to be critical tools to help understand and solve complicated issues ranging from understanding the process of infection, diagnosis and discovery of the precise molecular details, to developing possible interventions and safety profiling of possible treatments.
2021: Pacific Symposium on Biocomputing
#10
JOURNAL ARTICLE
Bi Zhao, Akila Katuwawala, Christopher J Oldfield, A Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz Kurgan
We present DescribePROT, the database of predicted amino acid-level descriptors of structure and function of proteins. DescribePROT delivers a comprehensive collection of 13 complementary descriptors predicted using 10 popular and accurate algorithms for 83 complete proteomes that cover key model organisms. The current version includes 7.8 billion predictions for close to 600 million amino acids in 1.4 million proteins. The descriptors encompass sequence conservation, position specific scoring matrix, secondary structure, solvent accessibility, intrinsic disorder, disordered linkers, signal peptides, MoRFs and interactions with proteins, DNA and RNAs...
October 29, 2020: Nucleic Acids Research
#11
REVIEW
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
A model that predicts levels of coronavirus (CoV) respiratory and fecal-oral transmission potentials based on the shell disorder has been built using neural network (artificial intelligence, AI) analysis of the percentage of disorder (PID) in the nucleocapsid, N, and membrane, M, proteins of the inner and outer viral shells, respectively. Using primarily the PID of N, SARS-CoV-2 is grouped as having intermediate levels of both respiratory and fecal-oral transmission potentials. Related studies, using similar methodologies, have found strong positive correlations between virulence and inner shell disorder among numerous viruses, including Nipah, Ebola, and Dengue viruses...
November 6, 2020: Journal of Proteome Research
#12
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
A model to predict the relative levels of respiratory and fecal-oral transmission potentials of coronaviruses (CoVs) by measuring the percentage of protein intrinsic disorder (PID) of the M (Membrane) and N (Nucleoprotein) proteins in their outer and inner shells, respectively, was built before the MERS-CoV outbreak. With MPID = 8.6% and NPID = 50.2%, the 2003 SARS-CoV falls into group B, which consists of CoVs with intermediate levels of both fecal-oral and respiratory transmission potentials. Further validation of the model came with MERS-CoV (MPID = 9%, NPID = 44%) and SARS-CoV-2 (MPID = 5...
August 13, 2020: Journal of Proteome Research
#13
JOURNAL ARTICLE
Jianhong Zhou, Christopher J Oldfield, Wenying Yan, Bairong Shen, A Keith Dunker
BACKGROUND: Intrinsically disordered proteins or regions (IDPs or IDRs) lack stable structures in solution, yet often fold upon binding with partners. IDPs or IDRs are highly abundant in all proteomes and represent a significant modification of sequence → structure → function paradigm. The Protein Data Bank (PDB) includes complexes containing disordered segments bound to globular proteins, but the molecular mechanisms of such binding interactions remain largely unknown. RESULTS: In this study, we present the results of various disorder predictions on a nonredundant set of PDB complexes...
July 28, 2020: ACS Omega
#14
JOURNAL ARTICLE
Christopher J Oldfield, Xiao Fan, Chen Wang, A Keith Dunker, Lukasz Kurgan
Intrinsically disordered proteins are either entirely disordered or contain disordered regions in their native state. These proteins and regions function without the prerequisite of a stable structure and were found to be abundant across all kingdoms of life. Experimental annotation of disorder lags behind the rapidly growing number of sequenced proteins, motivating the development of computational methods that predict disorder in protein sequences. DisCoP is a user-friendly webserver that provides accurate sequence-based prediction of protein disorder...
2020: Methods in Molecular Biology
#15
JOURNAL ARTICLE
Eshel Faraggi, A Keith Dunker, Robert L Jernigan, Andrzej Kloczkowski
Entropy should directly reflect the extent of disorder in proteins. By clustering structurally related proteins and studying the multiple-sequence-alignment of the sequences of these clusters, we were able to link between sequence, structure, and disorder information. We introduced several parameters as measures of fluctuations at a given MSA site and used these as representative of the sequence and structure entropy at that site. In general, we found a tendency for negative correlations between disorder and structure, and significant positive correlations between disorder and the fluctuations in the system...
August 2019: Entropy
#16
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
The coronavirus (CoV) family consists of viruses that infects a variety of animals including humans with various levels of respiratory and fecal-oral transmission levels depending on the behavior of the viruses' natural hosts and optimal viral fitness. A model to classify and predict the levels of respective respiratory and fecal-oral transmission potentials of the various viruses was built before the outbreak of MERS-CoV using AI and empirically-based molecular tools to predict the disorder level of proteins...
March 31, 2020: Microbial Pathogenesis
#17
EDITORIAL
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
The world is currently witnessing an outbreak of a new coronavirus spreading quickly across China and affecting at least 24 other countries. With almost 65,000 infected, a worldwide death toll of at least 1370 (as of 14 February 2020), and with the potential to affect up to two-thirds of the world population, COVID-19 is considered by the World Health Organization (WHO) to be a global health emergency. The speed of spread and infectivity of COVID-19 (also known as Wuhan-2019-nCoV) are dramatically exceeding those of the Middle East respiratory syndrome coronavirus (MERS-CoV) and severe acute respiratory syndrome coronavirus (SARS-CoV)...
February 19, 2020: Biomolecules
#18
JOURNAL ARTICLE
Gerard Kian-Meng Goh, A Keith Dunker, James A Foster, Vladimir N Uversky
The Nipah Virus (NiV) was first isolated during a 1998-9 outbreak in Malaysia. The outbreak initially infected farm pigs and then moved to humans from pigs with a case-fatality rate (CFR) of about 40%. After 2001, regular outbreaks occurred with higher CFRs (∼71%, 2001-5, ∼93%, 2008-12). The spread arose from drinking virus-laden palm date sap and human-to-human transmission. Intrinsic disorder analysis revealed strong correlation between the percentage of disorder in the N protein and CFR (Regression: r2 = 0...
January 12, 2020: Microbial Pathogenesis
#19
JOURNAL ARTICLE
Wei-Lun Alterovitz, Eshel Faraggi, Christopher J Oldfield, Jingwei Meng, Bin Xue, Fei Huang, Pedro Romero, Andrzej Kloczkowski, Vladimir N Uversky, A Keith Dunker
Disordered binding regions (DBRs), which are embedded within intrinsically disordered proteins or regions (IDPs or IDRs), enable IDPs or IDRs to mediate multiple protein-protein interactions. DBR-protein complexes were collected from the Protein Data Bank for which two or more DBRs having different amino acid sequences bind to the same (100% sequence identical) globular protein partner, a type of interaction herein called many-to-one binding. Two distinct binding profiles were identified: independent and overlapping...
2020: Pacific Symposium on Biocomputing
#20
JOURNAL ARTICLE
András Hatos, Borbála Hajdu-Soltész, Alexander M Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucia Chemes, Norman E Davey, Radoslav Davidović, A Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamas Horvath, Valentin Iglesias, Andrey V Kajava, Orsolya P Kovacs, John Lamb, Matteo Lambrughi, Tamas Lazar, Jeremy Y Leclercq, Emanuela Leonardi, Sandra Macedo-Ribeiro, Mauricio Macossay-Castillo, Emiliano Maiani, José A Manso, Cristina Marino-Buslje, Elizabeth Martínez-Pérez, Bálint Mészáros, Ivan Mičetić, Giovanni Minervini, Nikoletta Murvai, Marco Necci, Christos A Ouzounis, Mátyás Pajkos, Lisanna Paladin, Rita Pancsa, Elena Papaleo, Gustavo Parisi, Emilie Pasche, Pedro J Barbosa Pereira, Vasilis J Promponas, Jordi Pujols, Federica Quaglia, Patrick Ruch, Marco Salvatore, Eva Schad, Beata Szabo, Tamás Szaniszló, Stella Tamana, Agnes Tantos, Nevena Veljkovic, Salvador Ventura, Wim Vranken, Zsuzsanna Dosztányi, Peter Tompa, Silvio C E Tosatto, Damiano Piovesan
The Database of Protein Disorder (DisProt, URL: https://disprot.org) provides manually curated annotations of intrinsically disordered proteins from the literature. Here we report recent developments with DisProt (version 8), including the doubling of protein entries, a new disorder ontology, improvements of the annotation format and a completely new website. The website includes a redesigned graphical interface, a better search engine, a clearer API for programmatic access and a new annotation interface that integrates text mining technologies...
November 12, 2019: Nucleic Acids Research
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