1
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Cho D, Lee HM, Kim JA, Song JG, Hwang SH, Lee B, Park J, Tran KM, Kim J, Vo PNL, Bae J, Pimt T, Lee K, Gsponer J, Kim HW, Na D. Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms. Database (Oxford) 2024; 2024:baae085. [PMID: 39192607 DOI: 10.1093/database/baae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/30/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024]
Abstract
Autoinhibition, a crucial allosteric self-regulation mechanism in cell signaling, ensures signal propagation exclusively in the presence of specific molecular inputs. The heightened focus on autoinhibited proteins stems from their implication in human diseases, positioning them as potential causal factors or therapeutic targets. However, the absence of a comprehensive knowledgebase impedes a thorough understanding of their roles and applications in drug discovery. Addressing this gap, we introduce Autoinhibited Protein Database (AiPD), a curated database standardizing information on autoinhibited proteins. AiPD encompasses details on autoinhibitory domains (AIDs), their targets, regulatory mechanisms, experimental validation methods, and implications in diseases, including associated mutations and post-translational modifications. AiPD comprises 698 AIDs from 532 experimentally characterized autoinhibited proteins and 2695 AIDs from their 2096 homologs, which were retrieved from 864 published articles. AiPD also includes 42 520 AIDs of computationally predicted autoinhibited proteins. In addition, AiPD facilitates users in investigating potential AIDs within a query sequence through comparisons with documented autoinhibited proteins. As the inaugural autoinhibited protein repository, AiPD significantly aids researchers studying autoinhibition mechanisms and their alterations in human diseases. It is equally valuable for developing computational models, analyzing allosteric protein regulation, predicting new drug targets, and understanding intervention mechanisms AiPD serves as a valuable resource for diverse researchers, contributing to the understanding and manipulation of autoinhibition in cellular processes. Database URL: http://ssbio.cau.ac.kr/databases/AiPD.
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Affiliation(s)
- Daeahn Cho
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Ji Ah Kim
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Jae Gwang Song
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Su-Hee Hwang
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Bomi Lee
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Jinsil Park
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Kha Mong Tran
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Jiwon Kim
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Phuong Ngoc Lam Vo
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Jooeun Bae
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Teerapat Pimt
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
| | - Kangseok Lee
- Department of Life Science, Chung-Ang University, Seoul 06974, Republic of Korea
| | - Jörg Gsponer
- Center for High-Throughput Biology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Hyung Wook Kim
- Department of Bio-integrated Science and Technology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul 06974, South Korea
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2
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Kugler V, Schwaighofer S, Feichtner A, Enzler F, Fleischmann J, Strich S, Schwarz S, Wilson R, Tschaikner P, Troppmair J, Sexl V, Meier P, Kaserer T, Stefan E. Impact of protein and small molecule interactions on kinase conformations. eLife 2024; 13:RP94755. [PMID: 39088265 PMCID: PMC11293870 DOI: 10.7554/elife.94755] [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] [Indexed: 08/02/2024] Open
Abstract
Protein kinases act as central molecular switches in the control of cellular functions. Alterations in the regulation and function of protein kinases may provoke diseases including cancer. In this study we investigate the conformational states of such disease-associated kinases using the high sensitivity of the kinase conformation (KinCon) reporter system. We first track BRAF kinase activity conformational changes upon melanoma drug binding. Second, we also use the KinCon reporter technology to examine the impact of regulatory protein interactions on LKB1 kinase tumor suppressor functions. Third, we explore the conformational dynamics of RIP kinases in response to TNF pathway activation and small molecule interactions. Finally, we show that CDK4/6 interactions with regulatory proteins alter conformations which remain unaffected in the presence of clinically applied inhibitors. Apart from its predictive value, the KinCon technology helps to identify cellular factors that impact drug efficacies. The understanding of the structural dynamics of full-length protein kinases when interacting with small molecule inhibitors or regulatory proteins is crucial for designing more effective therapeutic strategies.
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Affiliation(s)
- Valentina Kugler
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Selina Schwaighofer
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Andreas Feichtner
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of InnsbruckInnsbruckAustria
| | - Jakob Fleischmann
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Sophie Strich
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Sarah Schwarz
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
| | - Rebecca Wilson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Philipp Tschaikner
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
- KinCon biolabs GmbHInnsbruckAustria
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of InnsbruckInnsbruckAustria
| | | | - Pascal Meier
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Teresa Kaserer
- Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute for Molecular Biology and Center for Molecular Biosciences Innsbruck (CMBI), University of InnsbruckInnsbruckAustria
- Tyrolean Cancer Research Institute (TKFI)InnsbruckAustria
- KinCon biolabs GmbHInnsbruckAustria
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3
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Holguin-Cruz JA, Bui JM, Jha A, Na D, Gsponer J. Widespread alteration of protein autoinhibition in human cancers. Cell Syst 2024; 15:246-263.e7. [PMID: 38366601 DOI: 10.1016/j.cels.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/20/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Autoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins. Reduced autoinhibition underlies the tumorigenic effect of some known cancer drivers, but whether autoinhibition is altered generally in cancer remains elusive. Here, we demonstrate that cancer-associated missense mutations, in-frame insertions/deletions, and fusion breakpoints are enriched within inhibitory allosteric switches (IASs) across all cancer types. Selection for IASs that are recurrently mutated in cancers identifies established and unknown cancer drivers. Recurrent missense mutations in IASs of these drivers are associated with distinct, cancer-specific changes in molecular signaling. For the specific case of PPP3CA, the catalytic subunit of calcineurin, we provide insights into the molecular mechanisms of altered autoinhibition by cancer mutations using biomolecular simulations, and demonstrate that such mutations are associated with transcriptome changes consistent with increased calcineurin signaling. Our integrative study shows that autoinhibition-modulating genetic alterations are positively selected for by cancer cells.
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Affiliation(s)
- Jorge A Holguin-Cruz
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer M Bui
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ashwani Jha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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4
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Venkat A, Watterson G, Byrne DP, O'Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. eLife 2023; 12:RP87958. [PMID: 37883155 PMCID: PMC10602587 DOI: 10.7554/elife.87958] [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] [Indexed: 10/27/2023] Open
Abstract
Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The doublecortin-like kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations, and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other calcium calmodulin kinases (CAMKs), and a 'Swiss Army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for autoregulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome-wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically divergent DCLK1 modulators, stabilizers, or degraders.
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Affiliation(s)
- Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Grace Watterson
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Dominic P Byrne
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Brady O'Boyle
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Safal Shrestha
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
| | - Nathan Gravel
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
| | - Emma E Fairweather
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Leonard A Daly
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
- Centre for Proteome Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Claire Bunn
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Wayland Yeung
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
| | - Ishan Aggarwal
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Samiksha Katiyar
- Department of Biochemistry and Molecular Biology, University of GeorgiaAthensUnited States
| | - Claire E Eyers
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
- Centre for Proteome Research, Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Patrick A Eyers
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Natarajan Kannan
- Institute of Bioinformatics, University of GeorgiaAthensUnited States
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5
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Venkat A, Watterson G, Byrne DP, O’Boyle B, Shrestha S, Gravel N, Fairweather EE, Daly LA, Bunn C, Yeung W, Aggarwal I, Katiyar S, Eyers CE, Eyers PA, Kannan N. Mechanistic and evolutionary insights into isoform-specific 'supercharging' in DCLK family kinases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.29.534689. [PMID: 37034755 PMCID: PMC10081240 DOI: 10.1101/2023.03.29.534689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Catalytic signaling outputs of protein kinases are dynamically regulated by an array of structural mechanisms, including allosteric interactions mediated by intrinsically disordered segments flanking the conserved catalytic domain. The Doublecortin Like Kinases (DCLKs) are a family of microtubule-associated proteins characterized by a flexible C-terminal autoregulatory 'tail' segment that varies in length across the various human DCLK isoforms. However, the mechanism whereby these isoform-specific variations contribute to unique modes of autoregulation is not well understood. Here, we employ a combination of statistical sequence analysis, molecular dynamics simulations and in vitro mutational analysis to define hallmarks of DCLK family evolutionary divergence, including analysis of splice variants within the DCLK1 sub-family, which arise through alternative codon usage and serve to 'supercharge' the inhibitory potential of the DCLK1 C-tail. We identify co-conserved motifs that readily distinguish DCLKs from all other Calcium Calmodulin Kinases (CAMKs), and a 'Swiss-army' assembly of distinct motifs that tether the C-terminal tail to conserved ATP and substrate-binding regions of the catalytic domain to generate a scaffold for auto-regulation through C-tail dynamics. Consistently, deletions and mutations that alter C-terminal tail length or interfere with co-conserved interactions within the catalytic domain alter intrinsic protein stability, nucleotide/inhibitor-binding, and catalytic activity, suggesting isoform-specific regulation of activity through alternative splicing. Our studies provide a detailed framework for investigating kinome-wide regulation of catalytic output through cis-regulatory events mediated by intrinsically disordered segments, opening new avenues for the design of mechanistically-divergent DCLK1 modulators, stabilizers or degraders.
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Affiliation(s)
- Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Grace Watterson
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Dominic P. Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Brady O’Boyle
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Safal Shrestha
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Nathan Gravel
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Emma E. Fairweather
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Leonard A. Daly
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Claire Bunn
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Ishan Aggarwal
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Samiksha Katiyar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Claire E. Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
- Centre for Proteome Research, Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Patrick A. Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
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6
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Holguin-Cruz JA, Foster LJ, Gsponer J. Where protein structure and cell diversity meet. Trends Cell Biol 2022; 32:996-1007. [PMID: 35537902 DOI: 10.1016/j.tcb.2022.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 01/21/2023]
Abstract
Protein-protein interaction networks - interactomes - are charted with the hope to understand how phenotypes emerge and how they are altered in disease states. Early efforts to map interactomes have focused on the assembly of context agnostic, reference networks. However, recent studies have mapped interactomes across different cell lines and tissues, finding highly variable interactomes due to the rewiring of protein-protein interactions in different contexts. Increasing evidence points to significant links between protein structure and interactome diversity seen across cell types and tissues. We discuss how recent findings support the key role of alternative splicing and phosphorylation, two well-established regulators of protein structural and functional diversity, in defining cell type- and tissue-specific interactomes. Moreover, we show that intrinsically disordered protein regions are most favorably equipped to support interactome rewiring by acting as hubs of protein structure and function regulation.
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Affiliation(s)
- Jorge A Holguin-Cruz
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
| | - Leonard J Foster
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada
| | - Jörg Gsponer
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, Canada.
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7
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Shinn MK, Cohan MC, Bullock JL, Ruff KM, Levin PA, Pappu RV. Connecting sequence features within the disordered C-terminal linker of Bacillus subtilis FtsZ to functions and bacterial cell division. Proc Natl Acad Sci U S A 2022; 119:e2211178119. [PMID: 36215496 PMCID: PMC9586301 DOI: 10.1073/pnas.2211178119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/20/2022] [Indexed: 11/21/2022] Open
Abstract
Intrinsically disordered regions (IDRs) can function as autoregulators of folded enzymes to which they are tethered. One example is the bacterial cell division protein FtsZ. This includes a folded core and a C-terminal tail (CTT) that encompasses a poorly conserved, disordered C-terminal linker (CTL) and a well-conserved 17-residue C-terminal peptide (CT17). Sites for GTPase activity of FtsZs are formed at the interface between GTP binding sites and T7 loops on cores of adjacent subunits within dimers. Here, we explore the basis of autoregulatory functions of the CTT in Bacillus subtilis FtsZ (Bs-FtsZ). Molecular simulations show that the CT17 of Bs-FtsZ makes statistically significant CTL-mediated contacts with the T7 loop. Statistical coupling analysis of more than 1,000 sequences from FtsZ orthologs reveals clear covariation of the T7 loop and the CT17 with most of the core domain, whereas the CTL is under independent selection. Despite this, we discover the conservation of nonrandom sequence patterns within CTLs across orthologs. To test how the nonrandom patterns of CTLs mediate CTT-core interactions and modulate FtsZ functionalities, we designed Bs-FtsZ variants by altering the patterning of oppositely charged residues within the CTL. Such alterations disrupt the core-CTT interactions, lead to anomalous assembly and inefficient GTP hydrolysis in vitro and protein degradation, aberrant assembly, and disruption of cell division in vivo. Our findings suggest that viable CTLs in FtsZs are likely to be IDRs that encompass nonrandom, functionally relevant sequence patterns that also preserve three-way covariation of the CT17, the T7 loop, and core domain.
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Affiliation(s)
- Min Kyung Shinn
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Megan C. Cohan
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Jessie L. Bullock
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Kiersten M. Ruff
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130
| | - Petra A. Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130
- Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130
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8
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Feichtner A, Kugler V, Schwaighofer S, Nuener T, Fleischmann J, Stefan E. Tracking mutation and drug-driven alterations of oncokinase conformations. MEMO 2022; 15:137-142. [PMID: 35677701 PMCID: PMC7612828 DOI: 10.1007/s12254-021-00790-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Numerous kinases act as central nodes of cellular signaling networks. As such, many of these enzymes function as molecular switches for coordinating spatiotemporal signal transmission. Typically, it is the compartmentalized phosphorylation of protein substrates which relays the transient input signal to determine decisive physiological cell responses. Genomic alterations affect kinase abundance and/or their activities which contribute to the malignant transformation, progression, and metastasis of human cancers. Thus, major drug discovery efforts have been made to identify lead molecules targeting clinically relevant oncokinases. The concept of personalized medicine aims to apply the therapeutic agent with the highest efficacy towards a patient-specific mutation. Here, we discuss the implementation of a cell-based reporter system which may foster the decision-making process to identify the most promising lead-molecules. We present a modular kinase conformation (KinCon) biosensor platform for live-cell analyses of kinase activity states. This biosensor facilitates the recording of kinase activity conformations of the wild-type and the respective mutated kinase upon lead molecule exposure. We reflect proof-of-principle studies demonstrating how this technology has been extended to profile drug properties of the full-length kinases BRAF and MEK1 in intact cells. Further, we pinpoint how this technology may open new avenues for systematic and patient-tailored drug discovery efforts. Overall, this precision-medicineoriented biosensor concept aims to determine kinase inhibitor specificity and anticipate their drug efficacies.
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Affiliation(s)
- Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Valentina Kugler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Selina Schwaighofer
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Thomas Nuener
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Jakob Fleischmann
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria; Tyrolean Cancer Research Institute, Innrain 66, 6020 Innsbruck, Austria
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9
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Morgan JL, Yeager A, Estelle AB, Gsponer J, Barbar E. Transient Tertiary Structures of Disordered Dynein Intermediate Chain Regulate its Interactions with Multiple Partners. J Mol Biol 2021; 433:167152. [PMID: 34273400 DOI: 10.1016/j.jmb.2021.167152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 11/24/2022]
Abstract
The N-terminal domain of dynein intermediate chain (N-IC) is central to the cytoplasmic dynein 'cargo attachment subcomplex' and regulation of motor activity. It is a prototypical intrinsically disordered protein (IDP), serving as a primarily disordered polybivalent molecular scaffold for numerous binding partners, including three dimeric dynein light chains and coiled coil domains of dynein partners dynactin p150Glued and NudE. At the very N-terminus, a 40 amino acid single alpha helix (SAH) forms the major binding site for both p150Glued and NudE, while a shorter nascent helix (H2) separated from SAH by a disordered linker, is necessary for tight binding to dynactin p150Glued but not to NudE. Here we demonstrate that transient tertiary interactions in this highly dynamic protein underlie the differences in its interactions with p150Glued and NudE. NMR paramagnetic relaxation enhancement experiments and restrained molecular dynamics simulations identify interactions between the two non-contiguous SAH and H2 helical regions, the extent of which correlates with the length and stability of H2, showing clearly that tertiary and secondary structure formation are coupled in IDPs. These interactions are significantly attenuated when N-IC is bound to NudE, suggesting that NudE binding shifts the conformational ensemble to one that is more extended and with less structure in H2. While the intrinsic disorder and flexibility in N-IC modulate its ability to serve as a binding platform for numerous partners, deviations of this protein from random-coil behavior provide a process for regulating these binding interactions and potentially the dynein motor.
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Affiliation(s)
- Jessica L Morgan
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States
| | - Andrew Yeager
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Aidan B Estelle
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States
| | - Jörg Gsponer
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Elisar Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, United States.
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Mutation-oriented profiling of autoinhibitory kinase conformations predicts RAF inhibitor efficacies. Proc Natl Acad Sci U S A 2020; 117:31105-31113. [PMID: 33229534 PMCID: PMC7733820 DOI: 10.1073/pnas.2012150117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Kinase-targeted therapies have the potential to improve the survival of patients with cancer. However, the cancer-specific spectrum of kinase alterations exhibits distinct functional properties and requires mutation-oriented drug treatments. Besides post-translational modifications and diverse intermolecular interactions of kinases, it is the distinct disease mutation which reshapes full-length kinase conformations, affecting their activity. Oncokinase mutation profiles differ between cancer types, as it was shown for BRAF in melanoma and non-small-cell lung cancers. Here, we present the target-oriented application of a kinase conformation (KinCon) reporter platform for live-cell measurements of autoinhibitory kinase activity states. The bioluminescence-based KinCon biosensor allows the tracking of conformation dynamics of full-length kinases in intact cells and real time. We show that the most frequent BRAF cancer mutations affect kinase conformations and thus the engagement and efficacy of V600E-specific BRAF inhibitors (BRAFi). We illustrate that the patient mutation harboring KinCon reporters display differences in the effectiveness of the three clinically approved BRAFi vemurafenib, encorafenib, and dabrafenib and the preclinical paradox breaker PLX8394. We confirmed KinCon-based drug efficacy predictions for BRAF mutations other than V600E in proliferation assays using patient-derived lung cancer cell lines and by analyzing downstream kinase signaling. The systematic implementation of such conformation reporters will allow to accelerate the decision process for the mutation-oriented RAF-kinase cancer therapy. Moreover, we illustrate that the presented kinase reporter concept can be extended to other kinases which harbor patient mutations. Overall, KinCon profiling provides additional mechanistic insights into full-length kinase functions by reporting protein-protein interaction (PPI)-dependent, mutation-specific, and drug-driven changes of kinase activity conformations.
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Enzler F, Tschaikner P, Schneider R, Stefan E. KinCon: Cell-based recording of full-length kinase conformations. IUBMB Life 2020; 72:1168-1174. [PMID: 32027084 PMCID: PMC7318358 DOI: 10.1002/iub.2241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/16/2020] [Indexed: 01/26/2023]
Abstract
The spectrum of kinase alterations displays distinct functional characteristics and requires kinase mutation-oriented strategies for therapeutic interference. Besides phosphotransferase activity, protein abundance, and intermolecular interactions, particular patient-mutations promote pathological kinase conformations. Despite major advances in identifying lead molecules targeting clinically relevant oncokinase functions, still many kinases are neglected and not part of drug discovery efforts. One explanation is attributed to challenges in tracking kinase activities. Chemical probes are needed to functionally annotate kinase functions, whose activities may not always depend on catalyzing phospho-transfer. Such non-catalytic kinase functions are related to transitions of full-length kinase conformations. Recent findings underline that cell-based reporter systems can be adapted to record conformation changes of kinases. Here, we discuss the possible applications of an extendable kinase conformation (KinCon) reporter toolbox for live-cell recording of kinase states. KinCon is a genetically encoded bioluminescence-based biosensor platform, which can be subjected for measurements of conformation dynamics of mutated kinases upon small molecule inhibitor exposure. We hypothesize that such biosensors can be utilized to delineate the molecular modus operandi for kinase and pseudokinase regulation. This should pave the path for full-length kinase-targeted drug discovery efforts aiming to identify single and combinatory kinase inhibitor therapies with increased specificity and efficacy.
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Affiliation(s)
- Florian Enzler
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Philipp Tschaikner
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Rainer Schneider
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of InnsbruckInnsbruckAustria
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12
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Zhou J, Oldfield CJ, Yan W, Shen B, Dunker AK. Intrinsically disordered domains: Sequence ➔ disorder ➔ function relationships. Protein Sci 2019; 28:1652-1663. [PMID: 31299122 DOI: 10.1002/pro.3680] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/29/2019] [Accepted: 07/03/2019] [Indexed: 02/05/2023]
Abstract
Disordered domains are long regions of intrinsic disorder that ideally have conserved sequences, conserved disorder, and conserved functions. These domains were first noticed in protein-protein interactions that are distinct from the interactions between two structured domains and the interactions between structured domains and linear motifs or molecular recognition features (MoRFs). So far, disordered domains have not been systematically characterized. Here, we present a bioinformatics investigation of the sequence-disorder-function relationships for a set of probable disordered domains (PDDs) identified from the Pfam database. All the Pfam seed proteins from those domains with at least one PDD sequence were collected. Most often, if a set contains one PDD sequence, then all members of the set are PDDs or nearly so. However, many seed sets have sequence collections that exhibit diverse proportions of predicted disorder and structure, thus giving the completely unexpected result that conserved sequences can vary substantially in predicted disorder and structure. In addition to the induction of structure by binding to protein partners, disordered domains are also induced to form structure by disulfide bond formation, by ion binding, and by complex formation with RNA or DNA. The two new findings, (a) that conserved sequences can vary substantially in their predicted disorder content and (b) that homologues from a single domain can evolve from structure to disorder (or vice versa), enrich our understanding of the sequence ➔ disorder ensemble ➔ function paradigm.
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Affiliation(s)
- Jianhong Zhou
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana.,School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | | | - Wenying Yan
- School of Biology & Basic Medical Sciences, Soochow University, Suzhou, China
| | - Bairong Shen
- Institutes for Systems Genetics, West China Hospital, Sichuan University, Chengdu, China
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana
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Röck R, Mayrhofer JE, Torres-Quesada O, Enzler F, Raffeiner A, Raffeiner P, Feichtner A, Huber RG, Koide S, Taylor SS, Troppmair J, Stefan E. BRAF inhibitors promote intermediate BRAF(V600E) conformations and binary interactions with activated RAS. SCIENCE ADVANCES 2019; 5:eaav8463. [PMID: 31453322 PMCID: PMC6693913 DOI: 10.1126/sciadv.aav8463] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 07/09/2019] [Indexed: 05/05/2023]
Abstract
Oncogenic BRAF mutations initiate tumor formation by unleashing the autoinhibited kinase conformation and promoting RAS-decoupled proliferative RAF-MEK-ERK signaling. We have engineered luciferase-based biosensors to systematically track full-length BRAF conformations and interactions affected by tumorigenic kinase mutations and GTP loading of RAS. Binding of structurally diverse αC-helix-OUT BRAF inhibitors (BRAFi) showed differences in specificity and efficacy by shifting patient mutation-containing BRAF reporters from the definitive opened to more closed conformations. Unexpectedly, BRAFi engagement with the catalytic pocket of V600E-mutated BRAF stabilized an intermediate and inactive kinase conformation that enhanced binary RAS:RAF interactions, also independently of RAF dimerization in melanoma cells. We present evidence that the interference with RAS interactions and nanoclustering antagonizes the sequential formation of drug-induced RAS:RAF tetramers. This suggests a previously unappreciated allosteric effect of anticancer drug-driven intramolecular communication between the kinase and RAS-binding domains of mutated BRAF, which may further promote paradoxical kinase activation and drug resistance mechanisms.
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Affiliation(s)
- Ruth Röck
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Johanna E. Mayrhofer
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Omar Torres-Quesada
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Florian Enzler
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Andrea Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Philipp Raffeiner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Andreas Feichtner
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Roland G. Huber
- Bioinformatics Institute (BII), Agency for Science Technology and Research (A*STAR), Singapore 138671, Singapore
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine and Laura and Isaac Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Susan S. Taylor
- Department of Pharmacology, Department of Chemistry and Biochemistry, and Howard Hughes Medical Institute, University of California, San Diego, San Diego, CA 92093, USA
| | - Jakob Troppmair
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innrain 66, 6020 Innsbruck, Austria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
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Yu MS, Lee HM, Park A, Park C, Ceong H, Rhee KH, Na D. In silico prediction of potential chemical reactions mediated by human enzymes. BMC Bioinformatics 2018; 19:207. [PMID: 29897324 PMCID: PMC5998764 DOI: 10.1186/s12859-018-2194-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background Administered drugs are often converted into an ineffective or activated form by enzymes in our body. Conventional in silico prediction approaches focused on therapeutically important enzymes such as CYP450. However, there are more than thousands of different cellular enzymes that potentially convert administered drug into other forms. Result We developed an in silico model to predict which of human enzymes including metabolic enzymes as well as CYP450 family can catalyze a given chemical compound. The prediction is based on the chemical and physical similarity between known enzyme substrates and a query chemical compound. Our in silico model was developed using multiple linear regression and the model showed high performance (AUC = 0.896) despite of the large number of enzymes. When evaluated on a test dataset, it also showed significantly high performance (AUC = 0.746). Interestingly, evaluation with literature data showed that our model can be used to predict not only enzymatic reactions but also drug conversion and enzyme inhibition. Conclusion Our model was able to predict enzymatic reactions of a query molecule with a high accuracy. This may foster to discover new metabolic routes and to accelerate the computational development of drug candidates by enabling the prediction of the potential conversion of administered drugs into active or inactive forms.
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Affiliation(s)
- Myeong-Sang Yu
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Hyang-Mi Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea
| | - Aaron Park
- School of Biological Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Chungoo Park
- School of Biological Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Hyithaek Ceong
- Department of Multimedia, Chonnam National University, Yeosu, Republic of Korea
| | - Ki-Hyeong Rhee
- College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, Republic of Korea.
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15
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Biophysical Characterization of the Tandem FHA Domain Regulatory Module from the Mycobacterium tuberculosis ABC Transporter Rv1747. Structure 2018; 26:972-986.e6. [PMID: 29861345 DOI: 10.1016/j.str.2018.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/13/2018] [Accepted: 04/27/2018] [Indexed: 11/23/2022]
Abstract
The Mycobacterium tuberculosis ATP-binding cassette transporter Rv1747 is a putative exporter of cell wall biosynthesis intermediates. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting Forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). The structures of FHA-1 and FHA-2 were determined by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, respectively. Relative to the canonical 11-strand β-sandwich FHA domain fold of FHA-1, FHA-2 is circularly permuted and lacking one β-strand. Nevertheless, the two share a conserved pThr-binding cleft. FHA-2 is less stable and more dynamic than FHA-1, yet binds model pThr peptides with moderately higher affinity (∼50 μM versus 500 μM equilibrium dissociation constants). Based on NMR relaxation and chemical shift perturbation measurements, when joined within a polypeptide chain, either FHA domain can bind either linker pThr to form intra- and intermolecular complexes. We hypothesize that this enables tunable phosphorylation-dependent multimerization to regulate Rv1747 transporter activity.
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Regulation of apoptosis by an intrinsically disordered region of Bcl-xL. Nat Chem Biol 2018; 14:458-465. [PMID: 29507390 PMCID: PMC5899648 DOI: 10.1038/s41589-018-0011-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 01/05/2018] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered regions (IDRs) of proteins often regulate function upon posttranslational modifications (PTMs) through interactions with folded domains. An IDR linking two α-helices (α1–α2) of the anti-apoptotic protein, Bcl-xL, experiences several PTMs, which reduce anti-apoptotic activity. Here, we report that PTMs within the α1–α2 IDR promote its interaction with the folded core of Bcl-xL that inhibits the pro-apoptotic activity of two types of regulatory targets, BH3-only proteins and p53. This autoregulation utilizes an allosteric pathway where, in one direction, the IDR induces a direct displacement of p53 from Bcl-xL coupled to allosteric displacement of simultaneously bound BH3-only partners. This pathway operates in the opposite direction when the BH3-only protein PUMA binds to the BH3 binding groove of Bcl-xL, directly displacing other bound BH3-only proteins, and allosterically remodeling the distal site, displacing p53. Our findings show how an IDR enhances functional versatility through PTM-dependent, allosteric regulation of a folded protein domain.
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Saravanan KM, Dunker AK, Krishnaswamy S. Sequence fingerprints distinguish erroneous from correct predictions of intrinsically disordered protein regions. J Biomol Struct Dyn 2017; 36:4338-4351. [PMID: 29228892 DOI: 10.1080/07391102.2017.1415822] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
More than 60 prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the World Wide Web. Nearly, all of these predictors give balanced accuracies in the ~65%-~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions. A higher occurrence of asparagine is observed in sequences of native IDP regions but not in sequences of false positive predictions of IDP regions. The occurrences of certain combinations of amino acids at the pentapeptide level provide a distinguishing feature in the IDPs with respect to globular proteins. The distinguishing features presented in this paper provide insights into the sequence fingerprints of amino acid residues in experimentally determined as compared to predicted IDP regions. These observations and additional work along these lines should enable the development of improvements in the accuracy of disorder prediction algorithm.
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Affiliation(s)
- Konda Mani Saravanan
- a Centre of Advanced Study in Crystallography & Biophysics , University of Madras , Guindy Campus, Chennai 600 025 , Tamilnadu , India
| | - A Keith Dunker
- b Centre for Computational Biology and Bioinformatics , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Sankaran Krishnaswamy
- c Institute of Mathematical Sciences , CIT Campus, Tharamani , Chennai 600 113 , Tamilnadu , India
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18
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Abstract
A new bioinformatics tool predicts natively disordered protein control elements that function in cis, opening the door to more systematic studies of this biomedically important class of protein modules.
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Affiliation(s)
- Toby J Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Manjeet Kumar
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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