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Nguyen TB, Myung Y, de Sá AGC, Pires DEV, Ascher DB. mmCSM-NA: accurately predicting effects of single and multiple mutations on protein-nucleic acid binding affinity. NAR Genom Bioinform 2021; 3:lqab109. [PMID: 34805992 PMCID: PMC8600011 DOI: 10.1093/nargab/lqab109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/20/2021] [Accepted: 10/27/2021] [Indexed: 02/02/2023] Open
Abstract
While protein-nucleic acid interactions are pivotal for many crucial biological processes, limited experimental data has made the development of computational approaches to characterise these interactions a challenge. Consequently, most approaches to understand the effects of missense mutations on protein-nucleic acid affinity have focused on single-point mutations and have presented a limited performance on independent data sets. To overcome this, we have curated the largest dataset of experimentally measured effects of mutations on nucleic acid binding affinity to date, encompassing 856 single-point mutations and 141 multiple-point mutations across 155 experimentally solved complexes. This was used in combination with an optimized version of our graph-based signatures to develop mmCSM-NA (http://biosig.unimelb.edu.au/mmcsm_na), the first scalable method capable of quantitatively and accurately predicting the effects of multiple-point mutations on nucleic acid binding affinities. mmCSM-NA obtained a Pearson's correlation of up to 0.67 (RMSE of 1.06 Kcal/mol) on single-point mutations under cross-validation, and up to 0.65 on independent non-redundant datasets of multiple-point mutations (RMSE of 1.12 kcal/mol), outperforming similar tools. mmCSM-NA is freely available as an easy-to-use web-server and API. We believe it will be an invaluable tool to shed light on the role of mutations affecting protein-nucleic acid interactions in diseases.
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Affiliation(s)
- Thanh Binh Nguyen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Yoochan Myung
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Alex G C de Sá
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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Usman S, Jamal A, Teh MT, Waseem A. Major Molecular Signaling Pathways in Oral Cancer Associated With Therapeutic Resistance. FRONTIERS IN ORAL HEALTH 2021; 1:603160. [PMID: 35047986 PMCID: PMC8757854 DOI: 10.3389/froh.2020.603160] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Accepted: 12/29/2020] [Indexed: 12/12/2022] Open
Abstract
Oral cancer is a sub-category of head and neck cancers that primarily initiates in the oral cavity. The primary treatment option for oral cancer remains surgery but it is associated with massive disfigurement, inability to carry out normal oral functions, psycho-social stress and exhaustive rehabilitation. Other treatment options such as chemotherapy and radiotherapy have their own limitations in terms of toxicity, intolerance and therapeutic resistance. Immunological treatments to enhance the body's ability to recognize cancer tissue as a foreign entity are also being used but they are new and underdeveloped. Although substantial progress has been made in the treatment of oral cancer, its complex heterogeneous nature still needs to be explored, to elucidate the molecular basis for developing resistance to therapeutic agents and how to overcome it, with the aim of improving the chances of patients' survival and their quality of life. This review provides an overview of up-to-date information on the complex role of the major molecules and associated signaling, epigenetic changes, DNA damage repair systems, cancer stem cells and micro RNAs in the development of therapeutic resistance and treatment failure in oral cancer. We have also summarized the current strategies being developed to overcome these therapeutic challenges. This review will help not only researchers but also oral oncologists in the management of the disease and in developing new therapeutic modalities.
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Affiliation(s)
| | | | | | - Ahmad Waseem
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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Hepburn M, Saltzberg DJ, Lee L, Fang S, Atkinson C, Strynadka NCJ, Sali A, Lees-Miller SP, Schriemer DC. The active DNA-PK holoenzyme occupies a tensed state in a staggered synaptic complex. Structure 2021; 29:467-478.e6. [PMID: 33412091 DOI: 10.1016/j.str.2020.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 11/14/2020] [Accepted: 12/09/2020] [Indexed: 01/06/2023]
Abstract
In the non-homologous end-joining (NHEJ) of a DNA double-strand break, DNA ends are bound and protected by DNA-PK, which synapses across the break to tether the broken ends and initiate repair. There is little clarity surrounding the nature of the synaptic complex and the mechanism governing the transition to repair. We report an integrative structure of the synaptic complex at a precision of 13.5 Å, revealing a symmetric head-to-head arrangement with a large offset in the DNA ends and an extensive end-protection mechanism involving a previously uncharacterized plug domain. Hydrogen/deuterium exchange mass spectrometry identifies an allosteric pathway connecting DNA end-binding with the kinase domain that places DNA-PK under tension in the kinase-active state. We present a model for the transition from end-protection to repair, where the synaptic complex supports hierarchical processing of the ends and scaffold assembly, requiring displacement of the catalytic subunit and tension release through kinase activity.
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Affiliation(s)
- Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Shujuan Fang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Claire Atkinson
- Department of Biochemistry and Molecular Biology and High-Resolution Macromolecular Electron Microscopy Facility, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Natalie C J Strynadka
- Department of Biochemistry and Molecular Biology and High-Resolution Macromolecular Electron Microscopy Facility, The University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Sciences, and California Institute for Quantitative Biomedical Sciences, University of California, San Francisco, CA 94158, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada; Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada; Department of Chemistry, University of Calgary, Calgary, AB, Canada.
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Dimers of DNA-PK create a stage for DNA double-strand break repair. Nat Struct Mol Biol 2020; 28:13-19. [DOI: 10.1038/s41594-020-00517-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/08/2020] [Indexed: 11/08/2022]
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Blundell TL, Gupta MN, Hasnain SE. Intrinsic disorder in proteins: Relevance to protein assemblies, drug design and host-pathogen interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2020; 156:34-42. [PMID: 32628954 DOI: 10.1016/j.pbiomolbio.2020.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
Intrinsic disorder in proteins resulting in considerable variation in structure can lead to multiple functions including multi-specificity and diverse pathologies. Protein interfaces can involve disordered regions that assemble through a concerted-fold-and-bind mechanism. The binding involves both enthalpic and entropic gains by exploiting 'hot spots' on the partner and displacing water molecules placed in thermodynamically unfavorable situations. The examples of Rad51-BRCA2 and Artemis-DNA-PKCs/LigIV complexes illustrate this in the context of drug design. This overview tracks the seamless involvement of protein disorder in multi-specificity of biocatalysts, protein assembly formations and host-pathogen interactions, where intrinsic disorder can in Mycobacteria, compensate for genome reduction by carrying out multiple functions and in some RNA viruses facilitate adaption to the host. These present challenging opportunities for designing new drugs and interventions.
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Affiliation(s)
- Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, CB21GA, UK
| | - Munishwar N Gupta
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Seyed E Hasnain
- Jamia Hamdard Institute of Molecular Medicine, Jamia Hamdard, Hamdard Nagar, New Delhi, India; Dr Reddy's Institute of Life Sciences, University of Hyderabad Campus, Prof C.R. Rao Road, Hyderabad, India.
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PAXX and its paralogs synergistically direct DNA polymerase λ activity in DNA repair. Nat Commun 2018; 9:3877. [PMID: 30250067 PMCID: PMC6155126 DOI: 10.1038/s41467-018-06127-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 08/09/2018] [Indexed: 12/20/2022] Open
Abstract
PAXX is a recently identified component of the nonhomologous end joining (NHEJ) DNA repair pathway. The molecular mechanisms of PAXX action remain largely unclear. Here we characterise the interactomes of PAXX and its paralogs, XLF and XRCC4, to show that these factors share the ability to interact with DNA polymerase λ (Pol λ), stimulate its activity and are required for recruitment of Pol λ to laser-induced DNA damage sites. Stimulation of Pol λ activity by XRCC4 paralogs requires a direct interaction between the SP/8 kDa domain of Pol λ and their N-terminal head domains to facilitate recognition of the 5′ end of substrate gaps. Furthermore, PAXX and XLF collaborate with Pol λ to promote joining of incompatible DNA ends and are redundant in supporting Pol λ function in vivo. Our findings identify Pol λ as a novel downstream effector of PAXX function and show XRCC4 paralogs act in synergy to regulate polymerase activity in NHEJ. PAXX functions as part of the nonhomologous end-joining pathway to repair double-strand DNA breaks. Here the authors show PAXX and its paralogs interact with polymerase lambda to promote joining of incompatible ends.
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Dissection of DNA double-strand-break repair using novel single-molecule forceps. Nat Struct Mol Biol 2018; 25:482-487. [PMID: 29786079 PMCID: PMC5990469 DOI: 10.1038/s41594-018-0065-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/13/2018] [Indexed: 02/02/2023]
Abstract
Repairing DNA double-strand breaks (DSBs) by nonhomologous end joining (NHEJ) requires multiple proteins to recognize and bind DNA ends, process them for compatibility, and ligate them together. We constructed novel DNA substrates for single-molecule nanomanipulation, allowing us to mechanically detect, probe, and rupture in real-time DSB synapsis by specific human NHEJ components. DNA-PKcs and Ku allow DNA end synapsis on the 100 ms timescale, and the addition of PAXX extends this lifetime to ~2 s. Further addition of XRCC4, XLF and ligase IV results in minute-scale synapsis and leads to robust repair of both strands of the nanomanipulated DNA. The energetic contribution of the different components to synaptic stability is typically on the scale of a few kilocalories per mole. Our results define assembly rules for NHEJ machinery and unveil the importance of weak interactions, rapidly ruptured even at sub-picoNewton forces, in regulating this multicomponent chemomechanical system for genome integrity.
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Ponikvar-Svet M, Zeiger DN, Liebman JF. Interplay of thermochemistry and Structural Chemistry, the journal (volume 28, 2017, issues 1–2) and the discipline. Struct Chem 2018. [DOI: 10.1007/s11224-018-1099-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Albanaz ATS, Rodrigues CHM, Pires DEV, Ascher DB. Combating mutations in genetic disease and drug resistance: understanding molecular mechanisms to guide drug design. Expert Opin Drug Discov 2017; 12:553-563. [PMID: 28490289 DOI: 10.1080/17460441.2017.1322579] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Mutations introduce diversity into genomes, leading to selective changes and driving evolution. These changes have contributed to the emergence of many of the current major health concerns of the 21st century, from the development of genetic diseases and cancers to the rise and spread of drug resistance. The experimental systematic testing of all mutations in a system of interest is impractical and not cost-effective, which has created interest in the development of computational tools to understand the molecular consequences of mutations to aid and guide rational experimentation. Areas covered: Here, the authors discuss the recent development of computational methods to understand the effects of coding mutations to protein function and interactions, particularly in the context of the 3D structure of the protein. Expert opinion: While significant progress has been made in terms of innovative tools to understand and quantify the different range of effects in which a mutation or a set of mutations can give rise to a phenotype, a great gap still exists when integrating these predictions and drawing causality conclusions linking variants. This often requires a detailed understanding of the system being perturbed. However, as part of the drug development process it can be used preemptively in a similar fashion to pharmacokinetics predictions, to guide development of therapeutics to help guide the design and analysis of clinical trials, patient treatment and public health policy strategies.
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Affiliation(s)
- Amanda T S Albanaz
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Carlos H M Rodrigues
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,b Department of Biochemistry and Immunology , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brazil
| | - Douglas E V Pires
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil
| | - David B Ascher
- a Centro de Pesquisas René Rachou, FIOCRUZ , Belo Horizonte , MG , Brazil.,c Department of Biochemistry , University of Cambridge , Cambridge , Cambridgeshire , UK.,d Department of Biochemistry and Molecular Biology , University of Melbourne , Melbourne , Victoria , Australia
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