1
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Yoo J, Lee J, Kim J. Structural basis for the selective methylation of 5-carboxymethoxyuridine in tRNA modification. Nucleic Acids Res 2023; 51:9432-9441. [PMID: 37587716 PMCID: PMC10516636 DOI: 10.1093/nar/gkad668] [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: 06/28/2023] [Revised: 07/26/2023] [Accepted: 08/09/2023] [Indexed: 08/18/2023] Open
Abstract
Posttranscriptional modifications of tRNA are widely conserved in all domains of life. Especially, those occurring within the anticodon often modulate translational efficiency. Derivatives of 5-hydroxyuridine are specifically found in bacterial tRNA, where 5-methoxyuridine and 5-carboxymethoxyuridine are the major species in Gram-positive and Gram-negative bacteria, respectively. In certain tRNA species, 5-carboxymethoxyuridine can be further methylated by CmoM to form the methyl ester. In this report, we present the X-ray crystal structure of Escherichia coli CmoM complexed with tRNASer1, which contains 5-carboxymethoxyuridine at the 5'-end of anticodon (the 34th position of tRNA). The 2.22 Å resolution structure of the enzyme-tRNA complex reveals that both the protein and tRNA undergo local conformational changes around the binding interface. Especially, the hypomodified uracil base is flipped out from the canonical stacked conformation enabling the specific molecular interactions with the enzyme. Moreover, the structure illustrates that the enzyme senses exclusively the anticodon arm region of the substrate tRNA and examines the presence of key determinants, 5-carboxymethoxyuridine at position 34 and guanosine at position 35, offering molecular basis for the discriminatory mechanism against non-cognate tRNAs.
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Affiliation(s)
- Jaehun Yoo
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jangmin Lee
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jungwook Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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2
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de Sá Ribeiro F, Lima LMTR. Linking B-factor and temperature-induced conformational transition. Biophys Chem 2023; 298:107027. [PMID: 37172417 DOI: 10.1016/j.bpc.2023.107027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
The crystallographic B-factor, also called temperature factor or Debye-Waller factor, has long been used as a surrogate for local protein flexibility. However, the use of the absolute B-factor as a probe for protein motion requires reproducible validation against conformational changes against chemical and physical variables. Here we report the investigation of the thermal dependence of the crystallographic B-factor and its correlation with conformational changes of the protein. We obtained the crystal protein structure coordinates and B-factors at high resolution (1.5 Å) over a broad temperature range (100 K to 325 K). The exponential thermal dependence of B-factor as a function of temperature was equal for both the diffraction intensity data (Wilson B-factor) and for all modeled atoms of the system (protein and non-protein atoms), with a thermal diffusion constant of about 0.0045 K-1, similar for all atoms. The extrapolated B-factor at zero Kelvin (or zero-point fluctuation) varies among the atoms, although with no apparent correlation with temperature-dependent protein conformational changes. These data suggest that the thermal vibration of the atom does not necessarily correlate with the conformational dynamics of the protein.
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Affiliation(s)
- Fernando de Sá Ribeiro
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Química Biológica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, 21941-902, Brazil
| | - Luís Maurício T R Lima
- Laboratório de Biotecnologia Farmacêutica (pbiotech), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Programa de Pós-Graduação em Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil; Instituto Nacional de Metrologia, Tecnologia e Qualidade (INMETRO), Duque de Caxias, RJ 25250-020, Brazil.
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3
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Lu C, Zhang Y, Liu X, Hou F, Cai R, Yu Z, Liu F, Yang G, Ding J, Xu J, Hua X, Cheng X, Pan X, Liu L, Lin K, Wang Z, Li X, Lu J, Zhang Q, Li Y, Hu C, Fan H, Liu X, Wang H, Jia R, Xu F, Wang X, Huang H, Zhao R, Li J, Cheng H, Jia W, Yang X. Heterologous boost with mRNA vaccines against SARS-CoV-2 Delta/Omicron variants following an inactivated whole-virus vaccine. Antiviral Res 2023; 212:105556. [PMID: 36871919 PMCID: PMC9985518 DOI: 10.1016/j.antiviral.2023.105556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 03/07/2023]
Abstract
The coronavirus SARS-CoV-2 has mutated quickly and caused significant global damage. This study characterizes two mRNA vaccines ZSVG-02 (Delta) and ZSVG-02-O (Omicron BA.1), and associating heterologous prime-boost strategy following the prime of a most widely administrated inactivated whole-virus vaccine (BBIBP-CorV). The ZSVG-02-O induces neutralizing antibodies that effectively cross-react with Omicron subvariants. In naïve animals, ZSVG-02 or ZSVG-02-O induce humoral responses skewed to the vaccine's targeting strains, but cellular immune responses cross-react to all variants of concern (VOCs) tested. Following heterologous prime-boost regimes, animals present comparable neutralizing antibody levels and superior protection against Delta and Omicron BA.1variants. Single-boost only generated ancestral and omicron dual-responsive antibodies, probably by "recall" and "reshape" the prime immunity. New Omicron-specific antibody populations, however, appeared only following the second boost with ZSVG-02-O. Overall, our results support a heterologous boost with ZSVG-02-O, providing the best protection against current VOCs in inactivated virus vaccine-primed populations.
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Affiliation(s)
- Changrui Lu
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | | | - Xiaohu Liu
- Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Fujun Hou
- Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Rujie Cai
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Zhibin Yu
- Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Fei Liu
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Guohuan Yang
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Jun Ding
- Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Jiang Xu
- Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Xianwu Hua
- Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Xinhua Cheng
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Xinping Pan
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Lianxiao Liu
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Kang Lin
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China
| | - Zejun Wang
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Xinguo Li
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Jia Lu
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Qiu Zhang
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Yuwei Li
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Chunxia Hu
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Huifen Fan
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Xiaoke Liu
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Hui Wang
- Wuhan Institute of Biological Products Co., LTD (WIBP), China
| | - Rui Jia
- China National Biotec Group (CNBG), China
| | | | | | - Hongwei Huang
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China; Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Ronghua Zhao
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China; Virogin Biotech (Shanghai) Ltd (Virogin), China
| | - Jing Li
- Shuimu BioSciences Ltd, China
| | | | - William Jia
- China National Biological Group-Virogin Biotech (Shanghai) Ltd (CNBG-Virogin), China; Virogin Biotech (Shanghai) Ltd (Virogin), China.
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4
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Chang Y, Hawkins BA, Du JJ, Groundwater PW, Hibbs DE, Lai F. A Guide to In Silico Drug Design. Pharmaceutics 2022; 15:pharmaceutics15010049. [PMID: 36678678 PMCID: PMC9867171 DOI: 10.3390/pharmaceutics15010049] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
The drug discovery process is a rocky path that is full of challenges, with the result that very few candidates progress from hit compound to a commercially available product, often due to factors, such as poor binding affinity, off-target effects, or physicochemical properties, such as solubility or stability. This process is further complicated by high research and development costs and time requirements. It is thus important to optimise every step of the process in order to maximise the chances of success. As a result of the recent advancements in computer power and technology, computer-aided drug design (CADD) has become an integral part of modern drug discovery to guide and accelerate the process. In this review, we present an overview of the important CADD methods and applications, such as in silico structure prediction, refinement, modelling and target validation, that are commonly used in this area.
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Affiliation(s)
- Yiqun Chang
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Bryson A. Hawkins
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Jonathan J. Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Paul W. Groundwater
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - David E. Hibbs
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
| | - Felcia Lai
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia
- Correspondence:
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5
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Dicks L, Wales DJ. Exploiting Sequence-Dependent Rotamer Information in Global Optimization of Proteins. J Phys Chem B 2022; 126:8381-8390. [PMID: 36257022 PMCID: PMC9623586 DOI: 10.1021/acs.jpcb.2c04647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Rotamers, namely amino acid side chain conformations common to many different peptides, can be compiled into libraries. These rotamer libraries are used in protein modeling, where the limited conformational space occupied by amino acid side chains is exploited. Here, we construct a sequence-dependent rotamer library from simulations of all possible tripeptides, which provides rotameric states dependent on adjacent amino acids. We observe significant sensitivity of rotamer populations to sequence and find that the library is successful in locating side chain conformations present in crystal structures. The library is designed for applications with basin-hopping global optimization, where we use it to propose moves in conformational space. The addition of rotamer moves significantly increases the efficiency of protein structure prediction within this framework, and we determine parameters to optimize efficiency.
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Affiliation(s)
- L. Dicks
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom,IBM
Research, The Hartree Centre STFC Laboratory,
Sci-Tech Daresbury, Warrington WA4 4AD, United Kingdom
| | - D. J. Wales
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom,
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6
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Bond PS, Cowtan KD. ModelCraft: an advanced automated model-building pipeline using Buccaneer. Acta Crystallogr D Struct Biol 2022; 78:1090-1098. [PMID: 36048149 PMCID: PMC9435595 DOI: 10.1107/s2059798322007732] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/01/2022] [Indexed: 01/16/2023] Open
Abstract
Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.
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7
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Villalobos-Alva J, Ochoa-Toledo L, Villalobos-Alva MJ, Aliseda A, Pérez-Escamirosa F, Altamirano-Bustamante NF, Ochoa-Fernández F, Zamora-Solís R, Villalobos-Alva S, Revilla-Monsalve C, Kemper-Valverde N, Altamirano-Bustamante MM. Protein Science Meets Artificial Intelligence: A Systematic Review and a Biochemical Meta-Analysis of an Inter-Field. Front Bioeng Biotechnol 2022; 10:788300. [PMID: 35875501 PMCID: PMC9301016 DOI: 10.3389/fbioe.2022.788300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 05/25/2022] [Indexed: 11/23/2022] Open
Abstract
Proteins are some of the most fascinating and challenging molecules in the universe, and they pose a big challenge for artificial intelligence. The implementation of machine learning/AI in protein science gives rise to a world of knowledge adventures in the workhorse of the cell and proteome homeostasis, which are essential for making life possible. This opens up epistemic horizons thanks to a coupling of human tacit–explicit knowledge with machine learning power, the benefits of which are already tangible, such as important advances in protein structure prediction. Moreover, the driving force behind the protein processes of self-organization, adjustment, and fitness requires a space corresponding to gigabytes of life data in its order of magnitude. There are many tasks such as novel protein design, protein folding pathways, and synthetic metabolic routes, as well as protein-aggregation mechanisms, pathogenesis of protein misfolding and disease, and proteostasis networks that are currently unexplored or unrevealed. In this systematic review and biochemical meta-analysis, we aim to contribute to bridging the gap between what we call binomial artificial intelligence (AI) and protein science (PS), a growing research enterprise with exciting and promising biotechnological and biomedical applications. We undertake our task by exploring “the state of the art” in AI and machine learning (ML) applications to protein science in the scientific literature to address some critical research questions in this domain, including What kind of tasks are already explored by ML approaches to protein sciences? What are the most common ML algorithms and databases used? What is the situational diagnostic of the AI–PS inter-field? What do ML processing steps have in common? We also formulate novel questions such as Is it possible to discover what the rules of protein evolution are with the binomial AI–PS? How do protein folding pathways evolve? What are the rules that dictate the folds? What are the minimal nuclear protein structures? How do protein aggregates form and why do they exhibit different toxicities? What are the structural properties of amyloid proteins? How can we design an effective proteostasis network to deal with misfolded proteins? We are a cross-functional group of scientists from several academic disciplines, and we have conducted the systematic review using a variant of the PICO and PRISMA approaches. The search was carried out in four databases (PubMed, Bireme, OVID, and EBSCO Web of Science), resulting in 144 research articles. After three rounds of quality screening, 93 articles were finally selected for further analysis. A summary of our findings is as follows: regarding AI applications, there are mainly four types: 1) genomics, 2) protein structure and function, 3) protein design and evolution, and 4) drug design. In terms of the ML algorithms and databases used, supervised learning was the most common approach (85%). As for the databases used for the ML models, PDB and UniprotKB/Swissprot were the most common ones (21 and 8%, respectively). Moreover, we identified that approximately 63% of the articles organized their results into three steps, which we labeled pre-process, process, and post-process. A few studies combined data from several databases or created their own databases after the pre-process. Our main finding is that, as of today, there are no research road maps serving as guides to address gaps in our knowledge of the AI–PS binomial. All research efforts to collect, integrate multidimensional data features, and then analyze and validate them are, so far, uncoordinated and scattered throughout the scientific literature without a clear epistemic goal or connection between the studies. Therefore, our main contribution to the scientific literature is to offer a road map to help solve problems in drug design, protein structures, design, and function prediction while also presenting the “state of the art” on research in the AI–PS binomial until February 2021. Thus, we pave the way toward future advances in the synthetic redesign of novel proteins and protein networks and artificial metabolic pathways, learning lessons from nature for the welfare of humankind. Many of the novel proteins and metabolic pathways are currently non-existent in nature, nor are they used in the chemical industry or biomedical field.
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Affiliation(s)
- Jalil Villalobos-Alva
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Luis Ochoa-Toledo
- Instituto de Ciencias Aplicadas y Tecnología (ICAT), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Mario Javier Villalobos-Alva
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Atocha Aliseda
- Instituto de Investigaciones Filosóficas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Fernando Pérez-Escamirosa
- Instituto de Ciencias Aplicadas y Tecnología (ICAT), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Francine Ochoa-Fernández
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Ricardo Zamora-Solís
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Sebastián Villalobos-Alva
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Cristina Revilla-Monsalve
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Nicolás Kemper-Valverde
- Instituto de Ciencias Aplicadas y Tecnología (ICAT), Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Myriam M. Altamirano-Bustamante
- Unidad de Investigación en Enfermedades Metabólicas, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
- *Correspondence: Myriam M. Altamirano-Bustamante,
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8
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The reproducible normality of the crystallographic B-factor. Anal Biochem 2022; 645:114594. [DOI: 10.1016/j.ab.2022.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 02/08/2022] [Indexed: 11/20/2022]
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9
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Alharbi E, Bond P, Calinescu R, Cowtan K. Predicting the performance of automated crystallographic model-building pipelines. Acta Crystallogr D Struct Biol 2021; 77:1591-1601. [PMID: 34866614 PMCID: PMC8647178 DOI: 10.1107/s2059798321010500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/10/2021] [Indexed: 12/02/2022] Open
Abstract
Proteins are macromolecules that perform essential biological functions which depend on their three-dimensional structure. Determining this structure involves complex laboratory and computational work. For the computational work, multiple software pipelines have been developed to build models of the protein structure from crystallographic data. Each of these pipelines performs differently depending on the characteristics of the electron-density map received as input. Identifying the best pipeline to use for a protein structure is difficult, as the pipeline performance differs significantly from one protein structure to another. As such, researchers often select pipelines that do not produce the best possible protein models from the available data. Here, a software tool is introduced which predicts key quality measures of the protein structures that a range of pipelines would generate if supplied with a given crystallographic data set. These measures are crystallographic quality-of-fit indicators based on included and withheld observations, and structure completeness. Extensive experiments carried out using over 2500 data sets show that the tool yields accurate predictions for both experimental phasing data sets (at resolutions between 1.2 and 4.0 Å) and molecular-replacement data sets (at resolutions between 1.0 and 3.5 Å). The tool can therefore provide a recommendation to the user concerning the pipelines that should be run in order to proceed most efficiently to a depositable model.
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Affiliation(s)
- Emad Alharbi
- Department of Computer Science, University of York, Heslington, York YO10 5GH, United Kingdom
- Department of Information Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Paul Bond
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
| | - Radu Calinescu
- Department of Computer Science, University of York, Heslington, York YO10 5GH, United Kingdom
| | - Kevin Cowtan
- Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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10
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Affiliation(s)
- Melanie Vollmar
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd., Harwell Science & Innovation Campus, Didcot, UK
- Rosalind Franklin Institute, Harwell Science & Innovation Campus, Didcot, UK
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11
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Pertici I, Taft MH, Greve JN, Fedorov R, Caremani M, Manstein DJ. Allosteric modulation of cardiac myosin mechanics and kinetics by the conjugated omega-7,9 trans-fat rumenic acid. J Physiol 2021; 599:3639-3661. [PMID: 33942907 DOI: 10.1113/jp281563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/28/2021] [Indexed: 01/23/2023] Open
Abstract
KEY POINTS Direct binding of rumenic acid to the cardiac myosin-2 motor domain increases the release rate for orthophosphate and increases the Ca2+ responsiveness of cardiac muscle at low load. Physiological cellular concentrations of rumenic acid affect the ATP turnover rates of the super-relaxed and disordered relaxed states of β-cardiac myosin, leading to a net increase in myocardial metabolic load. In Ca2+ -activated trabeculae, rumenic acid exerts a direct inhibitory effect on the force-generating mechanism without affecting the number of force-generating motors. In the presence of saturating actin concentrations rumenic acid binds to the β-cardiac myosin-2 motor domain with an EC50 of 200 nM. Molecular docking studies provide information about the binding site, the mode of binding, and associated allosteric communication pathways. Free rumenic acid may exceed thresholds in cardiomyocytes above which contractile efficiency is reduced and interference with small molecule therapeutics, targeting cardiac myosin, occurs. ABSTRACT Based on experiments using purified myosin motor domains, reconstituted actomyosin complexes and rat heart ventricular trabeculae, we demonstrate direct binding of rumenic acid, the cis-delta-9-trans-delta-11 isomer of conjugated linoleic acid, to an allosteric site located in motor domain of mammalian cardiac myosin-2 isoforms. In the case of porcine β-cardiac myosin, the EC50 for rumenic acid varies from 10.5 μM in the absence of actin to 200 nM in the presence of saturating concentrations of actin. Saturating concentrations of rumenic acid increase the maximum turnover of basal and actin-activated ATPase activity of β-cardiac myosin approximately 2-fold but decrease the force output per motor by 23% during isometric contraction. The increase in ATP turnover is linked to an acceleration of the release of the hydrolysis product orthophosphate. In the presence of 5 μM rumenic acid, the difference in the rate of ATP turnover by the super-relaxed and disordered relaxed states of cardiac myosin increases from 4-fold to 20-fold. The equilibrium between the two functional myosin states is not affected by rumenic acid. Calcium responsiveness is increased under zero-load conditions but unchanged under load. Molecular docking studies provide information about the rumenic acid binding site, the mode of binding, and associated allosteric communication pathways. They show how the isoform-specific replacement of residues in the binding cleft induces a different mode of rumenic acid binding in the case of non-muscle myosin-2C and blocks binding to skeletal muscle and smooth muscle myosin-2 isoforms.
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Affiliation(s)
- Irene Pertici
- PhysioLab, University of Florence, Florence, 50019, Italy.,Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Manuel H Taft
- Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Johannes N Greve
- Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Roman Fedorov
- Division of Structural Biochemistry, OE8830, Medizinische Hochschule Hannover, Hannover, 30625, Germany.,RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, Hannover, 30625, Germany
| | - Marco Caremani
- PhysioLab, University of Florence, Florence, 50019, Italy
| | - Dietmar J Manstein
- Institute for Biophysical Chemistry, OE4350, Medizinische Hochschule Hannover, Hannover, 30625, Germany.,Division of Structural Biochemistry, OE8830, Medizinische Hochschule Hannover, Hannover, 30625, Germany.,RESiST, Cluster of Excellence 2155, Medizinische Hochschule Hannover, Hannover, 30625, Germany
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12
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Cowtan K, Metcalfe S, Bond P. Shift-field refinement of macromolecular atomic models. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1192-1200. [PMID: 33263325 PMCID: PMC7709196 DOI: 10.1107/s2059798320013170] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 09/29/2020] [Indexed: 11/11/2022]
Abstract
The aim of crystallographic structure solution is typically to determine an atomic model which accurately accounts for an observed diffraction pattern. A key step in this process is the refinement of the parameters of an initial model, which is most often determined by molecular replacement using another structure which is broadly similar to the structure of interest. In macromolecular crystallography, the resolution of the data is typically insufficient to determine the positional and uncertainty parameters for each individual atom, and so stereochemical information is used to supplement the observational data. Here, a new approach to refinement is evaluated in which a `shift field' is determined which describes changes to model parameters affecting whole regions of the model rather than individual atoms only, with the size of the affected region being a key parameter of the calculation which can be changed in accordance with the resolution of the data. It is demonstrated that this approach can improve the radius of convergence of the refinement calculation while also dramatically reducing the calculation time.
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Affiliation(s)
- K Cowtan
- Department of Chemistry, University of York, York, United Kingdom
| | - S Metcalfe
- Derpartment of Mechanical Engineering, McGill University, Montréal, Canada
| | - P Bond
- Department of Chemistry, University of York, York, United Kingdom
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Cowtan K. Structural barriers to scientific progress. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:908-911. [PMID: 33021492 PMCID: PMC7543655 DOI: 10.1107/s2059798320011201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/15/2020] [Indexed: 11/11/2022]
Abstract
Structural biases, which are intrinsic in the social structures in which we function, play a key role in maintaining boundaries between traditionally privileged and underprivileged groups; however, they are particularly difficult to identify from within those societies. Two instances are highlighted in which the social structures of science appear to have discouraged collaboration, to the disadvantage of software and data users. Possible links are suggested to the strongly hierarchical structure of science and other factors which may in turn also serve to maintain sex and/or gender disparities in participation in the scientific endeavour.
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Affiliation(s)
- K Cowtan
- Department of Chemistry, University of York, York YO10 5DD, United Kingdom
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