1
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Chamberlain SR, Moore S, Grant TD. Fitting high-resolution electron density maps from atomic models to solution scattering data. Biophys J 2023; 122:4567-4581. [PMID: 37924208 PMCID: PMC10719074 DOI: 10.1016/j.bpj.2023.10.034] [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: 06/05/2023] [Revised: 08/29/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023] Open
Abstract
Solution scattering techniques, such as small- and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for one of the free fitting parameters commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated that uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high-quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization produces significantly more accurate predicted scattering profiles compared to the leading software. The algorithm is computationally efficient, comparable to the leading software and up to 10 times faster for large molecules. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package. In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms using SWAXS data and decreasing the risk of overfitting.
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Affiliation(s)
- Sarah R Chamberlain
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Stephen Moore
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York
| | - Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, New York.
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2
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Raviv U, Asor R, Shemesh A, Ginsburg A, Ben-Nun T, Schilt Y, Levartovsky Y, Ringel I. Insight into structural biophysics from solution X-ray scattering. J Struct Biol 2023; 215:108029. [PMID: 37741561 DOI: 10.1016/j.jsb.2023.108029] [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: 04/29/2023] [Revised: 08/09/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
The current challenges of structural biophysics include determining the structure of large self-assembled complexes, resolving the structure of ensembles of complex structures and their mass fraction, and unraveling the dynamic pathways and mechanisms leading to the formation of complex structures from their subunits. Modern synchrotron solution X-ray scattering data enable simultaneous high-spatial and high-temporal structural data required to address the current challenges of structural biophysics. These data are complementary to crystallography, NMR, and cryo-TEM data. However, the analysis of solution scattering data is challenging; hence many different analysis tools, listed in the SAS Portal (http://smallangle.org/), were developed. In this review, we start by briefly summarizing classical X-ray scattering analyses providing insight into fundamental structural and interaction parameters. We then describe recent developments, integrating simulations, theory, and advanced X-ray scattering modeling, providing unique insights into the structure, energetics, and dynamics of self-assembled complexes. The structural information is essential for understanding the underlying physical chemistry principles leading to self-assembled supramolecular architectures and computational structural refinement.
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Affiliation(s)
- Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel; The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel.
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yaelle Schilt
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Israel Ringel
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, 9112102 Jerusalem, Israel
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3
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Chamberlain SR, Moore S, Grant TD. Fitting high-resolution electron density maps from atomic models to solution scattering data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.02.543451. [PMID: 37398274 PMCID: PMC10312546 DOI: 10.1101/2023.06.02.543451] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Solution scattering techniques, such as small and wide-angle X-ray scattering (SWAXS), provide valuable insights into the structure and dynamics of biological macromolecules in solution. In this study, we present an approach to accurately predict solution X-ray scattering profiles at wide angles from atomic models by generating high-resolution electron density maps. Our method accounts for the excluded volume of bulk solvent by calculating unique adjusted atomic volumes directly from the atomic coordinates. This approach eliminates the need for a free fitting parameter commonly used in existing algorithms, resulting in improved accuracy of the calculated SWAXS profile. An implicit model of the hydration shell is generated which uses the form factor of water. Two parameters, namely the bulk solvent density and the mean hydration shell contrast, are adjusted to best fit the data. Results using eight publicly available SWAXS profiles show high quality fits to the data. In each case, the optimized parameter values show small adjustments demonstrating that the default values are close to the true solution. Disabling parameter optimization results in a significant improvement of the calculated scattering profiles compared to the leading software. The algorithm is computationally efficient, showing more than tenfold reduction in execution time compared to the leading software. The algorithm is encoded in a command line script called denss.pdb2mrc.py and is available open source as part of the DENSS v1.7.0 software package (https://github.com/tdgrant1/denss). In addition to improving the ability to compare atomic models to experimental SWAXS data, these developments pave the way for increasing the accuracy of modeling algorithms utilizing SWAXS data while decreasing the risk of overfitting.
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Affiliation(s)
- Sarah R. Chamberlain
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Stephen Moore
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
| | - Thomas D. Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, USA
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4
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Sonje J, Thakral S, Krueger S, Suryanarayanan R. Enabling Efficient Design of Biological Formulations Through Advanced Characterization. Pharm Res 2023; 40:1459-1477. [PMID: 36959413 DOI: 10.1007/s11095-023-03495-z] [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: 11/23/2022] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
The present review summarizes the use of differential scanning calorimetry (DSC) and scattering techniques in the context of protein formulation design and characterization. The scattering techniques include wide angle X-ray diffractometry (XRD), small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS). While DSC is valuable for understanding thermal behavior of the excipients, XRD provides critical information about physical state of solutes during freezing, annealing and in the final lyophile. However, as these techniques lack the sensitivity to detect biomolecule-related transitions, complementary characterization techniques such as small-angle scattering can provide valuable insights.
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Affiliation(s)
- Jayesh Sonje
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA
- BioTherapeutics, Pharmaceutical Sciences, Pfizer Inc., 1 Burtt Road, Andover, USA
| | - Seema Thakral
- Boehringer Ingelheim Pharmaceuticals, Inc, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Susan Krueger
- Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Raj Suryanarayanan
- Department of Pharmaceutics, College of Pharmacy, University of Minnesota, 308 Harvard St. SE, Minneapolis, MN, 55455, USA.
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5
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Trewhella J, Jeffries CM, Whitten AE. 2023 update of template tables for reporting biomolecular structural modelling of small-angle scattering data. Acta Crystallogr D Struct Biol 2023; 79:122-132. [PMID: 36762858 PMCID: PMC9912924 DOI: 10.1107/s2059798322012141] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 12/23/2022] [Indexed: 02/10/2023] Open
Abstract
In 2017, guidelines were published for reporting structural modelling of small-angle scattering (SAS) data from biomolecules in solution that exemplified best-practice documentation of experiments and analysis. Since then, there has been significant progress in SAS data and model archiving, and the IUCr journal editors announced that the IUCr biology journals will require the deposition of SAS data used in biomolecular structure solution into a public archive, as well as adherence to the 2017 reporting guidelines. In this context, the reporting template tables accompanying the 2017 publication guidelines have been reviewed with a focus on making them both easier to use and more general. With input from the SAS community via the IUCr Commission on SAS and attendees of the triennial 2022 SAS meeting (SAS2022, Campinas, Brazil), an updated reporting template table has been developed that includes standard descriptions for proteins, glycosylated proteins, DNA and RNA, with some reorganization of the data to improve readability and interpretation. In addition, a specialized template has been developed for reporting SAS contrast-variation (SAS-cv) data and models that incorporates the additional reporting requirements from the 2017 guidelines for these more complicated experiments. To demonstrate their utility, examples of reporting with these new templates are provided for a SAS study of a DNA-protein complex and a SAS-cv experiment on a protein complex. The examples demonstrate how the tabulated information promotes transparent reporting that, in combination with the recommended figures and additional information best presented in the main text, enables the reader of the work to readily draw their own conclusions regarding the quality of the data and the validity of the models presented.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, Notkestrasse 85, c/o Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Andrew E. Whitten
- Australian Nuclear Science and Technology Organisation, New Illawarra Road, Lucas Heights, NSW 2234, Australia
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6
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Wu Z, Jayaraman A. Machine Learning-Enhanced Computational Reverse-Engineering Analysis for Scattering Experiments (CREASE) for Analyzing Fibrillar Structures in Polymer Solutions. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c02165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zijie Wu
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware19716, United States
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, Delaware19716, United States
- Department of Materials Science and Engineering, University of Delaware, 201 DuPont Hall, Newark, Delaware19716, United States
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7
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Data quality assurance, model validation, and data sharing for biomolecular structures from small-angle scattering. Methods Enzymol 2022; 678:1-22. [PMID: 36641205 DOI: 10.1016/bs.mie.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Key to small-angle scattering (SAS) maturing and becoming a mainstream structural biology technique was the work done by the SAS community to establish standards for data quality, model validation and data sharing. Through a consultative process spanning more than a decade and a half, guidelines for publication have been established that include criteria for evaluating data quality and for model validation. In this process gaps were identified that stimulated innovation and development of new tools, for example new measures of model ambiguity and of the goodness-of-fit of a model to SAS data that complement the traditional global fit parameter χ2. The need for a global repository for biomolecular SAS data and models was identified and the SASBDB was established as a searchable, curated, freely accessible, downloadable database of experimental data, experimental conditions, sample details, derived models, and their fit to the data. Importantly, the SASBDB uses a common dictionary format that supports archiving of structures solved using integrative methods to support seamless data exchange with a federated system of public databanks that includes the world-wide Protein Data Bank (wwPDB) as the major repository for structural biology. Thus, biomolecular SAS is now well-positioned to achieve its full potential as a mainstream structural biology technique contributing at the frontier of integrative structural biology and meeting "best practice" standards for data quality assurance and data sharing.
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8
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Abstract
Ab initio modeling methods have proven to be powerful means of interpreting solution scattering data. In the absence of atomic models, or complementary to them, ab initio modeling approaches can be used for generating low-resolution particle envelopes using only solution scattering profiles. Recently, a new ab initio reconstruction algorithm has been introduced to the scientific community, called DENSS. DENSS is unique among ab initio modeling algorithms in that it solves the inverse scattering problem, i.e., the 1D scattering intensities are directly used to determine the 3D particle density. The reconstruction of particle density has several advantages over conventional uniform density modeling approaches, including the ability to reconstruct a much wider range of particle types and the ability to visualize low-resolution density fluctuations inside the particle envelope. In this chapter we will discuss the theory behind this new approach, how to use DENSS, and how to interpret the results. Several examples with experimental and simulated data will be provided.
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Affiliation(s)
- Thomas D Grant
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, SUNY University at Buffalo, Buffalo, NY, United States.
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9
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Chinnam NB, Syed A, Hura GL, Hammel M, Tainer JA, Tsutakawa SE. Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution. Methods Enzymol 2022; 678:351-376. [PMID: 36641214 PMCID: PMC10132260 DOI: 10.1016/bs.mie.2022.09.023] [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: 11/11/2022]
Abstract
Accurate protein structure predictions, enabled by recent advances in machine learning algorithms, provide an entry point to probing structural mechanisms and to integrating and querying many types of biochemical and biophysical results. Limitations in such protein structure predictions can be reduced and addressed through comparison to experimental Small Angle X-ray Scattering (SAXS) data that provides protein structural information in solution. SAXS data can not only validate computational predictions, but can improve conformational and assembly prediction to produce atomic models that are consistent with solution data and biologically relevant states. Here, we describe how to obtain protein structure predictions, compare them to experimental SAXS data and improve models to reflect experimental information from SAXS data. Furthermore, we consider the potential for such experimentally-validated protein structure predictions to broadly improve functional annotation in proteins identified in metagenomics and to identify functional clustering on conserved sites despite low sequence homology.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States; Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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10
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Lyons NS, Bogner AN, Tanner JJ, Sobrado P. Kinetic and Structural Characterization of a Flavin-Dependent Putrescine N-Hydroxylase from Acinetobacter baumannii. Biochemistry 2022; 61:2607-2620. [DOI: 10.1021/acs.biochem.2c00493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Noah S. Lyons
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Alexandra N. Bogner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Pablo Sobrado
- Department of Biochemistry and Center for Drug Discovery, Virginia Tech, Blacksburg, Virginia 24061, United States
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11
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San Emeterio J, Pabit SA, Pollack L. Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis. Methods Enzymol 2022; 677:41-83. [PMID: 36410957 PMCID: PMC10015503 DOI: 10.1016/bs.mie.2022.08.007] [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: 11/19/2022]
Abstract
Proteins and nucleic acids, alone and in complex are among the essential building blocks of living organisms. Obtaining a molecular level understanding of their structures, and the changes that occur as they interact, is critical for expanding our knowledge of life processes or disease progression. Here, we motivate and describe an application of solution small angle X-ray scattering (SAXS) which provides valuable information about the structures, ensembles, compositions and dynamics of protein-nucleic acid complexes in solution, in equilibrium and time-resolved studies. Contrast variation (CV-) SAXS permits the visualization of the distinct molecular constituents (protein and/or nucleic acid) within a complex. CV-SAXS can be implemented in two modes. In the simplest, the protein within the complex is effectively rendered invisible by the addition of an inert contrast agent at an appropriate concentration. Under these conditions, the structure, or structural changes of only the nucleic acid component of the complex can be studied in detail. The second mode permits observation of both components of the complex: the protein and the nucleic acid. This approach requires the acquisition of SAXS profiles on the complex at different concentrations of a contrast agent. Here, we review CV-SAXS as applied to protein-nucleic acid complexes in both modes. We provide some theoretical framework for CV-SAXS but focus primarily on providing the necessary information required to implement a successful experiment including experimental design, sample quality assessment, and data analysis.
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Affiliation(s)
- Josue San Emeterio
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, United States.
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12
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Chinnam NB, Syed A, Burnett KH, Hura GL, Tainer JA, Tsutakawa SE. Universally Accessible Structural Data on Macromolecular Conformation, Assembly, and Dynamics by Small Angle X-Ray Scattering for DNA Repair Insights. Methods Mol Biol 2022; 2444:43-68. [PMID: 35290631 PMCID: PMC9020468 DOI: 10.1007/978-1-0716-2063-2_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Structures provide a critical breakthrough step for biological analyses, and small angle X-ray scattering (SAXS) is a powerful structural technique to study dynamic DNA repair proteins. As toxic and mutagenic repair intermediates need to be prevented from inadvertently harming the cell, DNA repair proteins often chaperone these intermediates through dynamic conformations, coordinated assemblies, and allosteric regulation. By measuring structural conformations in solution for both proteins, DNA, RNA, and their complexes, SAXS provides insight into initial DNA damage recognition, mechanisms for validation of their substrate, and pathway regulation. Here, we describe exemplary SAXS analyses of a DNA damage response protein spanning from what can be derived directly from the data to obtaining super resolution through the use of SAXS selection of atomic models. We outline strategies and tactics for practical SAXS data collection and analysis. Making these structural experiments in reach of any basic and clinical researchers who have protein, SAXS data can readily be collected at government-funded synchrotrons, typically at no cost for academic researchers. In addition to discussing how SAXS complements and enhances cryo-electron microscopy, X-ray crystallography, NMR, and computational modeling, we furthermore discuss taking advantage of recent advances in protein structure prediction in combination with SAXS analysis.
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Affiliation(s)
- Naga Babu Chinnam
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Aleem Syed
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kathryn H Burnett
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Greg L Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Chemistry and Biochemistry Department, University of California Santa Cruz, Santa Cruz, CA, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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13
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Monsen RC, Chakravarthy S, Dean WL, Chaires JB, Trent JO. The solution structures of higher-order human telomere G-quadruplex multimers. Nucleic Acids Res 2021; 49:1749-1768. [PMID: 33469644 PMCID: PMC7897503 DOI: 10.1093/nar/gkaa1285] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/21/2020] [Accepted: 01/13/2021] [Indexed: 12/17/2022] Open
Abstract
Human telomeres contain the repeat DNA sequence 5′-d(TTAGGG), with duplex regions that are several kilobases long terminating in a 3′ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate models proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5′-d(TTAGGG)n, with n = 8, 12 and 16, fold into multimeric structures containing the maximal number (2, 3 and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of ∼34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville Medical School, Louisville, KY 40202, USA.,James Graham Brown Cancer Center, University of Louisville Medical School, Louisville, KY 40202, USA.,Department of Medicine, University of Louisville Medical School, Louisville, KY 40202, USA
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14
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Narvekar A, Gawali SL, Hassan PA, Jain R, Dandekar P. pH dependent aggregation and conformation changes of rituximab using SAXS and its comparison with the standard regulatory approach of biophysical characterization. Int J Biol Macromol 2020; 164:3084-3097. [PMID: 32835797 DOI: 10.1016/j.ijbiomac.2020.08.148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 10/23/2022]
Abstract
Development of biologics and biosimilars involves extensive physical and structural characterization, which underlines the further course of its implementation. These characterization techniques require considerable standardization and are labor intensive. It is therefore, important to have an immediate, independent and affordable characterization strategy that may meet the regulatory guidelines. In this study, we have compared the standard biophysical characterization of an anti-CD 20 antibody with characterization by small angle x ray scattering (SAXS). Aggregation of this mAb was analyzed using standard techniques like size exclusion HPLC, dynamic light scattering and sedimentation velocity - analytical ultracentrifugation, whereas structure analysis was conducted using mass spectrometry, circular dichroism spectroscopy and fluorescence spectroscopy. Our results demonstrated that the inferences about the state of mAb aggregation and its structure deduced using the standard approaches were comparable to the data interpreted using SAXS. The radius of gyration and the P(r) distribution plot obtained using the SAXS scattering data allowed analysis of aggregation and conformation of mAb via a single experiment. Thus, SAXS can be used as an independent technique to complement orthogonal analysis for determining the aggregation profile and structure of mAbs.
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Affiliation(s)
- Aditya Narvekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India
| | - Santosh L Gawali
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Puthusserickal A Hassan
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India
| | - Ratnesh Jain
- Department of Chemical Engineering, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
| | - Prajakta Dandekar
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai 400019, India.
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15
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Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo T, Chakravarthy S, Chaires JB, Trent JO. The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res 2020; 48:5720-5734. [PMID: 32083666 PMCID: PMC7261196 DOI: 10.1093/nar/gkaa107] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - Lynn DeLeeuw
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - T Michael Sabo
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
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16
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Treece BW, Heinrich F, Ramanathan A, Lösche M. Steering Molecular Dynamics Simulations of Membrane-Associated Proteins with Neutron Reflection Results. J Chem Theory Comput 2020; 16:3408-3419. [DOI: 10.1021/acs.jctc.0c00136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Bradley W. Treece
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- The NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Arvind Ramanathan
- Data Science and Learning, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- The NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
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17
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Koukos P, Bonvin A. Integrative Modelling of Biomolecular Complexes. J Mol Biol 2020; 432:2861-2881. [DOI: 10.1016/j.jmb.2019.11.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 12/31/2022]
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18
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Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A. SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:92-102. [PMID: 31570166 DOI: 10.1016/j.pbiomolbio.2019.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023]
Abstract
X-ray crystallography and electron microscopy maps resolved to 3-8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone model as an optimization problem, which requires three main components: the representation of the system, the scoring function, and the optimization method. The method is implemented in the open source Integrative Modeling Platform (IMP) (https://integrativemodeling.org), allowing a number of different terms in the scoring function. We apply this method to localizing the sequence assignment within a 199-residue disordered region of three structured and sequence unassigned helices in the DNA-PKcs crystallographic structure, using chemical crosslinks, hydrogen deuterium exchange, and sequence connectivity. The resulting ensemble of threading models provides two major solutions, one of which suggests that the crucial ABCDE cluster of phosphorylation sites cannot undergo intra-molecular autophosphorylation without a conformational rearrangement. The ensemble of solutions embodies the most accurate and precise sequence threading given the available information.
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Affiliation(s)
- Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA.
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Kala Bharath Pilla
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
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19
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Chen PC, Shevchuk R, Strnad FM, Lorenz C, Karge L, Gilles R, Stadler AM, Hennig J, Hub JS. Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4687-4698. [DOI: 10.1021/acs.jctc.9b00292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Roman Shevchuk
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Felix M. Strnad
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Charlotte Lorenz
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Lukas Karge
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Ralph Gilles
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
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20
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Braitbard M, Schneidman-Duhovny D, Kalisman N. Integrative Structure Modeling: Overview and Assessment. Annu Rev Biochem 2019; 88:113-135. [PMID: 30830798 DOI: 10.1146/annurev-biochem-013118-111429] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Integrative structure modeling computationally combines data from multiple sources of information with the aim of obtaining structural insights that are not revealed by any single approach alone. In the first part of this review, we survey the commonly used sources of structural information and the computational aspects of model building. Throughout the past decade, integrative modeling was applied to various biological systems, with a focus on large protein complexes. Recent progress in the field of cryo-electron microscopy (cryo-EM) has resolved many of these complexes to near-atomic resolution. In the second part of this review, we compare a range of published integrative models with their higher-resolution counterparts with the aim of critically assessing their accuracy. This comparison gives a favorable view of integrative modeling and demonstrates its ability to yield accurate and informative results. We discuss possible roles of integrative modeling in the new era of cryo-EM and highlight future challenges and directions.
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Affiliation(s)
- Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; .,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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21
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Influence of energy bandwidth of pink beam on small angle X-ray scattering. RADIATION DETECTION TECHNOLOGY AND METHODS 2019. [DOI: 10.1007/s41605-018-0047-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Ferrari AJR, Gozzo FC, Martínez L. Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints. Bioinformatics 2019; 35:3005-3012. [DOI: 10.1093/bioinformatics/btz013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 12/03/2018] [Accepted: 01/04/2019] [Indexed: 12/22/2022] Open
Abstract
Abstract
Motivation
Chemical cross-linking/mass spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms.
Results
A force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. First, the strategy suggests that XL constraints should be set to shorter distances than usually assumed. Second, the complete statistical force-field improves the models obtained and can be easily incorporated into current modeling methods and software. The force-field was implemented and is distributed to be used within the Rosetta ab initio relax protocol.
Availability and implementation
Force-field parameters and usage instructions are freely available online (http://m3g.iqm.unicamp.br/topolink/xlff).
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Allan J R Ferrari
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
| | - Fabio C Gozzo
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
| | - Leandro Martínez
- Institute of Chemistry, University of Campinas, Campinas, SP, Brazil
- Center for Computing in Engineering & Sciences, University of Campinas, Campinas, SP, Brazil
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23
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Kappel K, Das R. Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking. Structure 2018; 27:140-151.e5. [PMID: 30416038 DOI: 10.1016/j.str.2018.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/27/2018] [Accepted: 10/05/2018] [Indexed: 10/27/2022]
Abstract
RNA-protein complexes underlie numerous cellular processes including translation, splicing, and posttranscriptional regulation of gene expression. The structures of these complexes are crucial to their functions but often elude high-resolution structure determination. Computational methods are needed that can integrate low-resolution data for RNA-protein complexes while modeling de novo the large conformational changes of RNA components upon complex formation. To address this challenge, we describe RNP-denovo, a Rosetta method to simultaneously fold-and-dock RNA to a protein surface. On a benchmark set of diverse RNA-protein complexes not solvable with prior strategies, RNP-denovo consistently sampled native-like structures with better than nucleotide resolution. We revisited three past blind modeling challenges involving the spliceosome, telomerase, and a methyltransferase-ribosomal RNA complex in which previous methods gave poor results. When coupled with the same sparse FRET, crosslinking, and functional data used previously, RNP-denovo gave models with significantly improved accuracy. These results open a route to modeling global folds of RNA-protein complexes from low-resolution data.
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Affiliation(s)
- Kalli Kappel
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Physics, Stanford University, Stanford, CA 94305, USA.
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24
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Blanco MA, Hatch HW, Curtis JE, Shen VK. A methodology to calculate small-angle scattering profiles of macromolecular solutions from molecular simulations in the grand-canonical ensemble. J Chem Phys 2018; 149:084203. [PMID: 30193476 DOI: 10.1063/1.5029274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The theoretical framework to evaluate small-angle scattering (SAS) profiles for multi-component macromolecular solutions is re-examined from the standpoint of molecular simulations in the grand-canonical ensemble, where the chemical potentials of all species in solution are fixed. This statistical mechanical ensemble resembles more closely scattering experiments, capturing concentration fluctuations that arise from the exchange of molecules between the scattering volume and the bulk solution. The resulting grand-canonical expression relates scattering intensities to the different intra- and intermolecular pair distribution functions, as well as to the distribution of molecular concentrations on the scattering volume. This formulation represents a generalized expression that encompasses most of the existing methods to evaluate SAS profiles from molecular simulations. The grand-canonical SAS methodology is probed for a series of different implicit-solvent, homogeneous systems at conditions ranging from dilute to concentrated. These systems consist of spherical colloids, dumbbell particles, and highly flexible polymer chains. Comparison of the resulting SAS curves against classical methodologies based on either theoretical approaches or canonical simulations (i.e., at a fixed number of molecules) shows equivalence between the different scattering intensities so long as interactions between molecules are net repulsive or weakly attractive. On the other hand, for strongly attractive interactions, grand-canonical SAS profiles deviate in the low- and intermediate-q range from those calculated in a canonical ensemble. Such differences are due to the distribution of molecules becoming asymmetric, which yields a higher contribution from configurations with molecular concentrations larger than the nominal value. Additionally, for flexible systems, explicit discrimination between intra- and inter-molecular SAS contributions permits the implementation of model-free, structural analysis such as Guinier's plots at high molecular concentrations, beyond what the traditional limits are for such analysis.
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Affiliation(s)
- Marco A Blanco
- Chemical Informatics Group, Chemical Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Harold W Hatch
- Chemical Informatics Group, Chemical Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Vincent K Shen
- Chemical Informatics Group, Chemical Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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25
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Aprahamian ML, Chea EE, Jones LM, Lindert S. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Anal Chem 2018; 90:7721-7729. [PMID: 29874044 DOI: 10.1021/acs.analchem.8b01624] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years mass spectrometry-based covalent labeling techniques such as hydroxyl radical footprinting (HRF) have emerged as valuable structural biology techniques, yielding information on protein tertiary structure. These data, however, are not sufficient to predict protein structure unambiguously, as they provide information only on the relative solvent exposure of certain residues. Despite some recent advances, no software currently exists that can utilize covalent labeling mass spectrometry data to predict protein tertiary structure. We have developed the first such tool, which incorporates mass spectrometry derived protection factors from HRF labeling as a new centroid score term for the Rosetta scoring function to improve the prediction of protein tertiary structures. We tested our method on a set of four soluble benchmark proteins with known crystal structures and either published HRF experimental results or internally acquired data. Using the HRF labeling data, we rescored large decoy sets of structures predicted with Rosetta for each of the four benchmark proteins. As a result, the model quality improved for all benchmark proteins as compared to when scored with Rosetta alone. For two of the four proteins we were even able to identify atomic resolution models with the addition of HRF data.
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Affiliation(s)
- Melanie L Aprahamian
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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26
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Interpreting solution X-ray scattering data using molecular simulations. Curr Opin Struct Biol 2018; 49:18-26. [DOI: 10.1016/j.sbi.2017.11.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/20/2017] [Accepted: 11/04/2017] [Indexed: 01/23/2023]
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27
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Abstract
Despite the central role of Nuclear Pore Complexes (NPCs) as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm, their large size and dynamic nature have impeded a full structural and functional elucidation. Here, we have determined a subnanometer precision structure for the entire 552-protein yeast NPC by satisfying diverse data including stoichiometry, a cryo-electron tomography map, and chemical cross-links. The structure reveals the NPC’s functional elements in unprecedented detail. The NPC is built of sturdy diagonal columns to which are attached connector cables, imbuing both strength and flexibility, while tying together all other elements of the NPC, including membrane-interacting regions and RNA processing platforms. Inwardly-directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized in distinct functional units. Taken together, this integrative structure allows us to rationalize the architecture, transport mechanism, and evolutionary origins of the NPC.
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28
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Ogorzalek TL, Hura GL, Belsom A, Burnett KH, Kryshtafovych A, Tainer JA, Rappsilber J, Tsutakawa SE, Fidelis K. Small angle X-ray scattering and cross-linking for data assisted protein structure prediction in CASP 12 with prospects for improved accuracy. Proteins 2018; 86 Suppl 1:202-214. [PMID: 29314274 DOI: 10.1002/prot.25452] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/18/2017] [Accepted: 01/01/2018] [Indexed: 12/13/2022]
Abstract
Experimental data offers empowering constraints for structure prediction. These constraints can be used to filter equivalently scored models or more powerfully within optimization functions toward prediction. In CASP12, Small Angle X-ray Scattering (SAXS) and Cross-Linking Mass Spectrometry (CLMS) data, measured on an exemplary set of novel fold targets, were provided to the CASP community of protein structure predictors. As solution-based techniques, SAXS and CLMS can efficiently measure states of the full-length sequence in its native solution conformation and assembly. However, this experimental data did not substantially improve prediction accuracy judged by fits to crystallographic models. One issue, beyond intrinsic limitations of the algorithms, was a disconnect between crystal structures and solution-based measurements. Our analyses show that many targets had substantial percentages of disordered regions (up to 40%) or were multimeric or both. Thus, solution measurements of flexibility and assembly support variations that may confound prediction algorithms trained on crystallographic data and expecting globular fully-folded monomeric proteins. Here, we consider the CLMS and SAXS data collected, the information in these solution measurements, and the challenges in incorporating them into computational prediction. As improvement opportunities were only partly realized in CASP12, we provide guidance on how data from the full-length biological unit and the solution state can better aid prediction of the folded monomer or subunit. We furthermore describe strategic integrations of solution measurements with computational prediction programs with the aim of substantially improving foundational knowledge and the accuracy of computational algorithms for biologically-relevant structure predictions for proteins in solution.
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Affiliation(s)
- Tadeusz L Ogorzalek
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Greg L Hura
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Adam Belsom
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, U.K
| | - Kathryn H Burnett
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Andriy Kryshtafovych
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, CA, 95616, USA
| | - John A Tainer
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, 77030, USA
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, U.K.,Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
| | - Susan E Tsutakawa
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Krzysztof Fidelis
- Protein Structure Prediction Center, Genome and Biomedical Sciences Facilities, University of California, Davis, CA, 95616, USA
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29
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Abstract
Small-angle X-ray scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. SAXS profiles can be utilized in a variety of molecular modeling applications, such as comparing solution and crystal structures, structural characterization of flexible proteins, assembly of multi-protein complexes, and modeling of missing regions in the high-resolution structure. Here, we describe protocols for modeling atomic structures based on SAXS profiles. The first protocol is for comparing solution and crystal structures including modeling of missing regions and determination of the oligomeric state. The second protocol performs multi-state modeling by finding a set of conformations and their weights that fit the SAXS profile starting from a single-input structure. The third protocol is for protein-protein docking based on the SAXS profile of the complex. We describe the underlying software, followed by demonstrating their application on interleukin 33 (IL33) with its primary receptor ST2 and DNA ligase IV-XRCC4 complex.
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Affiliation(s)
- Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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30
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Hybrid Methods for Modeling Protein Structures Using Molecular Dynamics Simulations and Small-Angle X-Ray Scattering Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:237-258. [PMID: 30617833 DOI: 10.1007/978-981-13-2200-6_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Small-angle X-ray scattering (SAXS) is an efficient experimental tool to measure the overall shape of macromolecular structures in solution. However, due to the low resolution of SAXS data, high-resolution data obtained from X-ray crystallography or NMR and computational methods such as molecular dynamics (MD) simulations are complementary to SAXS data for understanding protein functions based on their structures at atomic resolution. Because MD simulations provide a physicochemically proper structural ensemble for flexible proteins in solution and a precise description of solvent effects, the hybrid analysis of SAXS and MD simulations is a promising method to estimate reasonable solution structures and structural ensembles in solution. Here, we review typical and useful in silico methods for modeling three dimensional protein structures, calculating theoretical SAXS profiles, and analyzing ensemble structures consistent with experimental SAXS profiles. We also review two examples of the hybrid analysis, termed MD-SAXS method in which MD simulations are carried out without any knowledge of experimental SAXS data, and the experimental SAXS data are used only to assess the consistency of the solution model from MD simulations with those observed in experiments. One example is an investigation of the intrinsic dynamics of EcoO109I using the computational method to obtain a theoretical profile from the trajectory of an MD simulation. The other example is a structural investigation of the vitamin D receptor ligand-binding domain using snapshots generated by MD simulations and assessment of the snapshots by experimental SAXS data.
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31
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Trewhella J. Small Angle Scattering and Structural Biology: Data Quality and Model Validation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1105:77-100. [PMID: 30617825 DOI: 10.1007/978-981-13-2200-6_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This chapter provides a brief review of the current state-of-the-art in small-angle scattering (SAS) from biomolecules in solution in regard to: (1) sample preparation and instrumentation, (2) data reduction and analysis, and (3) three-dimensional structural modelling and validation. In this context, areas of ongoing research in regard to the interpretation of SAS data will be discussed with a particular focus on structural modelling using computational methods and data from different experimental techniques, including SAS (hybrid methods). Finally, progress made in establishing community accepted publication guidelines and a standard reporting framework that includes SAS data deposition in a public data bank will be described. Importantly, SAS data with associated meta-data can now be held in a format that supports exchange between data archives and seamless interoperability with the world-wide Protein Data Bank (wwPDB). Biomolecular SAS is thus well positioned to contribute to an envisioned federation of data archives in support of hybrid structural biology.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia. .,Department of Chemistry, University of Utah, Salt Lake City, UT, USA.
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32
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Assessment of data-assisted prediction by inclusion of crosslinking/mass-spectrometry and small angle X-ray scattering data in the 12thCritical Assessment of protein Structure Prediction experiment. Proteins 2017; 86 Suppl 1:215-227. [DOI: 10.1002/prot.25442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/16/2017] [Accepted: 12/10/2017] [Indexed: 12/26/2022]
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33
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Lehmann LC, Hewitt G, Aibara S, Leitner A, Marklund E, Maslen SL, Maturi V, Chen Y, van der Spoel D, Skehel JM, Moustakas A, Boulton SJ, Deindl S. Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1. Mol Cell 2017; 68:847-859.e7. [PMID: 29220652 PMCID: PMC5745148 DOI: 10.1016/j.molcel.2017.10.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Revised: 08/16/2017] [Accepted: 10/17/2017] [Indexed: 02/07/2023]
Abstract
Human ALC1 is an oncogene-encoded chromatin-remodeling enzyme required for DNA repair that possesses a poly(ADP-ribose) (PAR)-binding macro domain. Its engagement with PARylated PARP1 activates ALC1 at sites of DNA damage, but the underlying mechanism remains unclear. Here, we establish a dual role for the macro domain in autoinhibition of ALC1 ATPase activity and coupling to nucleosome mobilization. In the absence of DNA damage, an inactive conformation of the ATPase is maintained by juxtaposition of the macro domain against predominantly the C-terminal ATPase lobe through conserved electrostatic interactions. Mutations within this interface displace the macro domain, constitutively activate the ALC1 ATPase independent of PARylated PARP1, and alter the dynamics of ALC1 recruitment at DNA damage sites. Upon DNA damage, binding of PARylated PARP1 by the macro domain induces a conformational change that relieves autoinhibitory interactions with the ATPase motor, which selectively activates ALC1 remodeling upon recruitment to sites of DNA damage.
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Affiliation(s)
- Laura C Lehmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Shintaro Aibara
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17165 Solna, Sweden
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology, 8093 Zürich, Switzerland
| | - Emil Marklund
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Varun Maturi
- Department of Medical Biochemistry and Microbiology, and Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - Yang Chen
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Uppsala University, 75124 Uppsala, Sweden
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Aristidis Moustakas
- Department of Medical Biochemistry and Microbiology, and Ludwig Institute for Cancer Research, Science for Life Laboratory, Uppsala University, 75123 Uppsala, Sweden
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.
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34
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Gong Z, Liu Z, Dong X, Ding YH, Dong MQ, Tang C. Protocol for analyzing protein ensemble structures from chemical cross-links using DynaXL. BIOPHYSICS REPORTS 2017; 3:100-108. [PMID: 29238747 PMCID: PMC5719800 DOI: 10.1007/s41048-017-0044-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/18/2017] [Indexed: 12/16/2022] Open
Abstract
Chemical cross-linking coupled with mass spectroscopy (CXMS) is a powerful technique for investigating protein structures. CXMS has been mostly used to characterize the predominant structure for a protein, whereas cross-links incompatible with a unique structure of a protein or a protein complex are often discarded. We have recently shown that the so-called over-length cross-links actually contain protein dynamics information. We have thus established a method called DynaXL, which allow us to extract the information from the over-length cross-links and to visualize protein ensemble structures. In this protocol, we present the detailed procedure for using DynaXL, which comprises five steps. They are identification of highly confident cross-links, delineation of protein domains/subunits, ensemble rigid-body refinement, and final validation/assessment. The DynaXL method is generally applicable for analyzing the ensemble structures of multi-domain proteins and protein–protein complexes, and is freely available at www.tanglab.org/resources.
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Affiliation(s)
- Zhou Gong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
| | - Zhu Liu
- Department of Pharmacology, Institute of Neuroscience, Key Laboratory of Medical Neurobiology of the Ministry of Health of China, Zhejiang University School of Medicine, Hangzhou, 310057 China
| | - Xu Dong
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
| | - Yue-He Ding
- RNA Therapeutics Institute, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605 USA
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206 China
| | - Chun Tang
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, and National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China.,National Center for Magnetic Resonance at Wuhan, Wuhan Institute of Physics and Mathematics of the Chinese Academy of Sciences, Wuhan, 430071 China
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35
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Cordeiro TN, Chen PC, De Biasio A, Sibille N, Blanco FJ, Hub JS, Crehuet R, Bernadó P. Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly. Nucleic Acids Res 2017; 45:1501-1515. [PMID: 28180305 PMCID: PMC5388412 DOI: 10.1093/nar/gkw1183] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
The intrinsically disordered p15PAF regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15PAF and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling. By using explicit ensemble descriptions for the individual species, built using integrative approaches and molecular dynamics (MD) simulations, we collectively interpreted multiple SAXS profiles as population-weighted thermodynamic mixtures. The analysis demonstrates that the N-terminus of p15PAF penetrates the PCNA ring and emerges on the back face. This observation substantiates the role of p15PAF as a drag regulating PCNA processivity during DNA repair. Our study reveals the power of ensemble-based approaches to decode structural, dynamic, and thermodynamic information from SAXS data. This strategy paves the way for deciphering the structural bases of flexible, transient and multivalent macromolecular assemblies involved in pivotal biological processes.
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Affiliation(s)
- Tiago N Cordeiro
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
| | - Po-Chia Chen
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | | | - Nathalie Sibille
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
| | - Francisco J Blanco
- CIC-bioGUNE, Derio, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | - Ramon Crehuet
- Institute of Advanced Chemistry of Catalonia, CSIC, Barcelona 08034, Spain
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM-U1054, CNRS UMR-5048, Université de Montpellier, Montpellier, France
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36
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Hopkins JB, Gillilan RE, Skou S. BioXTAS RAW: improvements to a free open-source program for small-angle X-ray scattering data reduction and analysis. J Appl Crystallogr 2017; 50:1545-1553. [PMID: 29021737 PMCID: PMC5627684 DOI: 10.1107/s1600576717011438] [Citation(s) in RCA: 395] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 08/02/2017] [Indexed: 01/19/2023] Open
Abstract
BioXTAS RAW is a graphical-user-interface-based free open-source Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data. The software is designed for biological SAXS data and enables creation and plotting of one-dimensional scattering profiles from two-dimensional detector images, standard data operations such as averaging and subtraction and analysis of radius of gyration and molecular weight, and advanced analysis such as calculation of inverse Fourier transforms and envelopes. It also allows easy processing of inline size-exclusion chromatography coupled SAXS data and data deconvolution using the evolving factor analysis method. It provides an alternative to closed-source programs such as Primus and ScÅtter for primary data analysis. Because it can calibrate, mask and integrate images it also provides an alternative to synchrotron beamline pipelines that scientists can install on their own computers and use both at home and at the beamline.
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37
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Leelananda SP, Lindert S. Iterative Molecular Dynamics-Rosetta Membrane Protein Structure Refinement Guided by Cryo-EM Densities. J Chem Theory Comput 2017; 13:5131-5145. [PMID: 28949136 DOI: 10.1021/acs.jctc.7b00464] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Knowing atomistic details of proteins is essential not only for the understanding of protein function but also for the development of drugs. Experimental methods such as X-ray crystallography, NMR, and cryo-electron microscopy (cryo-EM) are the preferred forms of protein structure determination and have achieved great success over the most recent decades. Computational methods may be an alternative when experimental techniques fail. However, computational methods are severely limited when it comes to predicting larger macromolecule structures with little sequence similarity to known structures. The incorporation of experimental restraints in computational methods is becoming increasingly important to more reliably predict protein structure. One such experimental input used in structure prediction and refinement is cryo-EM densities. Recent advances in cryo-EM have arguably revolutionized the field of structural biology. Our previously developed cryo-EM-guided Rosetta-MD protocol has shown great promise in the refinement of soluble protein structures. In this study, we extended cryo-EM density-guided iterative Rosetta-MD to membrane proteins. We also improved the methodology in general by picking models based on a combination of their score and fit-to-density during the Rosetta model selection. By doing so, we have been able to pick models superior to those with the previous selection based on Rosetta score only and we have been able to further improve our previously refined models of soluble proteins. The method was tested with five membrane spanning protein structures. By applying density-guided Rosetta-MD iteratively we were able to refine the predicted structures of these membrane proteins to atomic resolutions. We also showed that the resolution of the density maps determines the improvement and quality of the refined models. By incorporating high-resolution density maps (∼4 Å), we were able to more significantly improve the quality of the models than when medium-resolution maps (6.9 Å) were used. Beginning from an average starting structure root mean square deviation (RMSD) to native of 4.66 Å, our protocol was able to refine the structures to bring the average refined structure RMSD to 1.66 Å when 4 Å density maps were used. The protocol also successfully refined the HIV-1 CTD guided by an experimental 5 Å density map.
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Affiliation(s)
- Sumudu P Leelananda
- Department of Chemistry and Biochemistry, Ohio State University , Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University , Columbus, Ohio 43210, United States
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38
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Sønderby P, Rinnan Å, Madsen JJ, Harris P, Bukrinski JT, Peters GHJ. Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape. J Chem Inf Model 2017; 57:2463-2475. [DOI: 10.1021/acs.jcim.6b00789] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Pernille Sønderby
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Åsmund Rinnan
- Department
of Food Science, Faculty of Science, University of Copenhagen, DK-1958 Frederiksberg C, Denmark
| | - Jesper J. Madsen
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
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39
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Trewhella J, Duff AP, Durand D, Gabel F, Guss JM, Hendrickson WA, Hura GL, Jacques DA, Kirby NM, Kwan AH, Pérez J, Pollack L, Ryan TM, Sali A, Schneidman-Duhovny D, Schwede T, Svergun DI, Sugiyama M, Tainer JA, Vachette P, Westbrook J, Whitten AE. 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallogr D Struct Biol 2017; 73:710-728. [PMID: 28876235 PMCID: PMC5586245 DOI: 10.1107/s2059798317011597] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/07/2017] [Indexed: 12/02/2022] Open
Abstract
In 2012, preliminary guidelines were published addressing sample quality, data acquisition and reduction, presentation of scattering data and validation, and modelling for biomolecular small-angle scattering (SAS) experiments. Biomolecular SAS has since continued to grow and authors have increasingly adopted the preliminary guidelines. In parallel, integrative/hybrid determination of biomolecular structures is a rapidly growing field that is expanding the scope of structural biology. For SAS to contribute maximally to this field, it is essential to ensure open access to the information required for evaluation of the quality of SAS samples and data, as well as the validity of SAS-based structural models. To this end, the preliminary guidelines for data presentation in a publication are reviewed and updated, and the deposition of data and associated models in a public archive is recommended. These guidelines and recommendations have been prepared in consultation with the members of the International Union of Crystallography (IUCr) Small-Angle Scattering and Journals Commissions, the Worldwide Protein Data Bank (wwPDB) Small-Angle Scattering Validation Task Force and additional experts in the field.
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Affiliation(s)
- Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Anthony P. Duff
- ANSTO, New Illawarra Road, Lucas Heights, NSW 2234, Australia
| | - Dominique Durand
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - Frank Gabel
- Université Grenoble Alpes, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Structurale (IBS), and Institut Laue–Langevin, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - J. Mitchell Guss
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Wayne A. Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Greg L. Hura
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David A. Jacques
- University of Technology Sydney, ithree Institute, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Nigel M. Kirby
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Ann H. Kwan
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Javier Pérez
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint-Aubin BP48, 91192 Gif-sur-Yvette CEDEX, France
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853-2501, USA
| | - Timothy M. Ryan
- Australian Synchrotron, 800 Blackburn Road, Clayton, VIC 3168, Australia
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Torsten Schwede
- Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL) Hamburg, c/o DESY, Nokestrasse 85, 22607 Hamburg, Germany
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan
| | - John A. Tainer
- Basic Science Research Division, Molecular and Cellular Oncology, MD Anderson Cancer Center, University of Texas, Houston, Texas, USA
| | - Patrice Vachette
- Institut de Biologie Intégrative de la Cellule, UMR 9198, Bâtiment 430, Université Paris-Sud, 91405 Orsay CEDEX, France
| | - John Westbrook
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, NJ 07102, USA
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40
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Wang H, Liu H. Determining Complex Structures using Docking Method with Single Particle Scattering Data. Front Mol Biosci 2017; 4:23. [PMID: 28487857 PMCID: PMC5403940 DOI: 10.3389/fmolb.2017.00023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/29/2017] [Indexed: 11/23/2022] Open
Abstract
Protein complexes are critical for many molecular functions. Due to intrinsic flexibility and dynamics of complexes, their structures are more difficult to determine using conventional experimental methods, in contrast to individual subunits. One of the major challenges is the crystallization of protein complexes. Using X-ray free electron lasers (XFELs), it is possible to collect scattering signals from non-crystalline protein complexes, but data interpretation is more difficult because of unknown orientations. Here, we propose a hybrid approach to determine protein complex structures by combining XFEL single particle scattering data with computational docking methods. Using simulations data, we demonstrate that a small set of single particle scattering data collected at random orientations can be used to distinguish the native complex structure from the decoys generated using docking algorithms. The results also indicate that a small set of single particle scattering data is superior to spherically averaged intensity profile in distinguishing complex structures. Given the fact that XFEL experimental data are difficult to acquire and at low abundance, this hybrid approach should find wide applications in data interpretations.
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Affiliation(s)
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research CenterBeijing, China
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41
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Cheng P, Peng J, Zhang Z. SAXS-Oriented Ensemble Refinement of Flexible Biomolecules. Biophys J 2017; 112:1295-1301. [PMID: 28402873 DOI: 10.1016/j.bpj.2017.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/21/2017] [Accepted: 02/16/2017] [Indexed: 12/29/2022] Open
Abstract
The conformational flexibility of a biomolecule may play a crucial role in its biological function. Small-angle x-ray scattering (SAXS) is a very popular technique for characterizing biomolecule flexibility. It can be used to determine a possible structural ensemble of the biomolecule in solution with the aid of a computer simulation. In this article, we present a tool written in Python, which iteratively runs multiple independent enhanced sampling simulations such as amplified collective motions and accelerated molecular dynamics, and an ensemble optimization method to drive the biomolecule toward an ensemble that fits the SAXS data well. The tool has been validated with a protein and an RNA system, i.e., the tandem WW domains of formin-binding protein 21 and the aptamer domain of SAM-1 riboswitch, respectively. These Python scripts are user-friendly and can be easily modified if a different simulation engine is preferred.
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Affiliation(s)
- Peng Cheng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Junhui Peng
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Zhiyong Zhang
- Hefei National Laboratory for Physical Science at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.
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42
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Chen S, E J, Luo SN. SLADS: a parallel code for direct simulations of scattering of large anisotropic dense nanoparticle systems. J Appl Crystallogr 2017. [DOI: 10.1107/s1600576717004162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SLADS(http://www.pims.ac.cn/Resources.html), a parallel code for direct simulations of X-ray scattering of large anisotropic dense nanoparticle systems of arbitrary species and atomic configurations, is presented. Particles can be of arbitrary shapes and dispersities, and interactions between particles are considered. Parallelization is achieved in real space for the sake of memory limitation. The system sizes attempted are up to one billion atoms, and particle concentrations in dense systems up to 0.36. Anisotropy is explored in terms of superlattices. One- and two-dimensional small-angle scattering or diffraction patterns are obtained.SLADSis validated self-consistently or against cases with analytical solutions.
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43
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Sysoeva TA. Assessing heterogeneity in oligomeric AAA+ machines. Cell Mol Life Sci 2017; 74:1001-1018. [PMID: 27669691 PMCID: PMC11107579 DOI: 10.1007/s00018-016-2374-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/13/2016] [Accepted: 09/19/2016] [Indexed: 10/20/2022]
Abstract
ATPases Associated with various cellular Activities (AAA+ ATPases) are molecular motors that use the energy of ATP binding and hydrolysis to remodel their target macromolecules. The majority of these ATPases form ring-shaped hexamers in which the active sites are located at the interfaces between neighboring subunits. Structural changes initiate in an active site and propagate to distant motor parts that interface and reshape the target macromolecules, thereby performing mechanical work. During the functioning cycle, the AAA+ motor transits through multiple distinct states. Ring architecture and placement of the catalytic sites at the intersubunit interfaces allow for a unique level of coordination among subunits of the motor. This in turn results in conformational differences among subunits and overall asymmetry of the motor ring as it functions. To date, a large amount of structural information has been gathered for different AAA+ motors, but even for the most characterized of them only a few structural states are known and the full mechanistic cycle cannot be yet reconstructed. Therefore, the first part of this work will provide a broad overview of what arrangements of AAA+ subunits have been structurally observed focusing on diversity of ATPase oligomeric ensembles and heterogeneity within the ensembles. The second part of this review will concentrate on methods that assess structural and functional heterogeneity among subunits of AAA+ motors, thus bringing us closer to understanding the mechanism of these fascinating molecular motors.
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Affiliation(s)
- Tatyana A Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
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44
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Antonov LD, Olsson S, Boomsma W, Hamelryck T. Bayesian inference of protein ensembles from SAXS data. Phys Chem Chem Phys 2017; 18:5832-8. [PMID: 26548662 DOI: 10.1039/c5cp04886a] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The inherent flexibility of intrinsically disordered proteins (IDPs) and multi-domain proteins with intrinsically disordered regions (IDRs) presents challenges to structural analysis. These macromolecules need to be represented by an ensemble of conformations, rather than a single structure. Small-angle X-ray scattering (SAXS) experiments capture ensemble-averaged data for the set of conformations. We present a Bayesian approach to ensemble inference from SAXS data, called Bayesian ensemble SAXS (BE-SAXS). We address two issues with existing methods: the use of a finite ensemble of structures to represent the underlying distribution, and the selection of that ensemble as a subset of an initial pool of structures. This is achieved through the formulation of a Bayesian posterior of the conformational space. BE-SAXS modifies a structural prior distribution in accordance with the experimental data. It uses multi-step expectation maximization, with alternating rounds of Markov-chain Monte Carlo simulation and empirical Bayes optimization. We demonstrate the method by employing it to obtain a conformational ensemble of the antitoxin PaaA2 and comparing the results to a published ensemble.
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Affiliation(s)
- L D Antonov
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
| | - S Olsson
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, Vladimir-Prelog-Weg 2, CH-8093 Zürich, Switzerland and Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, CH-6500 Bellinzona, Switzerland
| | - W Boomsma
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark
| | - T Hamelryck
- Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200 Copenhagen N, Denmark.
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45
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Designing and Performing Biological Solution Small-Angle Neutron Scattering Contrast Variation Experiments on Multi-component Assemblies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:65-85. [DOI: 10.1007/978-981-10-6038-0_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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46
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Small-angle scattering and 3D structure interpretation. Curr Opin Struct Biol 2016; 40:1-7. [DOI: 10.1016/j.sbi.2016.05.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 12/29/2022]
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Bastos VA, Gomes-Neto F, Perales J, Neves-Ferreira AGC, Valente RH. Natural Inhibitors of Snake Venom Metalloendopeptidases: History and Current Challenges. Toxins (Basel) 2016; 8:toxins8090250. [PMID: 27571103 PMCID: PMC5037476 DOI: 10.3390/toxins8090250] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/11/2016] [Accepted: 08/15/2016] [Indexed: 01/13/2023] Open
Abstract
The research on natural snake venom metalloendopeptidase inhibitors (SVMPIs) began in the 18th century with the pioneering work of Fontana on the resistance that vipers exhibited to their own venom. During the past 40 years, SVMPIs have been isolated mainly from the sera of resistant animals, and characterized to different extents. They are acidic oligomeric glycoproteins that remain biologically active over a wide range of pH and temperature values. Based on primary structure determination, mammalian plasmatic SVMPIs are classified as members of the immunoglobulin (Ig) supergene protein family, while the one isolated from muscle belongs to the ficolin/opsonin P35 family. On the other hand, SVMPIs from snake plasma have been placed in the cystatin superfamily. These natural antitoxins constitute the first line of defense against snake venoms, inhibiting the catalytic activities of snake venom metalloendopeptidases through the establishment of high-affinity, non-covalent interactions. This review presents a historical account of the field of natural resistance, summarizing its main discoveries and current challenges, which are mostly related to the limitations that preclude three-dimensional structural determinations of these inhibitors using “gold-standard” methods; perspectives on how to circumvent such limitations are presented. Potential applications of these SVMPIs in medicine are also highlighted.
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Affiliation(s)
- Viviane A Bastos
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Francisco Gomes-Neto
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Jonas Perales
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Ana Gisele C Neves-Ferreira
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
| | - Richard H Valente
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro 21040-900, Brazil.
- National Institute of Science and Technology on Toxins (INCTTOX), CNPq, Brasilia 71605-001, Brazil.
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Tong D, Yang S, Lu L. Accurate optimization of amino acid form factors for computing small-angle X-ray scattering intensity of atomistic protein structures. J Appl Crystallogr 2016; 49:1148-1161. [PMID: 28074088 PMCID: PMC5223287 DOI: 10.1107/s1600576716007962] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/15/2016] [Indexed: 02/04/2023] Open
Abstract
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures. This EDM method is compared with and tested against other CG SAXS computing methods, and the resulting CG SAXS profiles from EDM agree better with all-atom theoretical SAXS data. By including the protein hydration shell represented by explicit CG water molecules and the correction of protein excluded volume, the developed CG form factors also reproduce the selected experimental SAXS profiles with very small deviations. Taken together, these EDM-derived CG form factors present an accurate and efficient computational approach for SAXS computing, especially when higher molecular details (represented by the q range of the SAXS data) become necessary for effective structure modelling.
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Affiliation(s)
- Dudu Tong
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, Case Western Reserve University, 10900 Euclid Avenue, BRB 929, Cleveland, OH 44106-4988, USA
| | - Lanyuan Lu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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49
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Emanuelle S, Brewer MK, Meekins DA, Gentry MS. Unique carbohydrate binding platforms employed by the glucan phosphatases. Cell Mol Life Sci 2016; 73:2765-2778. [PMID: 27147465 PMCID: PMC4920694 DOI: 10.1007/s00018-016-2249-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/19/2022]
Abstract
Glucan phosphatases are a family of enzymes that are functionally conserved at the enzymatic level in animals and plants. These enzymes bind and dephosphorylate glycogen in animals and starch in plants. While the enzymatic function is conserved, the glucan phosphatases employ distinct mechanisms to bind and dephosphorylate glycogen or starch. The founding member of the family is a bimodular human protein called laforin that is comprised of a carbohydrate binding module 20 (CBM20) followed by a dual specificity phosphatase domain. Plants contain two glucan phosphatases: Starch EXcess4 (SEX4) and Like Sex Four2 (LSF2). SEX4 contains a chloroplast targeting peptide, dual specificity phosphatase (DSP) domain, a CBM45, and a carboxy-terminal motif. LSF2 is comprised of simply a chloroplast targeting peptide, DSP domain, and carboxy-terminal motif. SEX4 employs an integrated DSP-CBM glucan-binding platform to engage and dephosphorylate starch. LSF2 lacks a CBM and instead utilizes two surface binding sites to bind and dephosphorylate starch. Laforin is a dimeric protein in solution and it utilizes a tetramodular architecture and cooperativity to bind and dephosphorylate glycogen. This chapter describes the biological role of glucan phosphatases in glycogen and starch metabolism and compares and contrasts their ability to bind and dephosphorylate glucans.
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Affiliation(s)
- Shane Emanuelle
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - M. Kathryn Brewer
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
| | - David A. Meekins
- Division of Biology, Kansas State University, Manhattan, KS 66506 USA
| | - Matthew S. Gentry
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536 USA
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50
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Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res 2016; 44:W424-9. [PMID: 27151198 PMCID: PMC4987932 DOI: 10.1093/nar/gkw389] [Citation(s) in RCA: 349] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022] Open
Abstract
Small Angle X-ray Scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. Here, we describe three web servers for modeling atomic structures based on SAXS profiles. FoXS (Fast X-Ray Scattering) rapidly computes a SAXS profile of a given atomistic model and fits it to an experimental profile. FoXSDock docks two rigid protein structures based on a SAXS profile of their complex. MultiFoXS computes a population-weighted ensemble starting from a single input structure by fitting to a SAXS profile of the protein in solution. We describe the interfaces and capabilities of the servers (salilab.org/foxs), followed by demonstrating their application on Interleukin-33 (IL-33) and its primary receptor ST2.
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Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA 94143, USA
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA 94143, USA
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