1
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Shor B, Schneidman-Duhovny D. Predicting structures of large protein assemblies using combinatorial assembly algorithm and AlphaFold2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541003. [PMID: 37293053 PMCID: PMC10245790 DOI: 10.1101/2023.05.16.541003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Deep learning models, such as AlphaFold2 and RosettaFold, enable high-accuracy protein structure prediction. However, large protein complexes are still challenging to predict due to their size and the complexity of interactions between multiple subunits. Here we present CombFold, a combinatorial and hierarchical assembly algorithm for predicting structures of large protein complexes utilizing pairwise interactions between subunits predicted by AlphaFold2. CombFold accurately predicted (TM-score > 0.7) 72% of the complexes among the Top-10 predictions in two datasets of 60 large, asymmetric assemblies. Moreover, the structural coverage of predicted complexes was 20% higher compared to corresponding PDB entries. We applied the method on complexes from Complex Portal with known stoichiometry but without known structure and obtained high-confidence predictions. CombFold supports the integration of distance restraints based on crosslinking mass spectrometry and fast enumeration of possible complex stoichiometries. CombFold's high accuracy makes it a promising tool for expanding structural coverage beyond monomeric proteins.
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Affiliation(s)
- Ben Shor
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
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2
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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3
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Cohen T, Halfon M, Carter L, Sharkey B, Jain T, Sivasubramanian A, Schneidman-Duhovny D. Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models. Methods Enzymol 2022; 678:237-262. [PMID: 36641210 DOI: 10.1016/bs.mie.2022.11.003] [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: 12/13/2022]
Abstract
Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray crystallography or cryo-electron microscopy provide atomic resolution characterization of the epitope, but the data collection process is typically long and the success rate is low. On the other hand, computational methods for modeling antibody-antigen structures from the individual components frequently suffer from a high false positive rate, rarely resulting in a unique solution. Recent deep learning models for structure prediction are also successful in predicting protein-protein complexes. However, they do not perform well for antibody-antigen complexes. Small Angle X-ray Scattering (SAXS) is a reliable technique for rapid structural characterization of protein samples in solution albeit at low resolution. Here, we present an integrative approach for modeling antigen-antibody complexes using the antibody sequence, antigen structure, and experimentally determined SAXS profiles of the antibody, antigen, and the complex. The method models antibody structures using a novel deep-learning approach, NanoNet. The structures of the antibodies and antigens are represented using multiple 3D conformations to account for compositional and conformational heterogeneity of the protein samples that are used to collect the SAXS data. The complexes are predicted by integrating the SAXS profiles with scoring functions for protein-protein interfaces that are based on statistical potentials and antibody-specific deep-learning models. We validated the method via application to four Fab:EGFR and one Fab:PCSK9 antibody:antigen complexes with experimentally available SAXS datasets. The integrative approach returns accurate predictions (interface RMSD<4Å) in the top five predictions for four out of five complexes (respective interface RMSD values of 1.95, 2.18, 2.66 and 3.87Å), providing support for the utility of such a computational pipeline for epitope characterization during therapeutic antibody discovery.
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Affiliation(s)
- Tomer Cohen
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matan Halfon
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lester Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - Beth Sharkey
- High-Throughput Expression, Adimab LLC, Lebanon, NH, United States
| | - Tushar Jain
- Computational Biology, Adimab LLC, Palo Alto, CA, United States
| | | | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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4
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Sun Y, Li X, Chen R, Liu F, Wei S. Recent advances in structural characterization of biomacromolecules in foods via small-angle X-ray scattering. Front Nutr 2022; 9:1039762. [PMID: 36466419 PMCID: PMC9714470 DOI: 10.3389/fnut.2022.1039762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/03/2022] [Indexed: 08/04/2023] Open
Abstract
Small-angle X-ray scattering (SAXS) is a method for examining the solution structure, oligomeric state, conformational changes, and flexibility of biomacromolecules at a scale ranging from a few Angstroms to hundreds of nanometers. Wide time scales ranging from real time (milliseconds) to minutes can be also covered by SAXS. With many advantages, SAXS has been extensively used, it is widely used in the structural characterization of biomacromolecules in food science and technology. However, the application of SAXS in charactering the structure of food biomacromolecules has not been reviewed so far. In the current review, the principle, theoretical calculations and modeling programs are summarized, technical advances in the experimental setups and corresponding applications of in situ capabilities: combination of chromatography, time-resolved, temperature, pressure, flow-through are elaborated. Recent applications of SAXS for monitoring structural properties of biomacromolecules in food including protein, carbohydrate and lipid are also highlighted, and limitations and prospects for developing SAXS based on facility upgraded and artificial intelligence to study the structural properties of biomacromolecules are finally discussed. Future research should focus on extending machine time, simplifying SAXS data treatment, optimizing modeling methods in order to achieve an integrated structural biology based on SAXS as a practical tool for investigating the structure-function relationship of biomacromolecules in food industry.
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Affiliation(s)
- Yang Sun
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Xiujuan Li
- Pharmaceutical Department, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
| | - Ruixin Chen
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Fei Liu
- College of Vocational and Technical Education, Yunnan Normal University, Kunming, China
| | - Song Wei
- Tumor Precise Intervention and Translational Medicine Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, China
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5
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Czaplewski C, Gong Z, Lubecka EA, Xue K, Tang C, Liwo A. Recent Developments in Data-Assisted Modeling of Flexible Proteins. Front Mol Biosci 2022; 8:765562. [PMID: 35004845 PMCID: PMC8740120 DOI: 10.3389/fmolb.2021.765562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this article, we review the recent developments in the concept and methods for the determination of the dynamic structures of flexible peptides and proteins. In particular, we describe ways to extract information from nuclear magnetic resonance small-angle X-ray scattering (SAXS), and chemical cross-linking coupled with mass spectroscopy (XL-MS) measurements. All these techniques can be used to obtain ensemble-averaged restraints or to re-weight the simulated conformational ensembles.
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Affiliation(s)
| | - Zhou Gong
- Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China
| | - Emilia A Lubecka
- Faculty of Electronics, Telecommunications and Informatics, Gdańsk University of Technology, Gdańsk, Poland
| | - Kai Xue
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chun Tang
- PKU-Tsinghua Center for Life Sciences, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
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6
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Garrigues RJ, Powell-Pierce AD, Hammel M, Skare JT, Garcia BL. A Structural Basis for Inhibition of the Complement Initiator Protease C1r by Lyme Disease Spirochetes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2856-2867. [PMID: 34759015 PMCID: PMC8612984 DOI: 10.4049/jimmunol.2100815] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/23/2021] [Indexed: 12/26/2022]
Abstract
Complement evasion is a hallmark of extracellular microbial pathogens such as Borrelia burgdorferi, the causative agent of Lyme disease. Lyme disease spirochetes express nearly a dozen outer surface lipoproteins that bind complement components and interfere with their native activities. Among these, BBK32 is unique in its selective inhibition of the classical pathway. BBK32 blocks activation of this pathway by selectively binding and inhibiting the C1r serine protease of the first component of complement, C1. To understand the structural basis for BBK32-mediated C1r inhibition, we performed crystallography and size-exclusion chromatography-coupled small angle X-ray scattering experiments, which revealed a molecular model of BBK32-C in complex with activated human C1r. Structure-guided site-directed mutagenesis was combined with surface plasmon resonance binding experiments and assays of complement function to validate the predicted molecular interface. Analysis of the structures shows that BBK32 inhibits activated forms of C1r by occluding substrate interaction subsites (i.e., S1 and S1') and reveals a surprising role for C1r B loop-interacting residues for full inhibitory activity of BBK32. The studies reported in this article provide for the first time (to our knowledge) a structural basis for classical pathway-specific inhibition by a human pathogen.
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Affiliation(s)
- Ryan J Garrigues
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC
| | - Alexandra D Powell-Pierce
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan/College Station, TX; and
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Jon T Skare
- Department of Microbial Pathogenesis and Immunology, College of Medicine, Texas A&M University, Bryan/College Station, TX; and
| | - Brandon L Garcia
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, NC;
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7
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Blumenthal DK, Cheng X, Fajer M, Ho KY, Rohrer J, Gerlits O, Taylor P, Juneja P, Kovalevsky A, Radić Z. Covalent inhibition of hAChE by organophosphates causes homodimer dissociation through long-range allosteric effects. J Biol Chem 2021; 297:101007. [PMID: 34324828 PMCID: PMC8384907 DOI: 10.1016/j.jbc.2021.101007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 11/26/2022] Open
Abstract
Acetylcholinesterase (EC 3.1.1.7), a key acetylcholine-hydrolyzing enzyme in cholinergic neurotransmission, is present in a variety of states in situ, including monomers, C-terminally disulfide-linked homodimers, homotetramers, and up to three tetramers covalently attached to structural subunits. Could oligomerization that ensures high local concentrations of catalytic sites necessary for efficient neurotransmission be affected by environmental factors? Using small-angle X-ray scattering (SAXS) and cryo-EM, we demonstrate that homodimerization of recombinant monomeric human acetylcholinesterase (hAChE) in solution occurs through a C-terminal four-helix bundle at micromolar concentrations. We show that diethylphosphorylation of the active serine in the catalytic gorge or isopropylmethylphosphonylation by the RP enantiomer of sarin promotes a 10-fold increase in homodimer dissociation. We also demonstrate the dissociation of organophosphate (OP)-conjugated dimers is reversed by structurally diverse oximes 2PAM, HI6, or RS194B, as demonstrated by SAXS of diethylphosphoryl-hAChE. However, binding of oximes to the native ligand-free hAChE, binding of high-affinity reversible ligands, or formation of an SP-sarin-hAChE conjugate had no effect on homodimerization. Dissociation monitored by time-resolved SAXS occurs in milliseconds, consistent with rates of hAChE covalent inhibition. OP-induced dissociation was not observed in the SAXS profiles of the double-mutant Y337A/F338A, where the active center gorge volume is larger than in wildtype hAChE. These observations suggest a key role of the tightly packed acyl pocket in allosterically triggered OP-induced dimer dissociation, with the potential for local reduction of acetylcholine-hydrolytic power in situ. Computational models predict allosteric correlated motions extending from the acyl pocket toward the four-helix bundle dimerization interface 25 Å away.
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Affiliation(s)
- Donald K Blumenthal
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, USA
| | - Xiaolin Cheng
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Mikolai Fajer
- Division of Medicinal Chemistry & Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Kwok-Yiu Ho
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA
| | - Jacqueline Rohrer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, Tennessee, USA
| | - Palmer Taylor
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA
| | - Puneet Juneja
- Cryo-EM Facility, Iowa State University, Ames, Iowa, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego, La Jolla, California, USA.
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8
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Transient and stabilized complexes of Nsp7, Nsp8, and Nsp12 in SARS-CoV-2 replication. Biophys J 2021; 120:3152-3165. [PMID: 34197805 PMCID: PMC8238635 DOI: 10.1016/j.bpj.2021.06.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/27/2021] [Accepted: 06/04/2021] [Indexed: 01/18/2023] Open
Abstract
The replication transcription complex (RTC) from the virus SARS-CoV-2 is responsible for recognizing and processing RNA for two principal purposes. The RTC copies viral RNA for propagation into new virus and for ribosomal transcription of viral proteins. To accomplish these activities, the RTC mechanism must also conform to a large number of imperatives, including RNA over DNA base recognition, basepairing, distinguishing viral and host RNA, production of mRNA that conforms to host ribosome conventions, interfacing with error checking machinery, and evading host immune responses. In addition, the RTC will discontinuously transcribe specific sections of viral RNA to amplify certain proteins over others. Central to SARS-CoV-2 viability, the RTC is therefore dynamic and sophisticated. We have conducted a systematic structural investigation of three components that make up the RTC: Nsp7, Nsp8, and Nsp12 (also known as RNA-dependent RNA polymerase). We have solved high-resolution crystal structures of the Nsp7/8 complex, providing insight into the interaction between the proteins. We have used small-angle x-ray and neutron solution scattering (SAXS and SANS) on each component individually as pairs and higher-order complexes and with and without RNA. Using size exclusion chromatography and multiangle light scattering-coupled SAXS, we defined which combination of components forms transient or stable complexes. We used contrast-matching to mask specific complex-forming components to test whether components change conformation upon complexation. Altogether, we find that individual Nsp7, Nsp8, and Nsp12 structures vary based on whether other proteins in their complex are present. Combining our crystal structure, atomic coordinates reported elsewhere, SAXS, SANS, and other biophysical techniques, we provide greater insight into the RTC assembly, mechanism, and potential avenues for disruption of the complex and its functions.
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9
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van Noort CW, Honorato RV, Bonvin AMJJ. Information-driven modeling of biomolecular complexes. Curr Opin Struct Biol 2021; 70:70-77. [PMID: 34139639 DOI: 10.1016/j.sbi.2021.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 11/15/2022]
Abstract
Proteins play crucial roles in every cellular process by interacting with each other, nucleic acids, metabolites, and other molecules. The resulting assemblies can be very large and intricate and pose challenges to experimental methods. In the current era of integrative modeling, it is often only by a combination of various experimental techniques and computations that three-dimensional models of those molecular machines can be obtained. Among the various computational approaches available, molecular docking is often the method of choice when it comes to predicting three-dimensional structures of complexes. Docking can generate particularly accurate models when taking into account the available information on the complex of interest. We review here the use of experimental and bioinformatics data in protein-protein docking, describing recent software developments and highlighting applications for the modeling of antibody-antigen complexes and membrane protein complexes, and the use of evolutionary and shape information.
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Affiliation(s)
- Charlotte W van Noort
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584CH, Netherlands
| | - Rodrigo V Honorato
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584CH, Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science, Department of Chemistry, Utrecht University, Padualaan 8, Utrecht, 3584CH, Netherlands.
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10
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Sagar A, Herranz-Trillo F, Langkilde AE, Vestergaard B, Bernadó P. Structure and thermodynamics of transient protein-protein complexes by chemometric decomposition of SAXS datasets. Structure 2021; 29:1074-1090.e4. [PMID: 33862013 DOI: 10.1016/j.str.2021.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
Transient biomolecular interactions play crucial roles in many cellular signaling and regulation processes. However, deciphering the structure of these assemblies is challenging owing to the difficulties in isolating complexes from the individual partners. The additive nature of small-angle X-ray scattering (SAXS) data allows for probing the species present in these mixtures, but decomposition into structural and thermodynamic information is difficult. We present a chemometric approach enabling the decomposition of titration SAXS data into species-specific information. Using extensive synthetic SAXS data, we demonstrate that robust decomposition can be achieved for titrations with a maximum fraction of complex of 0.5 that can be extended to 0.3 when two orthogonal titrations are simultaneously analyzed. The effect of the structural features, titration points, relative concentrations, and noise are thoroughly analyzed. The validation of the strategy with experimental data highlights the power of the approach to provide unique insights into this family of biomolecular assemblies.
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Affiliation(s)
- Amin Sagar
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
| | - Fátima Herranz-Trillo
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Annette Eva Langkilde
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bente Vestergaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Pau Bernadó
- Centre de Biochimie Structurale (CBS), INSERM, CNRS and Université de Montpellier, 29, rue de Navacelles, 34090 Montpellier, France.
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11
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Abstract
Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.
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12
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Aderinwale T, Christoffer CW, Sarkar D, Alnabati E, Kihara D. Computational structure modeling for diverse categories of macromolecular interactions. Curr Opin Struct Biol 2020; 64:1-8. [PMID: 32599506 PMCID: PMC7665979 DOI: 10.1016/j.sbi.2020.05.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/06/2020] [Accepted: 05/21/2020] [Indexed: 01/23/2023]
Abstract
Computational protein-protein docking is one of the most intensively studied topics in structural bioinformatics. The field has made substantial progress through over three decades of development. The development began with methods for rigid-body docking of two proteins, which have now been extended in different directions to cover the various macromolecular interactions observed in a cell. Here, we overview the recent developments of the variations of docking methods, including multiple protein docking, peptide-protein docking, and disordered protein docking methods.
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Affiliation(s)
- Tunde Aderinwale
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Eman Alnabati
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA.
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13
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Liao CC, Shankar S, Pi WC, Chang CC, Ahmed GR, Chen WY, Hsia KC. Karyopherin Kap114p-mediated trans-repression controls ribosomal gene expression under saline stress. EMBO Rep 2020; 21:e48324. [PMID: 32484313 DOI: 10.15252/embr.201948324] [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: 04/18/2019] [Revised: 04/16/2020] [Accepted: 04/30/2020] [Indexed: 01/01/2023] Open
Abstract
Nuclear accessibility of transcription factors controls gene expression, co-regulated by Ran-dependent nuclear localization and a competitive regulatory network. Here, we reveal that nuclear import factor-facilitated transcriptional repression attenuates ribosome biogenesis under chronic salt stress. Kap114p, one of the karyopherin-βs (Kap-βs) that mediates nuclear import of yeast TATA-binding protein (yTBP), exhibits a yTBP-binding affinity four orders of magnitude greater than its counterparts and suppresses binding of yTBP with DNA. Our crystal structure of Kap114p reveals an extensively negatively charged concave surface, accounting for high-affinity basic-protein binding. KAP114 knockout in yeast leads to a high-salt growth defect, with transcriptomic analyses revealing that Kap114p modulates expression of genes associated with ribosomal biogenesis by suppressing yTBP binding to target promoters, a trans-repression mechanism we attribute to reduced nuclear Ran levels under salinity stress. Our findings reveal that Ran integrates the nuclear transport pathway and transcription regulatory network, allowing yeast to respond to environmental stresses.
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Affiliation(s)
- Chung-Chi Liao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Sahana Shankar
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Chih-Chia Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | | | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Kuo-Chiang Hsia
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.,Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang-Ming University, Taipei, Taiwan
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14
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Rosell M, Fernández-Recio J. Docking approaches for modeling multi-molecular assemblies. Curr Opin Struct Biol 2020; 64:59-65. [PMID: 32615514 PMCID: PMC7324114 DOI: 10.1016/j.sbi.2020.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/13/2020] [Accepted: 05/21/2020] [Indexed: 12/12/2022]
Abstract
Computational docking approaches aim to overcome the limited availability of experimental structural data on protein-protein interactions, which are key in biology. The field is rapidly moving from the traditional docking methodologies for modeling of binary complexes to more integrative approaches using template-based, data-driven modeling of multi-molecular assemblies. We will review here the predictive capabilities of current docking methods in blind conditions, based on the results from the most recent community-wide blind experiments. Integration of template-based and ab initio docking approaches is emerging as the optimal strategy for modeling protein complexes and multimolecular assemblies. We will also review the new methodological advances on ab initio docking and integrative modeling.
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Affiliation(s)
- Mireia Rosell
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja - Gobierno de La Rioja, 26007 Logroño, Spain.
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15
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Yan Y, Tao H, He J, Huang SY. The HDOCK server for integrated protein–protein docking. Nat Protoc 2020; 15:1829-1852. [DOI: 10.1038/s41596-020-0312-x] [Citation(s) in RCA: 288] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 02/03/2020] [Indexed: 12/27/2022]
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16
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Nam J, Lim HK, Kim NH, Park JK, Kang ES, Kim YT, Heo C, Lee OS, Kim SG, Yun WS, Suh M, Kim YH. Supramolecular Peptide Hydrogel-Based Soft Neural Interface Augments Brain Signals through a Three-Dimensional Electrical Network. ACS NANO 2020; 14:664-675. [PMID: 31895542 DOI: 10.1021/acsnano.9b07396] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Recording neural activity from the living brain is of great interest in neuroscience for interpreting cognitive processing or neurological disorders. Despite recent advances in neural technologies, development of a soft neural interface that integrates with neural tissues, increases recording sensitivity, and prevents signal dissipation still remains a major challenge. Here, we introduce a biocompatible, conductive, and biostable neural interface, a supramolecular β-peptide-based hydrogel that allows signal amplification via tight neural/hydrogel contact without neuroinflammation. The non-biodegradable β-peptide forms a multihierarchical structure with conductive nanomaterial, creating a three-dimensional electrical network, which can augment brain signal efficiently. By achieving seamless integration in brain tissue with increased contact area and tight neural tissue coupling, the epidural and intracortical neural signals recorded with the hydrogel were augmented, especially in the high frequency range. Overall, our tissuelike chronic neural interface will facilitate a deeper understanding of brain oscillation in broad brain states and further lead to more efficient brain-computer interfaces.
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Affiliation(s)
- Jiyoung Nam
- Center for Neuroscience Imaging Research , Institute for Basic Science (IBS) , Suwon 16419 , Korea
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Hyun-Kyoung Lim
- Center for Neuroscience Imaging Research , Institute for Basic Science (IBS) , Suwon 16419 , Korea
- Department of Biological Sciences , Sungkyunkwan University , Suwon 16419 , Korea
| | - Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Jong Kwan Park
- Department of Chemistry , Sungkyunkwan University , Suwon 16419 , Korea
| | - Eun Sung Kang
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Yong-Tae Kim
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Chaejeong Heo
- Center for Neuroscience Imaging Research , Institute for Basic Science (IBS) , Suwon 16419 , Korea
| | - One-Sun Lee
- Qatar Environment and Energy Research Institute , Hamad Bin Khalifa University , Doha , Qatar
| | - Seong-Gi Kim
- Center for Neuroscience Imaging Research , Institute for Basic Science (IBS) , Suwon 16419 , Korea
- Department of Biomedical Engineering , Sungkyunkwan University , Suwon 16419 , Korea
| | - Wan Soo Yun
- Department of Chemistry , Sungkyunkwan University , Suwon 16419 , Korea
| | - Minah Suh
- Center for Neuroscience Imaging Research , Institute for Basic Science (IBS) , Suwon 16419 , Korea
- Department of Biomedical Engineering , Sungkyunkwan University , Suwon 16419 , Korea
- Biomedical Institute for Convergence at SKKU (BICS) , Sungkyunkwan University , Suwon 16419 , Korea
| | - Yong Ho Kim
- Center for Neuroscience Imaging Research , Institute for Basic Science (IBS) , Suwon 16419 , Korea
- SKKU Advanced Institute of Nanotechnology (SAINT) , Sungkyunkwan University , Suwon 16419 , Korea
- Department of Chemistry , Sungkyunkwan University , Suwon 16419 , Korea
- Biomedical Institute for Convergence at SKKU (BICS) , Sungkyunkwan University , Suwon 16419 , Korea
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17
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Jiménez-García B, Bernadó P, Fernández-Recio J. Structural Characterization of Protein-Protein Interactions with pyDockSAXS. Methods Mol Biol 2020; 2112:131-144. [PMID: 32006283 DOI: 10.1007/978-1-0716-0270-6_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Structural characterization of protein-protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical purposes. Unfortunately, the 3D structure is available for only a small fraction of all possible protein-protein interactions, due to the technical limitations of high-resolution structural determination methods. In this context, low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be combined with computational docking to provide structural models of protein-protein interactions at large scale. In this chapter, we describe the pyDockSAXS web server ( https://life.bsc.es/pid/pydocksaxs ), which uses pyDock docking and scoring to provide structural models that optimally satisfy the input SAXS data. This server, which is freely available to the scientific community, provides an automatic pipeline to model the structure of a protein-protein complex from SAXS data.
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Affiliation(s)
- Brian Jiménez-García
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht, The Netherlands
| | - Pau Bernadó
- Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.
- Institut de Biologia Molecular de Barcelona (IBMB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas (CSIC), Logroño, Spain.
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18
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Dasgupta B, Miyashita O, Tama F. Reconstruction of low-resolution molecular structures from simulated atomic force microscopy images. Biochim Biophys Acta Gen Subj 2019; 1864:129420. [PMID: 31472175 DOI: 10.1016/j.bbagen.2019.129420] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Atomic Force Microscopy (AFM) is an experimental technique to study structure-function relationship of biomolecules. AFM provides images of biomolecules at nanometer resolution. High-speed AFM experiments produce a series of images following dynamics of biomolecules. To further understand biomolecular functions, information on three-dimensional (3D) structures is beneficial. METHOD We aim to recover 3D information from an AFM image by computational modeling. The AFM image includes only low-resolution representation of a molecule; therefore we represent the structures by a coarse grained model (Gaussian mixture model). Using Monte-Carlo sampling, candidate models are generated to increase similarity between AFM images simulated from the models and target AFM image. RESULTS The algorithm was tested on two proteins to model their conformational transitions. Using a simulated AFM image as reference, the algorithm can produce a low-resolution 3D model of the target molecule. Effect of molecular orientations captured in AFM images on the 3D modeling performance was also examined and it is shown that similar accuracy can be obtained for many orientations. CONCLUSIONS The proposed algorithm can generate 3D low-resolution protein models, from which conformational transitions observed in AFM images can be interpreted in more detail. GENERAL SIGNIFICANCE High-speed AFM experiments allow us to directly observe biomolecules in action, which provides insights on biomolecular function through dynamics. However, as only partial structural information can be obtained from AFM data, this new AFM based hybrid modeling method would be useful to retrieve 3D information of the entire biomolecule.
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Affiliation(s)
- Bhaskar Dasgupta
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Osamu Miyashita
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan.
| | - Florence Tama
- Center for Computational Science, RIKEN, Kobe, Hyogo, 650-0047, Japan; Department of Physics, Graduate School of Science, Nagoya University, Aichi, 464-8602, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Aichi, 464-8601, Japan.
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19
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Vallat B, Webb B, Westbrook J, Sali A, Berman HM. Archiving and disseminating integrative structure models. JOURNAL OF BIOMOLECULAR NMR 2019; 73:385-398. [PMID: 31278630 PMCID: PMC6692293 DOI: 10.1007/s10858-019-00264-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/25/2019] [Indexed: 05/04/2023]
Abstract
Limitations in the applicability, accuracy, and precision of individual structure characterization methods can sometimes be overcome via an integrative modeling approach that relies on information from all available sources, including all available experimental data and prior models. The open-source Integrative Modeling Platform (IMP) is one piece of software that implements all computational aspects of integrative modeling. To maximize the impact of integrative structures, the coordinates should be made publicly available, as is already the case for structures based on X-ray crystallography, NMR spectroscopy, and electron microscopy. Moreover, the associated experimental data and modeling protocols should also be archived, such that the original results can easily be reproduced. Finally, it is essential that the integrative structures are validated as part of their publication and deposition. A number of research groups have already developed software to implement integrative modeling and have generated a number of structures, prompting the formation of an Integrative/Hybrid Methods Task Force. Following the recommendations of this task force, the existing PDBx/mmCIF data representation used for atomic PDB structures has been extended to address the requirements for archiving integrative structural models. This IHM-dictionary adds a flexible model representation, including coarse graining, models in multiple states and/or related by time or other order, and multiple input experimental information sources. A prototype archiving system called PDB-Dev ( https://pdb-dev.wwpdb.org ) has also been created to archive integrative structural models, together with a Python library to facilitate handling of integrative models in PDBx/mmCIF format.
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Affiliation(s)
- Brinda Vallat
- Institute for Quantitative Biomedicine, Piscataway, USA
| | - Benjamin Webb
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA, 94143, USA
| | - John Westbrook
- Institute for Quantitative Biomedicine, Piscataway, USA
- RCSB Protein Data Bank, Piscataway, USA
| | - Andrej Sali
- RCSB Protein Data Bank, Piscataway, USA.
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA, 94143, USA.
- Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, 94143, USA.
- Lead Contacts, San Francisco, USA.
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
- Lead Contacts, Piscataway, USA.
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20
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Rose HR, Maggiolo AO, McBride MJ, Palowitch GM, Pandelia ME, Davis KM, Yennawar NH, Boal AK. Structures of Class Id Ribonucleotide Reductase Catalytic Subunits Reveal a Minimal Architecture for Deoxynucleotide Biosynthesis. Biochemistry 2019; 58:1845-1860. [PMID: 30855138 PMCID: PMC6456427 DOI: 10.1021/acs.biochem.8b01252] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Class I ribonucleotide reductases (RNRs) share a common mechanism of nucleotide reduction in a catalytic α subunit. All RNRs initiate catalysis with a thiyl radical, generated in class I enzymes by a metallocofactor in a separate β subunit. Class Id RNRs use a simple mechanism of cofactor activation involving oxidation of a MnII2 cluster by free superoxide to yield a metal-based MnIIIMnIV oxidant. This simple cofactor assembly pathway suggests that class Id RNRs may be representative of the evolutionary precursors to more complex class Ia-c enzymes. X-ray crystal structures of two class Id α proteins from Flavobacterium johnsoniae ( Fj) and Actinobacillus ureae ( Au) reveal that this subunit is distinctly small. The enzyme completely lacks common N-terminal ATP-cone allosteric motifs that regulate overall activity, a process that normally occurs by dATP-induced formation of inhibitory quaternary structures to prevent productive β subunit association. Class Id RNR activity is insensitive to dATP in the Fj and Au enzymes evaluated here, as expected. However, the class Id α protein from Fj adopts higher-order structures, detected crystallographically and in solution. The Au enzyme does not exhibit these quaternary forms. Our study reveals structural similarity between bacterial class Id and eukaryotic class Ia α subunits in conservation of an internal auxiliary domain. Our findings with the Fj enzyme illustrate that nucleotide-independent higher-order quaternary structures can form in simple RNRs with truncated or missing allosteric motifs.
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Affiliation(s)
- Hannah R. Rose
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Ailiena O. Maggiolo
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Molly J. McBride
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Gavin M. Palowitch
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Katherine M. Davis
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - Neela H. Yennawar
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802
| | - Amie K. Boal
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
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21
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Wollacott AM, Robinson LN, Ramakrishnan B, Tissire H, Viswanathan K, Shriver Z, Babcock GJ. Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data. J Mol Recognit 2019; 32:e2778. [DOI: 10.1002/jmr.2778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/21/2018] [Accepted: 12/06/2018] [Indexed: 12/29/2022]
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22
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Kempf G, Stjepanovic G, Sloan J, Hendricks A, Lapouge K, Sinning I. The Escherichia coli SRP Receptor Forms a Homodimer at the Membrane. Structure 2018; 26:1440-1450.e5. [PMID: 30146170 DOI: 10.1016/j.str.2018.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/14/2018] [Accepted: 07/22/2018] [Indexed: 01/19/2023]
Abstract
The Escherichia coli signal recognition particle (SRP) receptor, FtsY, plays a fundamental role in co-translational targeting of membrane proteins via the SRP pathway. Efficient targeting relies on membrane interaction of FtsY and heterodimerization with the SRP protein Ffh, which is driven by detachment of α helix (αN1) in FtsY. Here we show that apart from the heterodimer, FtsY forms a nucleotide-dependent homodimer on the membrane, and upon αN1 removal also in solution. Homodimerization triggers reciprocal stimulation of GTP hydrolysis and occurs in vivo. Biochemical characterization together with integrative modeling suggests that the homodimer employs the same interface as the heterodimer. Structure determination of FtsY NG+1 with GMPPNP shows that a dimerization-induced conformational switch of the γ-phosphate is conserved in Escherichia coli, filling an important gap in SRP GTPase activation. Our findings add to the current understanding of SRP GTPases and may challenge previous studies that did not consider homodimerization of FtsY.
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Affiliation(s)
- Georg Kempf
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Goran Stjepanovic
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Jeremy Sloan
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Astrid Hendricks
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Karine Lapouge
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany
| | - Irmgard Sinning
- Heidelberg University Biochemistry Centre, Heidelberg 69120, Germany.
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23
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Ignatov M, Kazennov A, Kozakov D. ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking. J Mol Biol 2018; 430:2249-2255. [DOI: 10.1016/j.jmb.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 02/01/2023]
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24
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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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25
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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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26
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Karczyńska AS, Mozolewska MA, Krupa P, Giełdoń A, Liwo A, Czaplewski C. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information. Proteins 2017; 86 Suppl 1:228-239. [PMID: 29134679 DOI: 10.1002/prot.25421] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022]
Abstract
A new approach to assisted protein-structure prediction has been proposed, which is based on running multiplexed replica exchange molecular dynamics simulations with the coarse-grained UNRES force field with restraints derived from knowledge-based models and distance distribution from small angle X-ray scattering (SAXS) measurements. The latter restraints are incorporated into the target function as a maximum-likelihood term that guides the shape of the simulated structures towards that defined by SAXS. The approach was first verified with the 1KOY protein, for which the distance distribution was calculated from the experimental structure, and subsequently used to predict the structures of 11 data-assisted targets in the CASP12 experiment. Major improvement of the GDT_TS was obtained for 2 targets, minor improvement for other 2 while, for 6 target GDT_TS deteriorated compared with that calculated for predictions without the SAXS data, partly because of assuming a wrong multimeric state (for Ts866) or because the crystal conformation was more compact than the solution conformation (for Ts942). Particularly good results were obtained for Ts909, in which use of SAXS data resulted in the selection of a correctly packed trimer and, subsequently, increased the GDT_TS of monomer prediction. It was found that running simulations with correct oligomeric state is essential for the success in SAXS-data-assisted prediction.
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Affiliation(s)
| | - Magdalena A Mozolewska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warsaw, 01-248, Poland
| | - Paweł Krupa
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,Institute of Physics, Polish Academy of Sciences, Aleja Lotników 32/46, Warsaw, PL-02668, Poland
| | - Artur Giełdoń
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.,School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul, 130-722, Republic of Korea
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland
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27
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Bernadó P, Shimizu N, Zaccai G, Kamikubo H, Sugiyama M. Solution scattering approaches to dynamical ordering in biomolecular systems. Biochim Biophys Acta Gen Subj 2017; 1862:253-274. [PMID: 29107147 DOI: 10.1016/j.bbagen.2017.10.015] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 01/09/2023]
Abstract
Clarification of solution structure and its modulation in proteins and protein complexes is crucially important to understand dynamical ordering in macromolecular systems. Small-angle x-ray scattering (SAXS) and small-angle neutron scattering (SANS) are among the most powerful techniques to derive structural information. Recent progress in sample preparation, instruments and software analysis is opening up a new era for small-angle scattering. In this review, recent progress and trends of SAXS and SANS are introduced from the point of view of instrumentation and analysis, touching on general features and standard methods of small-angle scattering. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Pau Bernadó
- Centre de Biochimie Structurale, INSERM, CNRS, Université de Montpellier, France
| | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Giuseppe Zaccai
- Institut Laue Langevin, Institut de Biologie Structurale, CNRS, CNRS, UGA, Grenoble, France
| | - Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.
| | - Masaaki Sugiyama
- Research Reactor Institute, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan..
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28
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Wallen JR, Zhang H, Weis C, Cui W, Foster BM, Ho CMW, Hammel M, Tainer JA, Gross ML, Ellenberger T. Hybrid Methods Reveal Multiple Flexibly Linked DNA Polymerases within the Bacteriophage T7 Replisome. Structure 2017; 25:157-166. [PMID: 28052235 DOI: 10.1016/j.str.2016.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/02/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
The physical organization of DNA enzymes at a replication fork enables efficient copying of two antiparallel DNA strands, yet dynamic protein interactions within the replication complex complicate replisome structural studies. We employed a combination of crystallographic, native mass spectrometry and small-angle X-ray scattering experiments to capture alternative structures of a model replication system encoded by bacteriophage T7. Two molecules of DNA polymerase bind the ring-shaped primase-helicase in a conserved orientation and provide structural insight into how the acidic C-terminal tail of the primase-helicase contacts the DNA polymerase to facilitate loading of the polymerase onto DNA. A third DNA polymerase binds the ring in an offset manner that may enable polymerase exchange during replication. Alternative polymerase binding modes are also detected by small-angle X-ray scattering with DNA substrates present. Our collective results unveil complex motions within T7 replisome higher-order structures that are underpinned by multivalent protein-protein interactions with functional implications.
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Affiliation(s)
- Jamie R Wallen
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, NC 28723, USA.
| | - Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Caroline Weis
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Brittni M Foster
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, NC 28723, USA
| | - Chris M W Ho
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX 77054, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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29
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Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the Integrative Modeling Platform. Protein Sci 2017; 27:245-258. [PMID: 28960548 DOI: 10.1002/pro.3311] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/23/2017] [Accepted: 09/25/2017] [Indexed: 11/06/2022]
Abstract
Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use.
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Affiliation(s)
- Benjamin Webb
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | - Shruthi Viswanath
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | | | - Riccardo Pellarin
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Charles H Greenberg
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | - Daniel Saltzberg
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
| | - Andrej Sali
- California Institute for Quantitative Biosciences, University of California, San Francisco, California, 94158
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30
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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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31
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Borysik AJ. Simulated Isotope Exchange Patterns Enable Protein Structure Determination. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Antoni J. Borysik
- Department of Chemistry; King's College London; Britannia House London SE1 1DB UK
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32
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Borysik AJ. Simulated Isotope Exchange Patterns Enable Protein Structure Determination. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201704604] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Antoni J. Borysik
- Department of Chemistry; King's College London; Britannia House London SE1 1DB UK
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33
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Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics. Arch Biochem Biophys 2017; 628:33-41. [PMID: 28501583 PMCID: PMC5553349 DOI: 10.1016/j.abb.2017.05.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 05/05/2017] [Accepted: 05/08/2017] [Indexed: 01/25/2023]
Abstract
Small-angle X-ray scattering (SAXS) and Nuclear Magnetic Resonance (NMR) are established methods to analyze the structure and structural transitions of biological macromolecules in solution. Both methods are directly applicable to near-native macromolecular solutions and allow one to study structural responses to physical and chemical changes or ligand additions. Whereas SAXS is applied to elucidate overall structure, interactions and flexibility over a wide range of particle sizes, NMR yields atomic resolution detail for moderately sized macromolecules. NMR is arguably the most powerful technique for the experimental analysis of dynamics. The joint application of these two highly complementary techniques provides an extremely useful approach that facilitates comprehensive characterization of biomacromolecular solutions. SAXS and NMR are effective and highly complementary techniques in structural biology. Constraints from SAXS can be readily incorporated in NMR structure calculations. High resolution NMR models of domains can serve as building blocks for SAXS-based rigid body modeling. Flexible systems can be well described using ensemble approaches combining SAXS and NMR. Dynamics studies can be enhanced by combining SAXS and NMR.
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34
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Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. Nat Protoc 2017. [PMID: 28079879 DOI: 10.1038/nprot2016169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
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Affiliation(s)
- Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, USA
| | | | - Bing Xia
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Christine Yueh
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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35
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Formation of a repressive complex in the mammalian circadian clock is mediated by the secondary pocket of CRY1. Proc Natl Acad Sci U S A 2017; 114:1560-1565. [PMID: 28143926 DOI: 10.1073/pnas.1615310114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The basic helix-loop-helix PAS domain (bHLH-PAS) transcription factor CLOCK:BMAL1 (brain and muscle Arnt-like protein 1) sits at the core of the mammalian circadian transcription/translation feedback loop. Precise control of CLOCK:BMAL1 activity by coactivators and repressors establishes the ∼24-h periodicity of gene expression. Formation of a repressive complex, defined by the core clock proteins cryptochrome 1 (CRY1):CLOCK:BMAL1, plays an important role controlling the switch from repression to activation each day. Here we show that CRY1 binds directly to the PAS domain core of CLOCK:BMAL1, driven primarily by interaction with the CLOCK PAS-B domain. Integrative modeling and solution X-ray scattering studies unambiguously position a key loop of the CLOCK PAS-B domain in the secondary pocket of CRY1, analogous to the antenna chromophore-binding pocket of photolyase. CRY1 docks onto the transcription factor alongside the PAS domains, extending above the DNA-binding bHLH domain. Single point mutations at the interface on either CRY1 or CLOCK disrupt formation of the ternary complex, highlighting the importance of this interface for direct regulation of CLOCK:BMAL1 activity by CRY1.
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36
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Abstract
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
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37
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Hybrid Applications of Solution Scattering to Aid Structural Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:215-227. [PMID: 29218562 DOI: 10.1007/978-981-10-6038-0_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biomolecular applications of solution X-ray and neutron scattering (SAXS and SANS, respectively) started in late 1960s - early 1970s but were relatively limited in their ability to provide a detailed structural picture and lagged behind what became the two primary methods of experimental structural biology - X-ray crystallography and NMR. However, improvements in both data analysis and instrumentation led to an explosive growth in the number of studies that used small-angle scattering (SAS) for investigation of macromolecular structure, often in combination with other biophysical techniques. Such hybrid applications are nowadays quickly becoming a norm whenever scattering data are used for two reasons. First, it is generally accepted that SAS data on their own cannot lead to a uniquely defined high-resolution structural model, creating a need for supplementing them with information from complementary techniques. Second, solution scattering data are frequently applied in situations when a method such NMR or X-ray crystallography cannot provide a satisfactory structural picture, which makes these additional restraints highly desirable. Maturation of the hybrid bio-SAS approaches brings to light new questions including completeness of the conformational space sampling, model validation, and data compatibility.
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38
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Abstract
Genome sequencing projects have resulted in a rapid increase in the number of known protein sequences. In contrast, only about one-hundredth of these sequences have been characterized at atomic resolution using experimental structure determination methods. Computational protein structure modeling techniques have the potential to bridge this sequence-structure gap. In the following chapter, we present an example that illustrates the use of MODELLER to construct a comparative model for a protein with unknown structure. Automation of a similar protocol has resulted in models of useful accuracy for domains in more than half of all known protein sequences.
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Affiliation(s)
- Benjamin Webb
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, CA, 94143, USA
| | - 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, CA, 94143, USA.
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39
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Bonomi M, Camilloni C, Vendruscolo M. Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics. Sci Rep 2016; 6:31232. [PMID: 27561930 PMCID: PMC4999896 DOI: 10.1038/srep31232] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/11/2016] [Indexed: 01/23/2023] Open
Abstract
Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide.
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Affiliation(s)
- Massimiliano Bonomi
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Chemistry and Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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40
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Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA. Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. Structure 2016; 24:1248-1256. [PMID: 27396830 PMCID: PMC4972691 DOI: 10.1016/j.str.2016.05.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/25/2016] [Accepted: 05/12/2016] [Indexed: 01/14/2023]
Abstract
Cullin-RING E3 ligases (CRLs) are elongated and bowed protein complexes that transfer ubiquitin over 60 Å to proteins targeted for proteasome degradation. One such CRL contains the ankyrin repeat and SOCS box protein 9 (ASB9), which binds to and partially inhibits creatine kinase (CK). While current models for the ASB9-CK complex contain some known interface residues, the overall structure and precise interface of the ASB9-CK complex remains unknown. Through an integrative modeling approach, we report a third-generation model that reveals precisely the interface interactions and also fits the shape of the ASB9-CK complex as determined by small-angle X-ray scattering. We constructed an atomic model for the entire CK-targeting CRL to uncover dominant modes of motion that could permit ubiquitin transfer. Remarkably, only the correctly docked CK-containing E3 ligase and not incorrectly docked structures permitted close approach of ubiquitin to the CK substrate.
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Affiliation(s)
- Jamie M Schiffer
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
| | - Robert D Malmstrom
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA; National Biomedical Computation Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA
| | - Jonathan Parnell
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA
| | - Cesar Ramirez-Sarmiento
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Javiera Reyes
- Departamento de Biologia, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Casilla 653, Santiago 7800003, Chile
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA; National Biomedical Computation Resource, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA.
| | - Elizabeth A Komives
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0378, USA.
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41
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Schindler C, de Vries S, Sasse A, Zacharias M. SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. Structure 2016; 24:1387-1397. [DOI: 10.1016/j.str.2016.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
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42
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Vestergaard B. Analysis of biostructural changes, dynamics, and interactions – Small-angle X-ray scattering to the rescue. Arch Biochem Biophys 2016; 602:69-79. [DOI: 10.1016/j.abb.2016.02.029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/17/2016] [Accepted: 02/26/2016] [Indexed: 12/27/2022]
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43
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Carter L, Kim SJ, Schneidman-Duhovny D, Stöhr J, Poncet-Montange G, Weiss TM, Tsuruta H, Prusiner SB, Sali A. Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering. Biophys J 2016; 109:793-805. [PMID: 26287631 DOI: 10.1016/j.bpj.2015.06.065] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/22/2015] [Accepted: 06/30/2015] [Indexed: 10/23/2022] Open
Abstract
Aberrant self-assembly, induced by structural misfolding of the prion proteins, leads to a number of neurodegenerative disorders. In particular, misfolding of the mostly α-helical cellular prion protein (PrP(C)) into a β-sheet-rich disease-causing isoform (PrP(Sc)) is the key molecular event in the formation of PrP(Sc) aggregates. The molecular mechanisms underlying the PrP(C)-to-PrP(Sc) conversion and subsequent aggregation remain to be elucidated. However, in persistently prion-infected cell-culture models, it was shown that treatment with monoclonal antibodies against defined regions of the prion protein (PrP) led to the clearing of PrP(Sc) in cultured cells. To gain more insight into this process, we characterized PrP-antibody complexes in solution using a fast protein liquid chromatography coupled with small-angle x-ray scattering (FPLC-SAXS) procedure. High-quality SAXS data were collected for full-length recombinant mouse PrP [denoted recPrP(23-230)] and N-terminally truncated recPrP(89-230), as well as their complexes with each of two Fab fragments (HuM-P and HuM-R1), which recognize N- and C-terminal epitopes of PrP, respectively. In-line measurements by fast protein liquid chromatography coupled with SAXS minimized data artifacts caused by a non-monodispersed sample, allowing structural analysis of PrP alone and in complex with Fab antibodies. The resulting structural models suggest two mechanisms for how these Fabs may prevent the conversion of PrP(C) into PrP(Sc).
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Affiliation(s)
- Lester Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Seung Joong Kim
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | - Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California
| | - Jan Stöhr
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California; Department of Neurology, University of California San Francisco, San Francisco, California
| | - Guillaume Poncet-Montange
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Hiro Tsuruta
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California; Department of Neurology, University of California San Francisco, San Francisco, California.
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences and Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California San Francisco, San Francisco, California.
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44
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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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45
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Protein-protein interactions: a supra-structural phenomenon demanding trans-disciplinary biophysical approaches. Curr Opin Struct Biol 2015; 35:76-86. [PMID: 26496626 DOI: 10.1016/j.sbi.2015.09.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 09/01/2015] [Accepted: 09/28/2015] [Indexed: 01/14/2023]
Abstract
Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers. The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can be obtained at increasing resolution, at relevant time-scales and under increasingly relevant experimental conditions, intricate data are interpreted reliably, and the questions posed and answered grow in complexity. With this review, highlights from the study of PPIs using a multitude of biophysical methods, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods.
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46
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Xia B, Mamonov A, Leysen S, Allen KN, Strelkov SV, Paschalidis IC, Vajda S, Kozakov D. Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro. J Comput Chem 2015; 36:1568-72. [PMID: 26095982 DOI: 10.1002/jcc.23952] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 12/29/2022]
Abstract
The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtaining low resolution structural information in solution. While not sufficient on its own to uniquely predict complex structures, accounting for SAXS data improves the ranking of models and facilitates the identification of the most accurate structure. Although SAXS profiles are currently available only for a small number of complexes, due to its simplicity the method is becoming increasingly popular. Since combining docking with SAXS experiments will provide a viable strategy for fairly high-throughput determination of protein complex structures, the option of using SAXS restraints is added to the ClusPro server. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Bing Xia
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
| | - Artem Mamonov
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
| | - Seppe Leysen
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Karen N Allen
- Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Sergei V Strelkov
- Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, 3000, Belgium
| | - Ioannis Ch Paschalidis
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, 02215
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
| | - Dima Kozakov
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215
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47
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Chen PC, Hub JS. Interpretation of solution x-ray scattering by explicit-solvent molecular dynamics. Biophys J 2015; 108:2573-2584. [PMID: 25992735 PMCID: PMC4457003 DOI: 10.1016/j.bpj.2015.03.062] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 02/19/2015] [Accepted: 03/09/2015] [Indexed: 11/19/2022] Open
Abstract
Small- and wide-angle x-ray scattering (SWAXS) and molecular dynamics (MD) simulations are complementary approaches that probe conformational transitions of biomolecules in solution, even in a time-resolved manner. However, the structural interpretation of the scattering signals is challenging, while MD simulations frequently suffer from incomplete sampling or from a force-field bias. To combine the advantages of both techniques, we present a method that incorporates solution scattering data as a differentiable energetic restraint into explicit-solvent MD simulations, termed SWAXS-driven MD, with the aim to direct the simulation into conformations satisfying the experimental data. Because the calculations fully rely on explicit solvent, no fitting parameters associated with the solvation layer or excluded solvent are required, and the calculations remain valid at wide angles. The complementarity of SWAXS and MD is illustrated using three biological examples, namely a periplasmic binding protein, aspartate carbamoyltransferase, and a nuclear exportin. The examples suggest that SWAXS-driven MD is capable of refining structures against SWAXS data without foreknowledge of possible reaction paths. In turn, the SWAXS data accelerates conformational transitions in MD simulations and reduces the force-field bias.
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Affiliation(s)
- Po-Chia Chen
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Lower Saxony, Germany.
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48
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Jiménez-García B, Pons C, Svergun DI, Bernadó P, Fernández-Recio J. pyDockSAXS: protein-protein complex structure by SAXS and computational docking. Nucleic Acids Res 2015; 43:W356-61. [PMID: 25897115 PMCID: PMC4489248 DOI: 10.1093/nar/gkv368] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/02/2015] [Indexed: 11/13/2022] Open
Abstract
Structural characterization of protein–protein interactions at molecular level is essential to understand biological processes and identify new therapeutic opportunities. However, atomic resolution structural techniques cannot keep pace with current advances in interactomics. Low-resolution structural techniques, such as small-angle X-ray scattering (SAXS), can be applied at larger scale, but they miss atomic details. For efficient application to protein–protein complexes, low-resolution information can be combined with theoretical methods that provide energetic description and atomic details of the interactions. Here we present the pyDockSAXS web server (http://life.bsc.es/pid/pydocksaxs) that provides an automatic pipeline for modeling the structure of a protein–protein complex from SAXS data. The method uses FTDOCK to generate rigid-body docking models that are subsequently evaluated by a combination of pyDock energy-based scoring function and their capacity to describe SAXS data. The only required input files are structural models for the interacting partners and a SAXS curve. The server automatically provides a series of structural models for the complex, sorted by the pyDockSAXS scoring function. The user can also upload a previously computed set of docking poses, which opens the possibility to filter the docking solutions by potential interface residues or symmetry restraints. The server is freely available to all users without restriction.
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Affiliation(s)
- Brian Jiménez-García
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, 22603 Hamburg, Germany
| | - Pau Bernadó
- Centre de Biochimie Structurale, INSERM U1054, CNRS UMR 5048, Université Montpellier 1 and 2, F-34090 Montpellier, France
| | - Juan Fernández-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, 08034 Barcelona, Spain
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Thach TT, Lee N, Shin D, Han S, Kim G, Kim H, Lee S. Molecular determinants of polyubiquitin recognition by continuous ubiquitin-binding domains of Rad18. Biochemistry 2015; 54:2136-48. [PMID: 25756347 DOI: 10.1021/bi5012546] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins through its bipartite ubiquitin-binding domains UBZ and LRM with extra residues between them. Rad18 binds K63-linked polyubiquitin chains as well as K48-linked ones and monoubiquitin. However, the detailed molecular basis of polyubiquitin recognition by UBZ and LRM remains unclear. Here, we examined the interaction of Rad18(201-240), including UBZ and LRM, with linear polyubiquitin chains that are structurally similar to the K63-linked ones. Rad18(201-240) binds linear polyubiquitin chains (Ub2-Ub4) with affinity similar to that of a K63-linked one for diubiquitin. Ab initio modeling suggests that LRM and the extra residues at the C-terminus of UBZ (residues 227-237) likely form a continuous helix, termed the "extended LR motif" (ELRM). We obtained a molecular envelope for Rad18 UBZ-ELRM:linear Ub2 by small-angle X-ray scattering and derived a structural model for the complex. The Rad18:linear Ub2 model indicates that ELRM enhances the binding of Rad18 with linear polyubiquitin by contacting the proximal ubiquitin moiety. Consistent with the structural analysis, mutational studies showed that residues in ELRM affect binding with linear Ub2, not monoubiquitin. In cell data support the idea that ELRM is crucial in the localization of Rad18 to DNA damage sites. Specifically, E227 seems to be the most critical in polyubiquitin binding and localization to nuclear foci. Finally, we reveal that the ubiquitin-binding domains of Rad18 bind linear Ub2 more tightly than those of RAP80, providing a quantitative basis for blockage of RAP80 at DSB sites. Taken together, our data demonstrate that Rad18(201-240) forms continuous ubiquitin-binding domains, comprising UBZ and ELRM, and provides a structural framework for polyubiquitin recognition by Rad18 in the DDR pathway at a molecular level.
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Affiliation(s)
- Trung Thanh Thach
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Namsoo Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Donghyuk Shin
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Seungsu Han
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Gyuhee Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Hongtae Kim
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746, Korea
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50
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Yang S. Methods for SAXS-based structure determination of biomolecular complexes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:7902-10. [PMID: 24888261 PMCID: PMC4285438 DOI: 10.1002/adma.201304475] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 03/10/2014] [Indexed: 05/20/2023]
Abstract
Measurements from small-angle X-ray scattering (SAXS) are highly informative to determine the structures of bimolecular complexes in solution. Here, current and recent SAXS-driven developments are described, with an emphasis on computational modeling. In particular, accurate methods to computing one theoretical scattering profile from a given structure model are discussed, with a key focus on structure factor coarse-graining and hydration contribution. Methods for reconstructing topological structures from an experimental SAXS profile are currently under active development. We report on several modeling tools designed for conformation generation that make use of either atomic-level or coarse-grained representations. Furthermore, since large, flexible biomolecules can adopt multiple well-defined conformations, a traditional single-conformation SAXS analysis is inappropriate, so we also discuss recent methods that utilize the concept of ensemble optimization, weighing in on the SAXS contributions of a heterogeneous mixture of conformations. These tools will ultimately posit the usefulness of SAXS data beyond a simple space-filling approach by providing a reliable structure characterization of biomolecular complexes under physiological conditions.
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Affiliation(s)
- Sichun Yang
- Center for Proteomics and Department of Pharmacology, Department of Physiology and Biophysics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106-4988, USA
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