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Potrzebowski W, Trewhella J, Andre I. Bayesian inference of protein conformational ensembles from limited structural data. PLoS Comput Biol 2018; 14:e1006641. [PMID: 30557358 PMCID: PMC6312354 DOI: 10.1371/journal.pcbi.1006641] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 12/31/2018] [Accepted: 11/13/2018] [Indexed: 11/21/2022] Open
Abstract
Many proteins consist of folded domains connected by regions with higher flexibility. The details of the resulting conformational ensemble play a central role in controlling interactions between domains and with binding partners. Small-Angle Scattering (SAS) is well-suited to study the conformational states adopted by proteins in solution. However, analysis is complicated by the limited information content in SAS data and care must be taken to avoid constructing overly complex ensemble models and fitting to noise in the experimental data. To address these challenges, we developed a method based on Bayesian statistics that infers conformational ensembles from a structural library generated by all-atom Monte Carlo simulations. The first stage of the method involves a fast model selection based on variational Bayesian inference that maximizes the model evidence of the selected ensemble. This is followed by a complete Bayesian inference of population weights in the selected ensemble. Experiments with simulated ensembles demonstrate that model evidence is capable of identifying the correct ensemble and that correct number of ensemble members can be recovered up to high level of noise. Using experimental data, we demonstrate how the method can be extended to include data from Nuclear Magnetic Resonance (NMR) and structural energies of conformers extracted from the all-atom energy functions. We show that the data from SAXS, NMR chemical shifts and energies calculated from conformers can work synergistically to improve the definition of the conformational ensemble.
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Affiliation(s)
- Wojciech Potrzebowski
- Data Management and Software Centre, European Spallation Source ERIC, Copenhagen, Denmark
- Biochemistry and Structural Biology, University of Lund, Lund, Sweden
| | - Jill Trewhella
- School of Life and Environmental Sciences, The University of Sydney, Sydney, Australia
| | - Ingemar Andre
- Biochemistry and Structural Biology, University of Lund, Lund, Sweden
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Berland M, Offmann B, Andre I, Remaud-Simeon M, Charton P. A web-based tool for rational screening of mutants libraries using ProSAR. Protein Eng Des Sel 2014; 27:375-81. [DOI: 10.1093/protein/gzu035] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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3
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Kesicky D, Andre I, Kesicka M. EPA-0284 – Pedophiles and (or) child molesters. Eur Psychiatry 2014. [DOI: 10.1016/s0924-9338(14)77731-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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4
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Izakova L, Baloghova B, Borovska M, Andre I, Novotny V. P-1049 - Toxic psychoses - comparison to schizophrenia. Eur Psychiatry 2012. [DOI: 10.1016/s0924-9338(12)75216-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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5
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Huang PS, Ban YEA, Richter F, Andre I, Vernon R, Schief WR, Baker D. RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS One 2011; 6:e24109. [PMID: 21909381 PMCID: PMC3166072 DOI: 10.1371/journal.pone.0024109] [Citation(s) in RCA: 233] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 07/29/2011] [Indexed: 12/12/2022] Open
Abstract
We describe RosettaRemodel, a generalized framework for flexible protein design that provides a versatile and convenient interface to the Rosetta modeling suite. RosettaRemodel employs a unified interface, called a blueprint, which allows detailed control over many aspects of flexible backbone protein design calculations. RosettaRemodel allows the construction and elaboration of customized protocols for a wide range of design problems ranging from loop insertion and deletion, disulfide engineering, domain assembly, loop remodeling, motif grafting, symmetrical units, to de novo structure modeling.
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Affiliation(s)
- Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Yih-En Andrew Ban
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | - Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Interdisciplinary Program in Biomolecular Structure and Design, University of Washington, Seattle, Washington, United States of America
| | - Ingemar Andre
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Robert Vernon
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada
| | - William R. Schief
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail: (WRS); (DB)
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, University of Washington, Seattle, Washington, United States of America
- * E-mail: (WRS); (DB)
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6
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Abstract
Modeling the conformational changes that occur on binding of macromolecules is an unsolved challenge. In previous rounds of the Critical Assessment of PRediction of Interactions (CAPRI), it was demonstrated that the Rosetta approach to macromolecular modeling could capture side chain conformational changes on binding with high accuracy. In rounds 13-19 we tested the ability of various backbone remodeling strategies to capture the main-chain conformational changes observed during binding events. These approaches span a wide range of backbone motions, from limited refinement of loops to relieve clashes in homologous docking, through extensive remodeling of loop segments, to large-scale remodeling of RNA. Although the results are encouraging, major improvements in sampling and energy evaluation are clearly required for consistent high accuracy modeling. Analysis of our failures in the CAPRI challenges suggest that conformational sampling at the termini of exposed beta strands is a particularly pressing area for improvement.
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Affiliation(s)
- Sarel J Fleishman
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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7
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Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL. A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms. Cell 2008; 134:1007-18. [PMID: 18805093 PMCID: PMC2701508 DOI: 10.1016/j.cell.2008.07.042] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2008] [Revised: 07/01/2008] [Accepted: 07/25/2008] [Indexed: 11/18/2022]
Abstract
Drosophila Dscam encodes a vast family of immunoglobulin (Ig)-containing proteins that exhibit isoform-specific homophilic binding. This diversity is essential for cell recognition events required for wiring the brain. Each isoform binds to itself but rarely to other isoforms. Specificity is determined by "matching" of three variable Ig domains within an approximately 220 kD ectodomain. Here, we present the structure of the homophilic binding region of Dscam, comprising the eight N-terminal Ig domains (Dscam(1-8)). Dscam(1-8) forms a symmetric homodimer of S-shaped molecules. This conformation, comprising two reverse turns, allows each pair of the three variable domains to "match" in an antiparallel fashion. Structural, genetic, and biochemical studies demonstrate that, in addition to variable domain "matching," intramolecular interactions between constant domains promote homophilic binding. These studies provide insight into how "matching" at all three pairs of variable domains in Dscam mediates isoform-specific recognition.
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Affiliation(s)
- Michael R. Sawaya
- Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, CA 90095, USA
| | - Woj M. Wojtowicz
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ingemar Andre
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Bin Qian
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Wei Wu
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David Baker
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - David Eisenberg
- Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, CA 90095, USA
- Correspondence: (D.E.), (S.L.Z.)
| | - S. Lawrence Zipursky
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Correspondence: (D.E.), (S.L.Z.)
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Wojtowicz WM, Wu W, Andre I, Qian B, Baker D, Zipursky SL. A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains. Cell 2007; 130:1134-45. [PMID: 17889655 PMCID: PMC2707357 DOI: 10.1016/j.cell.2007.08.026] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2007] [Revised: 08/08/2007] [Accepted: 08/10/2007] [Indexed: 11/15/2022]
Abstract
Dscam encodes a family of cell surface proteins required for establishing neural circuits in Drosophila. Alternative splicing of Drosophila Dscam can generate 19,008 distinct extracellular domains containing different combinations of three variable immunoglobulin domains. To test the binding properties of many Dscam isoforms, we developed a high-throughput ELISA-based binding assay. We provide evidence that 95% (>18,000) of Dscam isoforms exhibit striking isoform-specific homophilic binding. We demonstrate that each of the three variable domains binds to the same variable domain in an opposing isoform and identify the structural elements that mediate this self-binding of each domain. These studies demonstrate that self-binding domains can assemble in different combinations to generate an enormous family of homophilic binding proteins. We propose that this vast repertoire of Dscam recognition molecules is sufficient to provide each neuron with a unique identity and homotypic binding specificity, thereby allowing neuronal processes to distinguish between self and nonself.
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Affiliation(s)
- Woj M. Wojtowicz
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles California, USA
| | - Wei Wu
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles California, USA
| | - Ingemar Andre
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - Bin Qian
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - David Baker
- Department of Biochemistry, Howard Hughes Medical Institute, University of Washington, Seattle, Washington, USA
| | - S. Lawrence Zipursky
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles California, USA
- Correspondence:
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Abstract
A challenge in protein-protein docking is to account for the conformational changes in the monomers that occur upon binding. The RosettaDock method, which incorporates sidechain flexibility but keeps the backbone fixed, was found in previous CAPRI rounds (4 and 5) to generate docking models with atomic accuracy, provided that conformational changes were mainly restricted to protein sidechains. In the recent rounds of CAPRI (6-12), large backbone conformational changes occur upon binding for several target complexes. To address these challenges, we explicitly introduced backbone flexibility in our modeling procedures by combining rigid-body docking with protein structure prediction techniques such as modeling variable loops and building homology models. Encouragingly, using this approach we were able to correctly predict a significant backbone conformational change of an interface loop for Target 20 (12 A rmsd between those in the unbound monomer and complex structures), but accounting for backbone flexibility in protein-protein docking is still very challenging because of the significantly larger conformational space, which must be surveyed. Motivated by these CAPRI challenges, we have made progress in reformulating RosettaDock using a "fold-tree" representation, which provides a general framework for treating a wide variety of flexible-backbone docking problems.
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Affiliation(s)
- Chu Wang
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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10
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Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins 2007; 69 Suppl 8:118-28. [PMID: 17894356 DOI: 10.1002/prot.21636] [Citation(s) in RCA: 156] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We describe predictions made using the Rosetta structure prediction methodology for both template-based modeling and free modeling categories in the Seventh Critical Assessment of Techniques for Protein Structure Prediction. For the first time, aggressive sampling and all-atom refinement could be carried out for the majority of targets, an advance enabled by the Rosetta@home distributed computing network. Template-based modeling predictions using an iterative refinement algorithm improved over the best existing templates for the majority of proteins with less than 200 residues. Free modeling methods gave near-atomic accuracy predictions for several targets under 100 residues from all secondary structure classes. These results indicate that refinement with an all-atom energy function, although computationally expensive, is a powerful method for obtaining accurate structure predictions.
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Affiliation(s)
- Rhiju Das
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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11
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Abstract
Defective apoptosis is a mechanism which could possibly explain B chronic lymphocytic leukemia (B-CLL) cell accumulation. Differences in evolution and prognosis of B-CLL patients may be due to heterogeneity in apoptotic cell death. We studied the apoptotic response to in vitro gamma radiation of blood mononuclear cells from 18 untreated B-CLL patients. In cells irradiated with 2, 4 or 8 Gy and then cultured for 20 hours, the percentage of trypan blue excluding (viable) cells was not modified (>92%). An apoptotic response to irradiation was detected in the majority of the patients, but the individual percentage of apoptotic cells varied widely (8 to 81% after 8 Gy irradiation) in individual cases. The flow cytometric analysis of nick-end DNA labeling demonstrated a dose effect of irradiation, particularly in patients with an apoptotic response of over 20%. In the future, a valuable clue to the selection of irradiation regimens for B-CLL patients may be the investigation of correlations between in vitro radiation-induced apoptosis and the in vivo response to radiation therapy.
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MESH Headings
- Aged
- Apoptosis/radiation effects
- B-Lymphocytes/radiation effects
- Cell Survival/radiation effects
- Female
- Flow Cytometry
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/radiotherapy
- Leukocytes, Mononuclear/pathology
- Leukocytes, Mononuclear/radiation effects
- Male
- Middle Aged
- Phenotype
- Prognosis
- Tumor Cells, Cultured
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Affiliation(s)
- E Comby
- Université de Caen, UPRES EA 2128, and Service d'Immunologie et Immunopathologie, France
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Lesseve J, Stamatoullas A, Bastard C, Andre I, Fruchart C, Callat M, Rossi A, Lenormand B, Tilly H, Piguet H, Monconduit M. The 5q-syndrome: Clinical course of 12 patients. Leuk Res 1994. [DOI: 10.1016/0145-2126(94)90228-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Li XY, Mantovani R, Hooft van Huijsduijnen R, Andre I, Benoist C, Mathis D. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res 1992; 20:1087-91. [PMID: 1549471 PMCID: PMC312095 DOI: 10.1093/nar/20.5.1087] [Citation(s) in RCA: 125] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
NF-Y is a CCAAT-specific transcription factor thought to be involved in the regulation of a variety of eukaryotic genes. It shows a striking sequence similarity with the yeast factor HAP2/3. In an attempt to trace back its evolutionary history, we succeeded in isolating NF-Y cDNA clones from a plant and from several species of vertebrates. The patterns of sequence conservation delineate potential functional domains: A central, highly conserved, domain likely responsible for DNA-binding and subunit interaction; more evolutionarily flexible flanking regions, in which variability is clustered, individualizing conserved glutamine or acidic amino-acids putatively involved in protein-protein contacts.
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Affiliation(s)
- X Y Li
- Laboratoire de Génétique Moléculaire des Eucaryotes du CNRS, Unité 184 de Biologie Moléculaire et de Génie Génétique de I'INSERM, Institut de Chimie Biologique, Faculté de Médecine, Strasbourg, France
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