201
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Fagerberg E, Lenton S, Skepö M. Evaluating Models of Varying Complexity of Crowded Intrinsically Disordered Protein Solutions Against SAXS. J Chem Theory Comput 2019; 15:6968-6983. [DOI: 10.1021/acs.jctc.9b00723] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eric Fagerberg
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
| | - Samuel Lenton
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
- LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, 223 70 Lund, Sweden
| | - Marie Skepö
- Theoretical Chemistry, Lund University, POB 124, SE-221 00 Lund, Sweden
- LINXS - Lund Institute of Advanced Neutron and X-ray Science, Scheelevägen 19, 223 70 Lund, Sweden
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202
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Zhang S, Zhou P, Wang P, Li Y, Jiang L, Jia W, Wang H, Fan A, Wang D, Shi X, Fang X, Hammel M, Wang S, Wang X, Zhang L. Structural Definition of a Unique Neutralization Epitope on the Receptor-Binding Domain of MERS-CoV Spike Glycoprotein. Cell Rep 2019; 24:441-452. [PMID: 29996104 PMCID: PMC7104183 DOI: 10.1016/j.celrep.2018.06.041] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 04/27/2018] [Accepted: 06/08/2018] [Indexed: 02/05/2023] Open
Abstract
The major mechanism of antibody-mediated neutralization of the Middle East respiratory syndrome coronavirus (MERS-CoV) involves competition with the cellular receptor dipeptidyl peptidase 4 (DPP4) for binding to the receptor-binding domain (RBD) of the spike (S) glycoprotein. Here, we report a unique epitope and unusual neutralizing mechanism of the isolated human antibody MERS-4. Structurally, MERS-4 approached the RBD from the outside of the RBD-DPP4 binding interface. Such binding resulted in the folding of the β5-β6 loop toward a shallow groove on the RBD interface critical for accommodating DPP4. The key residues for binding are identified through site-directed mutagenesis. Structural modeling revealed that MERS-4 binds to RBD only in the “up” position in the S trimer. Furthermore, MERS-4 demonstrated synergy with several reported antibodies. These results indicate that MERS-4 neutralizes MERS-CoV by indirect rather than direct competition with DPP4. This mechanism provides a valuable addition for the combined use of antibodies against MERS-CoV infection. MERS-4 binds RBD from the outside of the RBD–DPP4 binding interface MERS-4 favors binding to the RBD in the “up” position in the S trimer MERS-4 neutralizes MERS-CoV by indirect rather than direct competition with DPP4 MERS-4 is a valuable addition to the combined use of MERS-CoV antibodies
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Affiliation(s)
- Senyan Zhang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Panpan Zhou
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Pengfei Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yangyang Li
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Liwei Jiang
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Wenxu Jia
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Han Wang
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Angela Fan
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Dongli Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xianyang Fang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Shuying Wang
- Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 701, Taiwan
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China; Collaborative Innovation Center for Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
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203
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Zhang Y, Liu H, Yang S, Luo R, Chen HF. Well-Balanced Force Field ff03 CMAP for Folded and Disordered Proteins. J Chem Theory Comput 2019; 15:6769-6780. [PMID: 31657215 DOI: 10.1021/acs.jctc.9b00623] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Molecular dynamics simulation as an important complement of experiment is widely used to study protein structures and functions. However, previous studies indicate that the current force fields cannot, simultaneously, provide accurate descriptions of folded proteins and intrinsically disordered proteins (IDPs). Therefore, a correction maps (CMAP)-optimized force field based on the Amber ff03 force field (termed ff03CMAP herein) was developed for a balanced sampling of folded proteins and IDPs. Extensive validations of short peptides, folded proteins, disordered proteins, and fast-folding proteins show that simulated chemical shifts, J-coupling constants, order parameters, and residual dipolar couplings (RDCs) with the ff03CMAP force field are in very good agreement with nuclear magnetic resonance measurements and are more accurate than other ff03-series force fields. The influence of solvent models was also investigated. It was found that the combination of ff03CMAP/TIP4P-Ew is suitable for folded proteins, and that of ff03CMAP/TIP4PD is better for disordered proteins. These findings confirm that the newly developed force field ff03CMAP can improve the balance of conformer sampling between folded proteins and IDPs.
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Affiliation(s)
- Yangpeng Zhang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Hao Liu
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Sheng Yang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Molecular Engineering, and Materials Science and Engineering, and Biomedical Engineering , University of California , Irvine , California 92697 , United States
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology , Shanghai Jiao Tong University , Shanghai 200240 , China.,Shanghai Center for Bioinformation Technology , Shanghai 200235 , China
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204
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Foster BM, Rosenberg D, Salvo H, Stephens KL, Bintz BJ, Hammel M, Ellenberger T, Gainey MD, Wallen JR. Combined Solution and Crystal Methods Reveal the Electrostatic Tethers That Provide a Flexible Platform for Replication Activities in the Bacteriophage T7 Replisome. Biochemistry 2019; 58:4466-4479. [PMID: 31659895 DOI: 10.1021/acs.biochem.9b00525] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Recent structural studies of the bacteriophage T7 DNA replication system have shed light on how multiple proteins assemble to copy two antiparallel DNA strands. In T7, acidic C-terminal tails of both the primase-helicase and single-stranded DNA binding protein bind to two basic patches on the DNA polymerase to aid in replisome assembly, processivity, and coordinated DNA synthesis. Although these electrostatic interactions are essential for DNA replication, the molecular details for how these tails bind the polymerase are unknown. We have determined an X-ray crystal structure of the T7 DNA polymerase bound to both a primer/template DNA and a peptide that mimics the C-terminal tail of the primase-helicase. The structure reveals that the essential C-terminal phenylalanine of the tail binds to a hydrophobic pocket that is surrounded by positive charge on the surface of the polymerase. We show that alterations of polymerase residues that engage the tail lead to defects in viral replication. In the structure, we also observe dTTP bound in the exonuclease active site and stacked against tryptophan 160. Using both primer/extension assays and high-throughput sequencing, we show how mutations in the exonuclease active site lead to defects in mismatch repair and an increase in the level of mutagenesis of the T7 genome. Finally, using small-angle X-ray scattering, we provide the first solution structures of a complex between the single-stranded DNA binding protein and the DNA polymerase and show how a single-stranded DNA binding protein dimer engages both one and two copies of DNA polymerase.
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Affiliation(s)
- Brittni M Foster
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Daniel Rosenberg
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Graduate Group in Biophysics , University of California, Berkeley , Berkeley , California 94720 , United States
| | - Henry Salvo
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Kasie L Stephens
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Brittania J Bintz
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics , Washington University School of Medicine , St. Louis , Missouri 63110 , United States
| | - Maria D Gainey
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
| | - Jamie R Wallen
- Department of Chemistry & Physics , Western Carolina University , Cullowhee , North Carolina 28723 , United States
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205
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Tomazini A, Higasi P, Manzine LR, Stott M, Sparling R, Levin DB, Polikarpov I. A novel thermostable GH5 β-xylosidase from Thermogemmatispora sp. T81. N Biotechnol 2019; 53:57-64. [DOI: 10.1016/j.nbt.2019.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Revised: 06/09/2019] [Accepted: 07/06/2019] [Indexed: 10/26/2022]
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206
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Lisnyansky Bar-El M, Lee SY, Ki AY, Kapelushnik N, Loewenstein A, Chung KY, Schneidman-Duhovny D, Giladi M, Newman H, Haitin Y. Structural Characterization of Full-Length Human Dehydrodolichyl Diphosphate Synthase Using an Integrative Computational and Experimental Approach. Biomolecules 2019; 9:E660. [PMID: 31661879 PMCID: PMC6921004 DOI: 10.3390/biom9110660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/25/2019] [Accepted: 10/26/2019] [Indexed: 01/13/2023] Open
Abstract
Dehydrodolichyl diphosphate synthase (DHDDS) is the catalytic subunit of the heteromeric human cis-prenyltransferase complex, synthesizing the glycosyl carrier precursor for N-linked protein glycosylation. Consistent with the important role of N-glycosylation in protein biogenesis, DHDDS mutations result in human diseases. Importantly, DHDDS encompasses a C-terminal region, which does not converge with any known conserved domains. Therefore, despite the clinical importance of DHDDS, our understating of its structure-function relations remains poor. Here, we provide a structural model for the full-length human DHDDS using a multidisciplinary experimental and computational approach. Size-exclusion chromatography multi-angle light scattering revealed that DHDDS forms a monodisperse homodimer in solution. Enzyme kinetics assays revealed that it exhibits catalytic activity, although reduced compared to that reported for the intact heteromeric complex. Our model suggests that the DHDDS C-terminus forms a helix-turn-helix motif, tightly packed against the core catalytic domain. This model is consistent with small-angle X-ray scattering data, indicating that the full-length DHDDS maintains a similar conformation in solution. Moreover, hydrogen-deuterium exchange mass-spectrometry experiments show time-dependent deuterium uptake in the C-terminal domain, consistent with its overall folded state. Finally, we provide a model for the DHDDS-NgBR heterodimer, offering a structural framework for future structural and functional studies of the complex.
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Affiliation(s)
- Michal Lisnyansky Bar-El
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel.
| | - Su Youn Lee
- School of Pharmacy, Sungkyunkwan University, Jangan-gu, Suwon 16419, Korea.
| | - Ah Young Ki
- School of Pharmacy, Sungkyunkwan University, Jangan-gu, Suwon 16419, Korea.
| | - Noa Kapelushnik
- Department of Ophthalmology, Sheba Medical Center, Ramat Gan 5265601, Israel.
| | - Anat Loewenstein
- Department of Ophthalmology, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Jangan-gu, Suwon 16419, Korea.
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
| | - Moshe Giladi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel.
- Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.
| | - Hadas Newman
- Department of Ophthalmology, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel.
| | - Yoni Haitin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 6997801, Israel.
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207
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Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae. CRYSTALS 2019. [DOI: 10.3390/cryst9110551] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Biosynthesis of branched-chain amino acids (BCAAs), including isoleucine, leucine and valine, is required for survival and virulence of a bacterial pathogen such as Streptococcus pneumoniae. IlvC, a ketol-acid reductoisomerase (E.C. 1.1.1.86) with NADP(H) and Mg2+ as cofactors from the pathogenic Streptococcus pneumoniae (SpIlvC), catalyzes the second step in the BCAA biosynthetic pathway. To elucidate the structural basis for the IlvC-mediated reaction, we determined the crystal structure of SpIlvC at 1.69 Å resolution. The crystal structure of SpIlvC contains an asymmetric dimer in which one subunit is in apo-form and the other in NADP(H) and Mg2+-bound form. Crystallographic analysis combined with an activity assay and small-angle X-ray scattering suggested that SpIlvC retains dimeric arrangement in solution and that D83 in the NADP(H) binding site and E195 in the Mg2+ binding site are the most critical in the catalytic activity of SpIlvC. Crystal structures of SpIlvC mutants (R49E, D83G, D191G and E195S) revealed local conformational changes only in the NADP(H) binding site. Taken together, our results establish the molecular mechanism for understanding functions of SpIlvC in pneumococcal growth and virulence.
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208
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Yang S, Liu H, Zhang Y, Lu H, Chen H. Residue-Specific Force Field Improving the Sample of Intrinsically Disordered Proteins and Folded Proteins. J Chem Inf Model 2019; 59:4793-4805. [DOI: 10.1021/acs.jcim.9b00647] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sheng Yang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- SJTU-Yale Joint Center for Biostatistics and Data Science, 800 Dongchuan Road, Shanghai, 200240, China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU−Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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209
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Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. Sci Rep 2019; 9:14645. [PMID: 31601934 PMCID: PMC6787221 DOI: 10.1038/s41598-019-51182-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 09/25/2019] [Indexed: 11/09/2022] Open
Abstract
Multidomain proteins represent a broad spectrum of the protein landscape and are involved in various interactions. They could be considered as modular building blocks assembled in distinct fashion and connected by linkers of varying lengths and sequences. Due to their intrinsic flexibility, these linkers provide proteins a subtle way to modulate interactions and explore a wide range of conformational space. In the present study, we are seeking to understand the effect of the flexibility and dynamics of the linker involved in the STAM2 UIM-SH3 dual domain protein with respect to molecular recognition. We have engineered several constructs of UIM-SH3 with different length linkers or domain deletion. By means of SAXS and NMR experiments, we have shown that the modification of the linker modifies the flexibility and the dynamics of UIM-SH3. Indeed, the global tumbling of both the UIM and SH3 domain is different but not independent from each other while the length of the linker has an impact on the ps-ns time scale dynamics of the respective domains. Finally, the modification of the flexibility and dynamics of the linker has a drastic effect on the interaction of UIM-SH3 with Lys63-linked diubiquitin with a roughly eight-time weaker dissociation constant.
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210
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Structural Organization and Dynamics of Homodimeric Cytohesin Family Arf GTPase Exchange Factors in Solution and on Membranes. Structure 2019; 27:1782-1797.e7. [PMID: 31601460 PMCID: PMC6948192 DOI: 10.1016/j.str.2019.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 09/03/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
Abstract
Membrane dynamic processes require Arf GTPase activation by guanine nucleotide exchange factors (GEFs) with a Sec7 domain. Cytohesin family Arf GEFs function in signaling and cell migration through Arf GTPase activation on the plasma membrane and endosomes. In this study, the structural organization of two cytohesins (Grp1 and ARNO) was investigated in solution by size exclusion-small angle X-ray scattering and negative stain-electron microscopy and on membranes by dynamic light scattering, hydrogen-deuterium exchange-mass spectrometry and guanosine diphosphate (GDP)/guanosine triphosphate (GTP) exchange assays. The results suggest that cytohesins form elongated dimers with a central coiled coil and membrane-binding pleckstrin-homology (PH) domains at opposite ends. The dimers display significant conformational heterogeneity, with a preference for compact to intermediate conformations. Phosphoinositide-dependent membrane recruitment is mediated by one PH domain at a time and alters the conformational dynamics to prime allosteric activation by Arf-GTP. A structural model for membrane targeting and allosteric activation of full-length cytohesin dimers is discussed.
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211
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Kim G, Azmi L, Jang S, Jung T, Hebert H, Roe AJ, Byron O, Song JJ. Aldehyde-alcohol dehydrogenase forms a high-order spirosome architecture critical for its activity. Nat Commun 2019; 10:4527. [PMID: 31586059 PMCID: PMC6778083 DOI: 10.1038/s41467-019-12427-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023] Open
Abstract
Aldehyde-alcohol dehydrogenase (AdhE) is a key enzyme in bacterial fermentation, converting acetyl-CoA to ethanol, via two consecutive catalytic reactions. Here, we present a 3.5 Å resolution cryo-EM structure of full-length AdhE revealing a high-order spirosome architecture. The structure shows that the aldehyde dehydrogenase (ALDH) and alcohol dehydrogenase (ADH) active sites reside at the outer surface and the inner surface of the spirosome respectively, thus topologically separating these two activities. Furthermore, mutations disrupting the helical structure abrogate enzymatic activity, implying that formation of the spirosome structure is critical for AdhE activity. In addition, we show that this spirosome structure undergoes conformational change in the presence of cofactors. This work presents the atomic resolution structure of AdhE and suggests that the high-order helical structure regulates its enzymatic activity. Aldehyde-alcohol dehydrogenase (AdhE) converts acetyl-CoA to ethanol and plays an important role in bacterial fermentation. Here the authors present the 3.5 Å cryo-EM structure of full-length E. coli AdhE, which reveals a right-handed helical spirosome structure and they show that the helical structure is required for AdhE activity.
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Affiliation(s)
- Gijeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Liyana Azmi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Seongmin Jang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea
| | - Taeyang Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.,School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden
| | - Hans Hebert
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Novum, SE-141 57, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, S-141 83, Huddinge, Sweden
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Ji-Joon Song
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Korea.
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212
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Brosey CA, Tainer JA. Evolving SAXS versatility: solution X-ray scattering for macromolecular architecture, functional landscapes, and integrative structural biology. Curr Opin Struct Biol 2019; 58:197-213. [PMID: 31204190 PMCID: PMC6778498 DOI: 10.1016/j.sbi.2019.04.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022]
Abstract
Small-angle X-ray scattering (SAXS) has emerged as an enabling integrative technique for comprehensive analyses of macromolecular structures and interactions in solution. Over the past two decades, SAXS has become a mainstay of the structural biologist's toolbox, supplying multiplexed measurements of molecular shape and dynamics that unveil biological function. Here, we discuss evolving SAXS theory, methods, and applications that extend the field of small-angle scattering beyond simple shape characterization. SAXS, coupled with size-exclusion chromatography (SEC-SAXS) and time-resolved (TR-SAXS) methods, is now providing high-resolution insight into macromolecular flexibility and ensembles, delineating biophysical landscapes, and facilitating high-throughput library screening to assess macromolecular properties and to create opportunities for drug discovery. Looking forward, we consider SAXS in the integrative era of hybrid structural biology methods, its potential for illuminating cellular supramolecular and mesoscale structures, and its capacity to complement high-throughput bioinformatics sequencing data. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.
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Affiliation(s)
- Chris A Brosey
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - John A Tainer
- Molecular and Cellular Oncology and Cancer Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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213
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Horst BG, Yokom AL, Rosenberg DJ, Morris KL, Hammel M, Hurley JH, Marletta MA. Allosteric activation of the nitric oxide receptor soluble guanylate cyclase mapped by cryo-electron microscopy. eLife 2019; 8:e50634. [PMID: 31566566 PMCID: PMC6839917 DOI: 10.7554/elife.50634] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/27/2019] [Indexed: 12/14/2022] Open
Abstract
Soluble guanylate cyclase (sGC) is the primary receptor for nitric oxide (NO) in mammalian nitric oxide signaling. We determined structures of full-length Manduca sexta sGC in both inactive and active states using cryo-electron microscopy. NO and the sGC-specific stimulator YC-1 induce a 71° rotation of the heme-binding β H-NOX and PAS domains. Repositioning of the β H-NOX domain leads to a straightening of the coiled-coil domains, which, in turn, use the motion to move the catalytic domains into an active conformation. YC-1 binds directly between the β H-NOX domain and the two CC domains. The structural elongation of the particle observed in cryo-EM was corroborated in solution using small angle X-ray scattering (SAXS). These structures delineate the endpoints of the allosteric transition responsible for the major cyclic GMP-dependent physiological effects of NO.
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Affiliation(s)
- Benjamin G Horst
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
| | - Adam L Yokom
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyUnited States
| | - Kyle L Morris
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Michal Hammel
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - James H Hurley
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
- Molecular Biophysics and Integrated BioimagingLawrence Berkeley National LaboratoryBerkeleyUnited States
- California Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyUnited States
| | - Michael A Marletta
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
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214
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Saltzberg DJ, Hepburn M, Pilla KB, Schriemer DC, Lees-Miller SP, Blundell TL, Sali A. SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:92-102. [PMID: 31570166 DOI: 10.1016/j.pbiomolbio.2019.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/09/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023]
Abstract
X-ray crystallography and electron microscopy maps resolved to 3-8 Å are generally sufficient for tracing the path of the polypeptide chain in space, while often insufficient for unambiguously registering the sequence on the path (i.e., threading). Frequently, however, additional information is available from other biophysical experiments, physical principles, statistical analyses, and other prior models. Here, we formulate an integrative approach for sequence assignment to a partial backbone model as an optimization problem, which requires three main components: the representation of the system, the scoring function, and the optimization method. The method is implemented in the open source Integrative Modeling Platform (IMP) (https://integrativemodeling.org), allowing a number of different terms in the scoring function. We apply this method to localizing the sequence assignment within a 199-residue disordered region of three structured and sequence unassigned helices in the DNA-PKcs crystallographic structure, using chemical crosslinks, hydrogen deuterium exchange, and sequence connectivity. The resulting ensemble of threading models provides two major solutions, one of which suggests that the crucial ABCDE cluster of phosphorylation sites cannot undergo intra-molecular autophosphorylation without a conformational rearrangement. The ensemble of solutions embodies the most accurate and precise sequence threading given the available information.
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Affiliation(s)
- Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA.
| | - Morgan Hepburn
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Kala Bharath Pilla
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, USA
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215
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Gabrielsen M, Buetow L, Kowalczyk D, Zhang W, Sidhu SS, Huang DT. Identification and Characterization of Mutations in Ubiquitin Required for Non-covalent Dimer Formation. Structure 2019; 27:1452-1459.e4. [PMID: 31303481 PMCID: PMC6720194 DOI: 10.1016/j.str.2019.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 05/29/2019] [Accepted: 06/21/2019] [Indexed: 11/26/2022]
Abstract
Ubiquitin (Ub) is a small protein that post-translationally modifies a variety of substrates in eukaryotic cells to modulate substrate function. The ability of Ub to interact with numerous protein domains makes Ub an attractive scaffold for engineering ubiquitin variants (UbVs) with high target specificity. Previously, we identified a UbV that formed a non-covalent stable dimer via a β-strand exchange, and in the current work we identified and characterized the minimal substitutions in the primary sequence of Ub required to form a higher ordered complex. Using solution angle scattering and X-ray crystallography, we show that a single substitution of residue Gly10 to either Ala or Val is sufficient to convert Ub from a monomer to a dimer. We also investigate contributions to dimer formation by the residues in the surrounding sequence. These results can be used to develop next-generation phage-display libraries of UbVs to engineer new interfaces for protein recognition.
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Affiliation(s)
- Mads Gabrielsen
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lori Buetow
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Dominika Kowalczyk
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
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216
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Knott GJ, Cress BF, Liu JJ, Thornton BW, Lew RJ, Al-Shayeb B, Rosenberg DJ, Hammel M, Adler BA, Lobba MJ, Xu M, Arkin AP, Fellmann C, Doudna JA. Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a. eLife 2019; 8:e49110. [PMID: 31397669 PMCID: PMC6711708 DOI: 10.7554/elife.49110] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 08/09/2019] [Indexed: 12/18/2022] Open
Abstract
CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by CRISPR-Cas has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function by wide-ranging mechanisms. We show here that the inhibitor AcrVA4 uses a previously undescribed strategy to recognize the L. bacterium Cas12a (LbCas12a) pre-crRNA processing nuclease, forming a Cas12a dimer, and allosterically inhibiting DNA binding. The Ac. species Cas12a (AsCas12a) enzyme, widely used for genome editing applications, contains an ancestral helical bundle that blocks AcrVA4 binding and allows it to escape anti-CRISPR recognition. Using biochemical, microbiological, and human cell editing experiments, we show that Cas12a orthologs can be rendered either sensitive or resistant to AcrVA4 through rational structural engineering informed by evolution. Together, these findings explain a new mode of CRISPR-Cas inhibition and illustrate how structural variability in Cas effectors can drive opportunistic co-evolution of inhibitors by bacteriophage.
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Affiliation(s)
- Gavin J Knott
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Brady F Cress
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Jun-Jie Liu
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Brittney W Thornton
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | | | - Basem Al-Shayeb
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Daniel J Rosenberg
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Graduate Group in BiophysicsUniversity of California, BerkeleyBerkeleyUnited States
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Benjamin A Adler
- UC Berkeley-UCSF Graduate Program in BioengineeringUniversity of California, BerkeleyBerkeleyUnited States
- Department of BioengineeringUniversity of California, BerkeleyBerkeleyUnited States
| | - Marco J Lobba
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
| | - Michael Xu
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
| | - Adam P Arkin
- Department of BioengineeringUniversity of California, BerkeleyBerkeleyUnited States
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
| | - Christof Fellmann
- Gladstone InstitutesSan FranciscoUnited States
- Department of Cellular and Molecular PharmacologyUniversity of California, San FranciscoSan FranciscoUnited States
| | - Jennifer A Doudna
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Gladstone InstitutesSan FranciscoUnited States
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyUnited States
- Department of ChemistryUniversity of California, BerkeleyBerkeleyUnited States
- Innovative Genomics InstituteUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3)University of California, BerkeleyBerkeleyUnited States
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217
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Zhou Y, Millott R, Kim HJ, Peng S, Edwards RA, Skene-Arnold T, Hammel M, Lees-Miller SP, Tainer JA, Holmes CFB, Glover JNM. Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis. Structure 2019; 27:1485-1496.e4. [PMID: 31402222 DOI: 10.1016/j.str.2019.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/14/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
ASPP (apoptosis-stimulating proteins of p53) proteins bind PP-1c (protein phosphatase 1) and regulate p53 impacting cancer cell growth and apoptosis. Here we determine the crystal structure of the oncogenic ASPP protein, iASPP, bound to PP-1c. The structure reveals a 1:1 complex that relies on interactions of the iASPP SILK and RVxF motifs with PP-1c, plus interactions of the PP-1c PxxPxR motif with the iASPP SH3 domain. Small-angle X-ray scattering analyses suggest that the crystal structure undergoes slow interconversion with more extended conformations in solution. We show that iASPP, and the tumor suppressor ASPP2, enhance the catalytic activity of PP-1c against the small-molecule substrate, pNPP as well as p53. The combined results suggest that PxxPxR binding to iASPP SH3 domain is critical for complex formation, and that the modular ASPP-PP-1c interface provides dynamic flexibility that enables functional binding and dephosphorylation of p53 and other diverse protein substrates.
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Affiliation(s)
- Yeyun Zhou
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Robyn Millott
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Hyeong Jin Kim
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shiyun Peng
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Tamara Skene-Arnold
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - 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
| | - Charles F B Holmes
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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218
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Asor R, Selzer L, Schlicksup CJ, Zhao Z, Zlotnick A, Raviv U. Assembly Reactions of Hepatitis B Capsid Protein into Capsid Nanoparticles Follow a Narrow Path through a Complex Reaction Landscape. ACS NANO 2019; 13:7610-7626. [PMID: 31173689 PMCID: PMC7243059 DOI: 10.1021/acsnano.9b00648] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
For many viruses, capsids (biological nanoparticles) assemble to protect genetic material and dissociate to release their cargo. To understand these contradictory properties, we analyzed capsid assembly for hepatitis B virus; an endemic pathogen with an icosahedral, 120-homodimer capsid. We used solution X-ray scattering to examine trapped and equilibrated assembly reactions. To fit experimental results, we generated a library of distinct intermediates, selected by umbrella sampling of Monte Carlo simulations. The number of possible capsid intermediates is immense, ∼1030, yet assembly reactions are rapid and completed with high fidelity. If the huge number of possible intermediates were actually present, maximum entropy analysis shows that assembly reactions would be blocked by an entropic barrier, resulting in incomplete nanoparticles. When an energetic term was applied to select the stable species that dominated the reaction mixture, we found only a few hundred intermediates, mapping out a narrow path through the immense reaction landscape. This is a solution to a viral application of the Levinthal paradox. With the correct energetic term, the match between predicted intermediates and scattering data was striking. The grand canonical free energy landscape for assembly, calibrated by our experimental results, supports a detailed analysis of this complex reaction. There is a narrow range of energies that supports on-path assembly. If association energy is too weak or too strong, progressively more intermediates will be entropically blocked, spilling into paths leading to dissociation or trapped incomplete nanoparticles, respectively. These results are relevant to many viruses and provide a basis for simplifying assembly models and identifying new targets for antiviral intervention. They provide a basis for understanding and designing biological and abiological self-assembly reactions.
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Affiliation(s)
- Roi Asor
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401 , Israel
| | - Lisa Selzer
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
- Department of Genetics , Stanford University School of Medicine , Stanford , California 94305 , United States
| | - Christopher John Schlicksup
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Zhongchao Zhao
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Uri Raviv
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , The Hebrew University of Jerusalem , Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401 , Israel
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219
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Perturbation of the interactions of calmodulin with GRK5 using a natural product chemical probe. Proc Natl Acad Sci U S A 2019; 116:15895-15900. [PMID: 31337679 DOI: 10.1073/pnas.1818547116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G protein-coupled receptor (GPCR) kinases (GRKs) are responsible for initiating desensitization of activated GPCRs. GRK5 is potently inhibited by the calcium-sensing protein calmodulin (CaM), which leads to nuclear translocation of GRK5 and promotion of cardiac hypertrophy. Herein, we report the architecture of the Ca2+·CaM-GRK5 complex determined by small-angle X-ray scattering and negative-stain electron microscopy. Ca2+·CaM binds primarily to the small lobe of the kinase domain of GRK5 near elements critical for receptor interaction and membrane association, thereby inhibiting receptor phosphorylation while activating the kinase for phosphorylation of soluble substrates. To define the role of each lobe of Ca2+·CaM, we utilized the natural product malbrancheamide as a chemical probe to show that the C-terminal lobe of Ca2+·CaM regulates membrane binding while the N-terminal lobe regulates receptor phosphorylation and kinase domain activation. In cells, malbrancheamide attenuated GRK5 nuclear translocation and effectively blocked the hypertrophic response, demonstrating the utility of this natural product and its derivatives in probing Ca2+·CaM-dependent hypertrophy.
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220
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Birtley JR, Alomary M, Zanini E, Antony J, Maben Z, Weaver GC, Von Arx C, Mura M, Marinho AT, Lu H, Morecroft EVN, Karali E, Chayen NE, Tate EW, Jurewicz M, Stern LJ, Recchi C, Gabra H. Inactivating mutations and X-ray crystal structure of the tumor suppressor OPCML reveal cancer-associated functions. Nat Commun 2019; 10:3134. [PMID: 31316070 PMCID: PMC6637204 DOI: 10.1038/s41467-019-10966-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/06/2019] [Indexed: 11/28/2022] Open
Abstract
OPCML, a tumor suppressor gene, is frequently silenced epigenetically in ovarian and other cancers. Here we report, by analysis of databases of tumor sequences, the observation of OPCML somatic missense mutations from various tumor types and the impact of these mutations on OPCML function, by solving the X-ray crystal structure of this glycoprotein to 2.65 Å resolution. OPCML consists of an extended arrangement of three immunoglobulin-like domains and homodimerizes via a network of contacts between membrane-distal domains. We report the generation of a panel of OPCML variants with representative clinical mutations and demonstrate clear phenotypic effects in vitro and in vivo including changes to anchorage-independent growth, interaction with activated cognate receptor tyrosine kinases, cellular migration, invasion in vitro and tumor growth in vivo. Our results suggest that clinically occurring somatic missense mutations in OPCML have the potential to contribute to tumorigenesis in a variety of cancers.
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Affiliation(s)
- James R Birtley
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
- UCB Pharma, Bath Road, Slough, SL1 3WE, UK
| | - Mohammad Alomary
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Elisa Zanini
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Jane Antony
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Zachary Maben
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Grant C Weaver
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Claudia Von Arx
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Manuela Mura
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Aline T Marinho
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Haonan Lu
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Eloise V N Morecroft
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
- Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Evdoxia Karali
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Naomi E Chayen
- Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, SW7 2AZ, UK
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Mollie Jurewicz
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Lawrence J Stern
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.
| | - Chiara Recchi
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK.
| | - Hani Gabra
- Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, Du Cane Road, London, W12 0NN, UK.
- Clinical Discovery Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, SG8 6HB, UK.
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221
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Complementary substrate specificity and distinct quaternary assembly of the Escherichia coli aerobic and anaerobic β-oxidation trifunctional enzyme complexes. Biochem J 2019; 476:1975-1994. [DOI: 10.1042/bcj20190314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 02/03/2023]
Abstract
AbstractThe trifunctional enzyme (TFE) catalyzes the last three steps of the fatty acid β-oxidation cycle. Two TFEs are present in Escherichia coli, EcTFE and anEcTFE. EcTFE is expressed only under aerobic conditions, whereas anEcTFE is expressed also under anaerobic conditions, with nitrate or fumarate as the ultimate electron acceptor. The anEcTFE subunits have higher sequence identity with the human mitochondrial TFE (HsTFE) than with the soluble EcTFE. Like HsTFE, here it is found that anEcTFE is a membrane-bound complex. Systematic enzyme kinetic studies show that anEcTFE has a preference for medium- and long-chain enoyl-CoAs, similar to HsTFE, whereas EcTFE prefers short chain enoyl-CoA substrates. The biophysical characterization of anEcTFE and EcTFE shows that EcTFE is heterotetrameric, whereas anEcTFE is purified as a complex of two heterotetrameric units, like HsTFE. The tetrameric assembly of anEcTFE resembles the HsTFE tetramer, although the arrangement of the two anEcTFE tetramers in the octamer is different from the HsTFE octamer. These studies demonstrate that EcTFE and anEcTFE have complementary substrate specificities, allowing for complete degradation of long-chain enoyl-CoAs under aerobic conditions. The new data agree with the notion that anEcTFE and HsTFE are evolutionary closely related, whereas EcTFE belongs to a separate subfamily.
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222
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Pyles H, Zhang S, De Yoreo JJ, Baker D. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature 2019; 571:251-256. [PMID: 31292559 PMCID: PMC6948101 DOI: 10.1038/s41586-019-1361-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/10/2019] [Indexed: 11/09/2022]
Abstract
The ability of proteins and other macromolecules to interact with inorganic surfaces is critical to biological function. The proteins involved in these interactions are highly charged and often rich in carboxylic acid side chains1-5, but the structures of most protein-inorganic interfaces are unknown. We explored the possibility of systematically designing structured protein-mineral interfaces guided by the example of ice-binding proteins, which present arrays of threonine residues matched to the ice lattice that order clathrate waters into an ice-like structure6. We designed proteins displaying arrays of up to 54 carboxylate residues geometrically matched to the K+ sublattice on muscovite mica (001). At low [K+] individual molecules bind independently to mica in the designed orientations, while at high [K+], the designs form 2D liquid-crystal phases, which accentuate the inherent structural bias in the muscovite lattice to produce protein arrays ordered over tens of millimeters. Incorporation of designed protein-protein interactions preserving the match between the proteins and the K+ lattice led to extended self-assembled structures on mica: designed end-to-end interactions produced micron long single protein-diameter wires, and a designed trimeric interface yielded extensive honeycomb arrays. The nearest neighbor distances in these hexagonal arrays could be set digitally between 7.5 and 15.9 nm with 2.1 nm selectivity by changing the number of repeat units in the monomer. These results demonstrate that protein-inorganic lattice interactions can be systematically programmed and set the stage for designing protein-inorganic hybrid materials.
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Affiliation(s)
- Harley Pyles
- Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Shuai Zhang
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA.,Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA
| | - James J De Yoreo
- Physical Sciences Division, Physical and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA. .,Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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223
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Shaffer R, DeMaria AM, Kagermazova L, Liu Y, Babaei M, Penix S, Cervantes A, Jehle S, Makowski L, Gilmore TD, Whitty A, Allen KN. A Central Region of NF-κB Essential Modulator Is Required for IKKβ-Induced Conformational Change and for Signal Propagation. Biochemistry 2019; 58:2906-2920. [PMID: 31145594 PMCID: PMC9295417 DOI: 10.1021/acs.biochem.8b01316] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
NF-κB essential modulator (NEMO) regulates NF-κB signaling by acting as a scaffold for the kinase IKKβ to direct its activity toward the NF-κB inhibitor, IκBα. Here, we show that a highly conserved central region of NEMO termed the intervening domain (IVD, amino acids 112-195) plays a key role in NEMO function. We determined a structural model of full-length NEMO by small-angle X-ray scattering and show that full-length, wild-type NEMO becomes more compact upon binding of a peptide comprising the NEMO binding domain of IKKβ (amino acids 701-745). Mutation of conserved IVD residues (9SG-NEMO) disrupts this conformational change in NEMO and abolishes the ability of NEMO to propagate NF-κB signaling in cells, although the affinity of 9SG-NEMO for IKKβ compared to that of the wild type is unchanged. On the basis of these results, we propose a model in which the IVD is required for a conformational change in NEMO that is necessary for its ability to direct phosphorylation of IκBα by IKKβ. Our findings suggest a molecular explanation for certain disease-associated mutations within the IVD and provide insight into the role of conformational change in signaling scaffold proteins.
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Affiliation(s)
- Robert Shaffer
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | | | | | - Yuekun Liu
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Milad Babaei
- Department of Biology, Boston University, Boston, MA 02215, USA
| | - Suhaily Penix
- Department of Biology, Boston University, Boston, MA 02215, USA
| | | | - Stefan Jehle
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | | | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Karen N. Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA
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224
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Gabel F, Engilberge S, Pérez J, Girard E. Medical contrast media as possible tools for SAXS contrast variation. IUCRJ 2019; 6:521-525. [PMID: 31316796 PMCID: PMC6608644 DOI: 10.1107/s2052252519005943] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/29/2019] [Indexed: 05/26/2023]
Abstract
Small-angle X-ray scattering (SAXS) is increasingly used to extract structural information from a multitude of soft-matter and biological systems in aqueous solution, including polymers, detergents, lipids, colloids, proteins and RNA/DNA. When SAXS data are recorded at multiple contrasts, i.e. at different electron densities of the solvent, the internal electron-density profile of solubilized molecular systems can be probed. However, contrast-variation SAXS has been limited by the range of electron densities available by conventional agents such as sugars, glycerol and salt, and by the fact that many soft-matter and biological systems are modified in their presence. Here we present a pioneering SAXS contrast-variation study on DDM (n-do-decyl-β-d-malto-pyran-oside) micelles by using two highly electron-rich contrast agents from biomedical imaging which belong to the families of gadolinium-based and iodinated molecules. The two agents, Gd-HPDO3A and iohexol, were allowed to attain modifications of the solvent electron density that are 50 to 100% higher than those obtained for sucrose, and are located between the electron densities of proteins and RNA/DNA. In the case of Gd-HPDO3A, an analysis of the internal micellar structure was possible and compared with results obtained with sucrose. In conclusion, medical contrast agents represent a promising class of molecules for SAXS contrast-variation experiments with potential appli-cations for numerous soft-matter and biological systems, including membrane proteins and protein-RNA/DNA complexes.
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Affiliation(s)
- Frank Gabel
- IBS, CEA, CNRS, UGA, 71 avenue des Martyrs, 38000 Grenoble, France
| | | | - Javier Pérez
- Synchrotron SOLEIL, Saint-Aubin BP 48, 91192 Gif-sur-Yvette, France
| | - Eric Girard
- IBS, CEA, CNRS, UGA, 71 avenue des Martyrs, 38000 Grenoble, France
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225
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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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226
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Chen PC, Shevchuk R, Strnad FM, Lorenz C, Karge L, Gilles R, Stadler AM, Hennig J, Hub JS. Combined Small-Angle X-ray and Neutron Scattering Restraints in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4687-4698. [DOI: 10.1021/acs.jctc.9b00292] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Po-chia Chen
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Roman Shevchuk
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Felix M. Strnad
- Institute for Microbiology and Genetics, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany
| | - Charlotte Lorenz
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Lukas Karge
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Ralph Gilles
- Heinz Maier-Leibnitz Zentrum, Technische Universität München, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute for Complex Systems ICS (ICS-1), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jochen S. Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Campus E2 6, 66123 Saarbrücken, Germany
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227
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Ge J, Remesh SG, Hammel M, Pan S, Mahan AD, Wang S, Wang X. Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling. Structure 2019; 27:1296-1307.e5. [PMID: 31257107 DOI: 10.1016/j.str.2019.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/09/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
The interleukin 1 (IL-1) receptor family, whose members contain three immunoglobulin-like domains (D1-D3) in the extracellular region, is responsible for transmitting pleiotropic signals of IL-1 cytokines. The inter-domain flexibility of IL-1 receptors and its functional roles have not been fully elucidated. In this study, we used small-angle X-ray scattering to show that ligand-binding primary receptors and co-receptors in the family all have inherent inter-domain flexibility due to the D2/D3 linker. Variants of the IL-1RAcP and IL-18Rβ co-receptors with mutated D2/D3 linkers cannot form a cytokine-receptor complex and mediate signaling. Our analysis further revealed that these mutated co-receptors exhibited a changed conformational ensemble, suggesting that loss of function is due to the alteration of receptor dynamics. Taken together, our results demonstrate that the D2/D3 linker is a critical functional determinant of IL-1 receptor and underscore the important roles of the inter-domain flexibility in cytokine/receptor binding and signaling.
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Affiliation(s)
- Jiwan Ge
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Soumya G Remesh
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Si Pan
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Andrew D Mahan
- Janssen Bio Therapeutics, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Shuying Wang
- Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan.
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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228
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Thomas WC, Brooks FP, Burnim AA, Bacik JP, Stubbe J, Kaelber JT, Chen JZ, Ando N. Convergent allostery in ribonucleotide reductase. Nat Commun 2019; 10:2653. [PMID: 31201319 PMCID: PMC6572854 DOI: 10.1038/s41467-019-10568-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/20/2019] [Indexed: 02/04/2023] Open
Abstract
Ribonucleotide reductases (RNRs) use a conserved radical-based mechanism to catalyze the conversion of ribonucleotides to deoxyribonucleotides. Within the RNR family, class Ib RNRs are notable for being largely restricted to bacteria, including many pathogens, and for lacking an evolutionarily mobile ATP-cone domain that allosterically controls overall activity. In this study, we report the emergence of a distinct and unexpected mechanism of activity regulation in the sole RNR of the model organism Bacillus subtilis. Using a hypothesis-driven structural approach that combines the strengths of small-angle X-ray scattering (SAXS), crystallography, and cryo-electron microscopy (cryo-EM), we describe the reversible interconversion of six unique structures, including a flexible active tetramer and two inhibited helical filaments. These structures reveal the conformational gymnastics necessary for RNR activity and the molecular basis for its control via an evolutionarily convergent form of allostery. Ribonucleotide reductase (RNR) catalyzes the conversion of ribonucleotides to deoxyribonucleotides, which is an essential step in DNA synthesis. Here the authors use small-angle X-ray scattering, X-ray crystallography, and cryo-electron microscopy to capture active and inactive forms of the Bacillus subtilis RNR and provide mechanistic insights into a convergent form of allosteric regulation.
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Affiliation(s)
- William C Thomas
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - F Phil Brooks
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Audrey A Burnim
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - John-Paul Bacik
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Jason T Kaelber
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - James Z Chen
- Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Nozomi Ando
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA. .,Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA.
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229
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Fox NG, Yu X, Feng X, Bailey HJ, Martelli A, Nabhan JF, Strain-Damerell C, Bulawa C, Yue WW, Han S. Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism. Nat Commun 2019; 10:2210. [PMID: 31101807 PMCID: PMC6525205 DOI: 10.1038/s41467-019-09989-y] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022] Open
Abstract
The core machinery for de novo biosynthesis of iron-sulfur clusters (ISC), located in the mitochondria matrix, is a five-protein complex containing the cysteine desulfurase NFS1 that is activated by frataxin (FXN), scaffold protein ISCU, accessory protein ISD11, and acyl-carrier protein ACP. Deficiency in FXN leads to the loss-of-function neurodegenerative disorder Friedreich's ataxia (FRDA). Here the 3.2 Å resolution cryo-electron microscopy structure of the FXN-bound active human complex, containing two copies of the NFS1-ISD11-ACP-ISCU-FXN hetero-pentamer, delineates the interactions of FXN with other component proteins of the complex. FXN binds at the interface of two NFS1 and one ISCU subunits, modifying the local environment of a bound zinc ion that would otherwise inhibit NFS1 activity in complexes without FXN. Our structure reveals how FXN facilitates ISC production through stabilizing key loop conformations of NFS1 and ISCU at the protein-protein interfaces, and suggests how FRDA clinical mutations affect complex formation and FXN activation.
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Affiliation(s)
- Nicholas G Fox
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
- Merck & Co, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Xiaodi Yu
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
- SMPS, Janssen Research and Development, 1400 McKean Rd, Spring House, PA, 19477, USA
| | - Xidong Feng
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA
| | - Henry J Bailey
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Alain Martelli
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Joseph F Nabhan
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Claire Strain-Damerell
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK
| | - Christine Bulawa
- Rare Disease Research Unit, Worldwide Research and Development, Pfizer Inc., 610 Main Street, Cambridge, MA, 02139, USA
| | - Wyatt W Yue
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Seungil Han
- Discovery Sciences, Worldwide Research and Development, Pfizer Inc., Eastern Point Road, Groton, CT, 06340, USA.
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230
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Powers KT, Gildenberg MS, Washington MT. Modeling Conformationally Flexible Proteins With X-ray Scattering and Molecular Simulations. Comput Struct Biotechnol J 2019; 17:570-578. [PMID: 31073392 PMCID: PMC6495069 DOI: 10.1016/j.csbj.2019.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/15/2019] [Accepted: 04/17/2019] [Indexed: 01/03/2023] Open
Abstract
Proteins and protein complexes with high conformational flexibility participate in a wide range of biological processes. These processes include genome maintenance, gene expression, signal transduction, cell cycle regulation, and many others. Gaining a structural understanding of conformationally flexible proteins and protein complexes is arguably the greatest problem facing structural biologists today. Over the last decade, some progress has been made toward understanding the conformational flexibility of such systems using hybrid approaches. One particularly fruitful strategy has been the combination of small-angle X-ray scattering (SAXS) and molecular simulations. In this article, we provide a brief overview of SAXS and molecular simulations and then discuss two general approaches for combining SAXS data and molecular simulations: minimal ensemble approaches and full ensemble approaches. In minimal ensemble approaches, one selects a minimal ensemble of structures from the simulations that best fit the SAXS data. In full ensemble approaches, one validates a full ensemble of structures from the simulations using SAXS data. We argue that full ensemble models are more realistic than minimal ensemble searches models and that full ensemble approaches should be used wherever possible.
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Key Words
- BD, Brownian dynamics
- CG, coarse-grained
- Cryo-EM, cryo-electron microscopy
- DNA polymerase
- DNA replication
- Dmax, maximal distance
- LD, Langevin dynamics
- MD, molecular dynamics
- Minimal ensemble search
- NMR, nuclear magnetic resonance
- PCNA, proliferating cell nuclear antigen
- Pol η, DNA polymerase eta
- Protein structure
- RPA, replication protein A
- Rg, radius of gyration
- SANS
- SANS, small-angle neutron scattering
- SAXS
- SAXS, small-angle X-ray scattering
- SEC, size exclusion chromatography
- SUMO, small ubiquitin-like modifie
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Affiliation(s)
| | | | - M. Todd Washington
- Department of Biochemistry, University of Iowa College of Medicine, Iowa City, IA 52242-1109, United States of America
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231
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Commonly used FRET fluorophores promote collapse of an otherwise disordered protein. Proc Natl Acad Sci U S A 2019; 116:8889-8894. [PMID: 30992378 DOI: 10.1073/pnas.1813038116] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt in the absence of denaturant remain controversial. We developed an analysis procedure for small-angle X-ray scattering (SAXS) profiles and used it to demonstrate that even relatively hydrophobic IDPs remain nearly as expanded in water as they are in high denaturant concentrations. In contrast, as demonstrated here, most fluorescence resonance energy transfer (FRET) measurements have indicated that relatively hydrophobic IDPs contract significantly in the absence of denaturant. We use two independent approaches to further explore this controversy. First, using SAXS we show that fluorophores employed in FRET can contribute to the observed discrepancy. Specifically, we find that addition of Alexa-488 to a normally expanded IDP causes contraction by an additional 15%, a value in reasonable accord with the contraction reported in FRET-based studies. Second, using our simulations and analysis procedure to accurately extract both the radius of gyration (Rg) and end-to-end distance (Ree) from SAXS profiles, we tested the recent suggestion that FRET and SAXS results can be reconciled if the Rg and Ree are "uncoupled" (i.e., no longer simply proportional), in contrast to the case for random walk homopolymers. We find, however, that even for unfolded proteins, these two measures of unfolded state dimensions remain proportional. Together, these results suggest that improved analysis procedures and a correction for significant, fluorophore-driven interactions are sufficient to reconcile prior SAXS and FRET studies, thus providing a unified picture of the nature of unfolded polypeptide chains in the absence of denaturant.
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232
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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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233
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Ramis R, Ortega-Castro J, Casasnovas R, Mariño L, Vilanova B, Adrover M, Frau J. A Coarse-Grained Molecular Dynamics Approach to the Study of the Intrinsically Disordered Protein α-Synuclein. J Chem Inf Model 2019; 59:1458-1471. [DOI: 10.1021/acs.jcim.8b00921] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rafael Ramis
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Joaquín Ortega-Castro
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Rodrigo Casasnovas
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Laura Mariño
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Bartolomé Vilanova
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Miquel Adrover
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
| | - Juan Frau
- Institut Universitari d’Investigació en Ciències de la Salut (IUNICS), Departament de Química, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
- Institut d’Investigació Sanitària Illes Balears (IdISBa), 07120 Palma de Mallorca, Spain
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234
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Paissoni C, Jussupow A, Camilloni C. Martini bead form factors for nucleic acids and their application in the refinement of protein–nucleic acid complexes against SAXS data. J Appl Crystallogr 2019. [DOI: 10.1107/s1600576719002450] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The use of small-angle X-ray scattering (SAXS) in combination with molecular dynamics simulation is hampered by its heavy computational cost. The calculation of SAXS from atomic structures can be speeded up by using a coarse-grain representation of the structure. Following the work of Niebling, Björling & Westenhoff [J. Appl. Cryst. (2014), 47, 1190–1198], the Martini bead form factors for nucleic acids have been derived and then implemented, together with those previously determined for proteins, in the publicly available PLUMED library. A hybrid multi-resolution strategy has also been implemented to perform SAXS restrained simulations at atomic resolution by calculating the virtual positions of the Martini beads on the fly and using them for the calculation of SAXS. The accuracy and efficiency of the method are demonstrated by refining the structure of two protein–nucleic acid complexes. Instrumental for this result is the use of metainference, which allows the consideration and alleviation of the approximations at play in the present SAXS calculations.
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235
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Weiel M, Reinartz I, Schug A. Rapid interpretation of small-angle X-ray scattering data. PLoS Comput Biol 2019; 15:e1006900. [PMID: 30901335 PMCID: PMC6447237 DOI: 10.1371/journal.pcbi.1006900] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 04/03/2019] [Accepted: 02/24/2019] [Indexed: 12/20/2022] Open
Abstract
The fundamental aim of structural analyses in biophysics is to reveal a mutual relation between a molecule’s dynamic structure and its physiological function. Small-angle X-ray scattering (SAXS) is an experimental technique for structural characterization of macromolecules in solution and enables time-resolved analysis of conformational changes under physiological conditions. As such experiments measure spatially averaged low-resolution scattering intensities only, the sparse information obtained is not sufficient to uniquely reconstruct a three-dimensional atomistic model. Here, we integrate the information from SAXS into molecular dynamics simulations using computationally efficient native structure-based models. Dynamically fitting an initial structure towards a scattering intensity, such simulations produce atomistic models in agreement with the target data. In this way, SAXS data can be rapidly interpreted while retaining physico-chemical knowledge and sampling power of the underlying force field. We demonstrate our method’s performance using the example of three protein systems. Simulations are faster than full molecular dynamics approaches by more than two orders of magnitude and consistently achieve comparable accuracy. Computational demands are reduced sufficiently to run the simulations on commodity desktop computers instead of high-performance computing systems. These results underline that scattering-guided structure-based simulations provide a suitable framework for rapid early-stage refinement of structures towards SAXS data with particular focus on minimal computational resources and time. Proteins are the molecular nanomachines in biological cells and thus vital to any known form of life. From the evolutionary perspective, viable protein structure emerges on the basis of a ‘form-follows-function’ principle. A protein’s designated function is inextricably linked to dynamic conformational changes, which can be observed by small-angle X-ray scattering. Intensities from SAXS contain low-resolution information on the protein’s shape at different steps of its functional cycle. We are interested in directly getting an atomistic model of this encoded structure. One powerful approach is to include the experimental data into computational simulations of the protein’s function-related physical motions. We combine scattering intensities with coarse-grained native structure-based models. These models are computationally highly efficient yet describe the system’s dynamics realistically. Here, we present our method for rapid interpretation of scattering intensities from SAXS to derive structural models, using minimal computational resources and time.
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Affiliation(s)
- Marie Weiel
- Department of Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Ines Reinartz
- Department of Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Alexander Schug
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Institute for Advanced Simulation, Jülich Supercomputing Center, Jülich, Germany
- * E-mail:
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236
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Chan-Yao-Chong M, Durand D, Ha-Duong T. Molecular Dynamics Simulations Combined with Nuclear Magnetic Resonance and/or Small-Angle X-ray Scattering Data for Characterizing Intrinsically Disordered Protein Conformational Ensembles. J Chem Inf Model 2019; 59:1743-1758. [PMID: 30840442 DOI: 10.1021/acs.jcim.8b00928] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The concept of intrinsically disordered proteins (IDPs) has emerged relatively slowly, but over the past 20 years, it has become an intense research area in structural biology. Indeed, because of their considerable flexibility and structural heterogeneity, the determination of IDP conformational ensemble is particularly challenging and often requires a combination of experimental measurements and computational approaches. With the improved accuracy of all-atom force fields and the increasing computing performances, molecular dynamics (MD) simulations have become more and more reliable to generate realistic conformational ensembles. And the combination of MD simulations with experimental approaches, such as nuclear magnetic resonance (NMR) and/or small-angle X-ray scattering (SAXS) allows one to converge toward a more accurate and exhaustive description of IDP structures. In this Review, we discuss the state of the art of MD simulations of IDP conformational ensembles, with a special focus on studies that back-calculated and directly compared theoretical and experimental NMR or SAXS observables, such as chemical shifts (CS), 3J-couplings (3Jc), residual dipolar couplings (RDC), or SAXS intensities. We organize the review in three parts. In the first section, we discuss the studies which used NMR and/or SAXS data to test and validate the development of force fields or enhanced sampling techniques. In the second part, we explore different methods for the refinement of MD-derived structural ensembles, such as NMR or SAXS data-restrained MD simulations or ensemble reweighting to better fit experiments. Finally, we survey some recent studies combining MD simulations with NMR and/or SAXS measurements to investigate the relationship between IDP conformational ensemble and biological activity, as well as their implication in human diseases. From this review, we noticed that quite a few studies compared MD-generated conformational ensembles with both NMR and SAXS measurements to validate IDP structures at both local and global levels. Yet, beside the IDP propensity to form local secondary structures, their dynamic extension or compactness also appears important for their activity. Thus, we believe that a close synergy between MD simulations, NMR, and SAXS experiments would be greatly appropriate to address the challenges of characterizing the disordered structures of proteins and their complexes, relative to their biological functions.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud , Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex, France
| | - Tâp Ha-Duong
- BioCIS, Université Paris-Sud, CNRS , Université Paris-Saclay , 92290 Châtenay-Malabry , France
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237
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Panmanee J, Bradley-Clarke J, Mato JM, O'Neill PM, Antonyuk SV, Hasnain SS. Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory β subunit and quinolone-based compounds. FEBS J 2019; 286:2135-2154. [PMID: 30776190 PMCID: PMC6850014 DOI: 10.1111/febs.14790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/17/2019] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
Methylation is an underpinning process of life and provides control for biological processes such as DNA synthesis, cell growth, and apoptosis. Methionine adenosyltransferases (MAT) produce the cellular methyl donor, S‐Adenosylmethionine (SAMe). Dysregulation of SAMe level is a relevant event in many diseases, including cancers such as hepatocellular carcinoma and colon cancer. In addition, mutation of Arg264 in MATα1 causes isolated persistent hypermethioninemia, which is characterized by low activity of the enzyme in liver and high level of plasma methionine. In mammals, MATα1/α2 and MATβV1/V2 are the catalytic and the major form of regulatory subunits, respectively. A gating loop comprising residues 113–131 is located beside the active site of catalytic subunits (MATα1/α2) and provides controlled access to the active site. Here, we provide evidence of how the gating loop facilitates the catalysis and define some of the key elements that control the catalytic efficiency. Mutation of several residues of MATα2 including Gln113, Ser114, and Arg264 lead to partial or total loss of enzymatic activity, demonstrating their critical role in catalysis. The enzymatic activity of the mutated enzymes is restored to varying degrees upon complex formation with MATβV1 or MATβV2, endorsing its role as an allosteric regulator of MATα2 in response to the levels of methionine or SAMe. Finally, the protein–protein interacting surface formed in MATα2:MATβ complexes is explored to demonstrate that several quinolone‐based compounds modulate the activity of MATα2 and its mutants, providing a rational for chemical design/intervention responsive to the level of SAMe in the cellular environment. Enzymes Methionine adenosyltransferase (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/5/1/6.html). Database Structural data are available in the RCSB PDB database under the PDB ID http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FBN (Q113A), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FBP (S114A: P22121), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FBO (S114A: I222), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FCB (P115G), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FCD (R264A), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6FAJ (wtMATα2: apo), http://www.rcsb.org/pdb/search/structidSearch.do?structureId=6G6R (wtMATα2: holo)
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Affiliation(s)
- Jiraporn Panmanee
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Jack Bradley-Clarke
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - Jose M Mato
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Parque Tecnologico de Bizkaia, Derio, Spain
| | - Paul M O'Neill
- Department of Chemistry, School of Physical Sciences, University of Liverpool, UK
| | - Svetlana V Antonyuk
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
| | - S Samar Hasnain
- Molecular Biophysics Group, Institute of Integrative Biology, Faculty of Health and Life Sciences, University of Liverpool, UK
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238
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Braitbard M, Schneidman-Duhovny D, Kalisman N. Integrative Structure Modeling: Overview and Assessment. Annu Rev Biochem 2019; 88:113-135. [PMID: 30830798 DOI: 10.1146/annurev-biochem-013118-111429] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Integrative structure modeling computationally combines data from multiple sources of information with the aim of obtaining structural insights that are not revealed by any single approach alone. In the first part of this review, we survey the commonly used sources of structural information and the computational aspects of model building. Throughout the past decade, integrative modeling was applied to various biological systems, with a focus on large protein complexes. Recent progress in the field of cryo-electron microscopy (cryo-EM) has resolved many of these complexes to near-atomic resolution. In the second part of this review, we compare a range of published integrative models with their higher-resolution counterparts with the aim of critically assessing their accuracy. This comparison gives a favorable view of integrative modeling and demonstrates its ability to yield accurate and informative results. We discuss possible roles of integrative modeling in the new era of cryo-EM and highlight future challenges and directions.
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Affiliation(s)
- Merav Braitbard
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Dina Schneidman-Duhovny
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel; .,School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
| | - Nir Kalisman
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel;
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239
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Chan-Yao-Chong M, Deville C, Pinet L, van Heijenoort C, Durand D, Ha-Duong T. Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data. Biophys J 2019; 116:1216-1227. [PMID: 30878202 DOI: 10.1016/j.bpj.2019.02.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/14/2019] [Accepted: 02/19/2019] [Indexed: 11/19/2022] Open
Abstract
Because of their large conformational heterogeneity, structural characterization of intrinsically disordered proteins (IDPs) is very challenging using classical experimental methods alone. In this study, we use NMR and small-angle x-ray scattering (SAXS) data with multiple molecular dynamics (MD) simulations to describe the conformational ensemble of the fully disordered verprolin homology domain of the neural Aldrich syndrome protein involved in the regulation of actin polymerization. First, we studied several back-calculation software of SAXS scattering intensity and optimized the adjustable parameters to accurately calculate the SAXS intensity from an atomic structure. We also identified the most appropriate force fields for MD simulations of this IDP. Then, we analyzed four conformational ensembles of neural Aldrich syndrome protein verprolin homology domain, two generated with the program flexible-meccano with or without NMR-derived information as input and two others generated by MD simulations with two different force fields. These four conformational ensembles were compared to available NMR and SAXS data for validation. We found that MD simulations with the AMBER-03w force field and the TIP4P/2005s water model are able to correctly describe the conformational ensemble of this 67-residue IDP at both local and global level.
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Affiliation(s)
- Maud Chan-Yao-Chong
- BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France; Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Célia Deville
- IGBMC, University of Strasbourg, CNRS UMR 7104, Illkirch, France
| | - Louise Pinet
- ICSN, CNRS UPR 2301, University Paris-Saclay, Gif-sur-Yvette, France
| | | | - Dominique Durand
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Tâp Ha-Duong
- BioCIS, University Paris-Sud, CNRS UMR 8076, University Paris-Saclay, Châtenay-Malabry, France.
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240
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, Raviv U. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. J Appl Crystallogr 2019; 52:219-242. [PMID: 31057345 PMCID: PMC6495662 DOI: 10.1107/s1600576718018046] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 11/10/2022] Open
Abstract
This paper presents the computer program D+ (https://scholars.huji.ac.il/uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars.huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/master/).
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Affiliation(s)
- Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401 Jerusalem, Israel
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Lea Fink
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Roee Tekoah
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Daniel Khaykelson
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Amos Fellig
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
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241
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Ginsburg A, Ben-Nun T, Asor R, Shemesh A, Fink L, Tekoah R, Levartovsky Y, Khaykelson D, Dharan R, Fellig A, Raviv U. D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures. J Appl Crystallogr 2019; 52:219-242. [PMID: 31057345 DOI: 10.26434/chemrxiv.7012622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 12/20/2018] [Indexed: 05/23/2023] Open
Abstract
This paper presents the computer program D+ (https://scholars.huji.ac.il/uriraviv/book/d-0), where the reciprocal-grid (RG) algorithm is implemented. D+ efficiently computes, at high-resolution, the X-ray scattering curves from complex structures that are isotropically distributed in random orientations in solution. Structures are defined in hierarchical trees in which subunits can be represented by geometric or atomic models. Repeating subunits can be docked into their assembly symmetries, describing their locations and orientations in space. The scattering amplitude of the entire structure can be calculated by computing the amplitudes of the basic subunits on 3D reciprocal-space grids, moving up in the hierarchy, calculating the RGs of the larger structures, and repeating this process for all the leaves and nodes of the tree. For very large structures (containing over 100 protein subunits), a hybrid method can be used to avoid numerical artifacts. In the hybrid method, only grids of smaller subunits are summed and used as subunits in a direct computation of the scattering amplitude. D+ can accurately analyze both small- and wide-angle solution X-ray scattering data. This article describes how D+ applies the RG algorithm, accounts for rotations and translations of subunits, processes atomic models, accounts for the contribution of the solvent as well as the solvation layer of complex structures in a scalable manner, writes and accesses RGs, interpolates between grid points, computes numerical integrals, enables the use of scripts to define complicated structures, applies fitting algorithms, accounts for several coexisting uncorrelated populations, and accelerates computations using GPUs. D+ may also account for different X-ray energies to analyze anomalous solution X-ray scattering data. An accessory tool that can identify repeating subunits in a Protein Data Bank file of a complex structure is provided. The tool can compute the orientation and translation of repeating subunits needed for exploiting the advantages of the RG algorithm in D+. A Python wrapper (https://scholars.huji.ac.il/uriraviv/book/python-api) is also available, enabling more advanced computations and integration of D+ with other computational tools. Finally, a large number of tests are presented. The results of D+ are compared with those of other programs when possible, and the use of D+ to analyze solution scattering data from dynamic microtubule structures with different protofilament number is demonstrated. D+ and its source code are freely available for academic users and developers (https://bitbucket.org/uriraviv/public-dplus/src/master/).
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Affiliation(s)
- Avi Ginsburg
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Tal Ben-Nun
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401 Jerusalem, Israel
| | - Roi Asor
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Asaf Shemesh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Lea Fink
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Roee Tekoah
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Yehonatan Levartovsky
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Daniel Khaykelson
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Raviv Dharan
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Amos Fellig
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
| | - Uri Raviv
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
- Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, 9190401, Jerusalem, Israel
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242
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Nandwani N, Surana P, Negi H, Mascarenhas NM, Udgaonkar JB, Das R, Gosavi S. A five-residue motif for the design of domain swapping in proteins. Nat Commun 2019; 10:452. [PMID: 30692525 PMCID: PMC6349918 DOI: 10.1038/s41467-019-08295-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 12/28/2018] [Indexed: 11/09/2022] Open
Abstract
Domain swapping is the process by which identical monomeric proteins exchange structural elements to generate dimers/oligomers. Although engineered domain swapping is a compelling strategy for protein assembly, its application has been limited due to the lack of simple and reliable design approaches. Here, we demonstrate that the hydrophobic five-residue 'cystatin motif' (QVVAG) from the domain-swapping protein Stefin B, when engineered into a solvent-exposed, tight surface loop between two β-strands prevents the loop from folding back upon itself, and drives domain swapping in non-domain-swapping proteins. High-resolution structural studies demonstrate that engineering the QVVAG stretch independently into various surface loops of four structurally distinct non-domain-swapping proteins enabled the design of different modes of domain swapping in these proteins, including single, double and open-ended domain swapping. These results suggest that the introduction of the QVVAG motif can be used as a mutational approach for engineering domain swapping in diverse β-hairpin proteins.
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Affiliation(s)
- Neha Nandwani
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Parag Surana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Hitendra Negi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.,Sastra University, Thanjavur, 613402, India
| | - Nahren M Mascarenhas
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.,Sacred Heart College, Tirupattur, Tamil Nadu, 635601, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India. .,Indian Institute of Science Education and Research, Pune, 411008, India.
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
| | - Shachi Gosavi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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243
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Latham AP, Zhang B. Improving Coarse-Grained Protein Force Fields with Small-Angle X-ray Scattering Data. J Phys Chem B 2019; 123:1026-1034. [PMID: 30620594 DOI: 10.1021/acs.jpcb.8b10336] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Small-angle X-ray scattering (SAXS) experiments provide valuable structural data for biomolecules in solution. We develop a highly efficient maximum entropy approach to fit SAXS data by introducing minimal biases to a coarse-grained protein force field, the associative memory, water mediated, structure, and energy model (AWSEM). We demonstrate that the resulting force field, AWSEM-SAXS, succeeds in reproducing scattering profiles and models protein structures with shapes that are in much better agreement with experimental results. Quantitative metrics further reveal a modest, but consistent, improvement in the accuracy of modeled structures when SAXS data are incorporated into the force field. Additionally, when applied to a multiconformational protein, we find that AWSEM-SAXS is able to recover the population of different protein conformations from SAXS data alone. We, therefore, conclude that the maximum entropy approach is effective in fine-tuning the force field to better characterize both protein structure and conformational fluctuation.
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Affiliation(s)
- Andrew P Latham
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Bin Zhang
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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244
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Hutchinson JA, Hamley IW, Torras J, Alemán C, Seitsonen J, Ruokolainen J. Self-Assembly of Lipopeptides Containing Short Peptide Fragments Derived from the Gastrointestinal Hormone PYY 3-36: From Micelles to Amyloid Fibrils. J Phys Chem B 2019; 123:614-621. [PMID: 30609361 PMCID: PMC7005981 DOI: 10.1021/acs.jpcb.8b11097] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We
investigate the impact of lipidation on the self-assembly of
two peptide fragments from the gastrointestinal peptide hormone PYY3–36. The lipopeptides C16IKPEAP and C16IKPEAPGE contain the first 6 and 8 amino acid residues, respectively,
from the PYY3–36 peptide sequence, with a palmitoyl
C16 tail attached at the N-terminus. These lipopeptides
form spherical micelles in aqueous solution, above a critical micelle
concentration (cmc), which is pH-dependent. Modeling of small-angle
X-ray scattering data along with molecular dynamics simulations shows
the formation of micelles with a hydrophobic interior and a well-hydrated
exterior. The lipopeptides have a disordered conformation over the
pH and temperature ranges studied. The cmc is found to be independent
of temperature, pointing to athermal micellization. In contrast to
the presence of hydrated micelles in solution, β-sheet amyloid
fibrils form in dried samples. Thus, the nanostructure of lipidated
PYY3–36 fragment peptides can be tuned by control
of pH or concentration, for future applications.
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Affiliation(s)
- Jessica A Hutchinson
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Ian W Hamley
- Department of Chemistry , University of Reading , Whiteknights , Reading RG6 6AD , United Kingdom
| | - Juan Torras
- Department of Chemical Engineering and Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya, Escola d'Enginyeria de Barcelona Est (EEBE) Campus Diagonal Besòs , C/Eduard Maristany 10-14 , 08019 Barcelona , Spain
| | - Carlos Alemán
- Department of Chemical Engineering and Barcelona Research Center for Multiscale Science and Engineering , Universitat Politècnica de Catalunya, Escola d'Enginyeria de Barcelona Est (EEBE) Campus Diagonal Besòs , C/Eduard Maristany 10-14 , 08019 Barcelona , Spain
| | - Jani Seitsonen
- Nanomicroscopy Center , Aalto University , Puumiehenkuja 2 , FIN-02150 Espoo , Finland
| | - Janne Ruokolainen
- Nanomicroscopy Center , Aalto University , Puumiehenkuja 2 , FIN-02150 Espoo , Finland
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245
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Fedorov BA, Smirnov AV, Yaroshenko VV, Porozov YB. SASCUBE: An Updated Method of Cubes for Calculation of the Intensity of X-Ray Scattering by Biopolymers in Solution. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350919010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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246
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Matsuo T, Kono F, Fujiwara S. Effects of the cardiomyopathy-causing E244D mutation of troponin T on the structures of cardiac thin filaments studied by small-angle X-ray scattering. J Struct Biol 2018; 205:196-205. [PMID: 30599212 DOI: 10.1016/j.jsb.2018.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/07/2018] [Accepted: 12/10/2018] [Indexed: 02/04/2023]
Abstract
Small-angle X-ray scattering experiments were carried out to investigate the structural changes of cardiac thin filaments induced by the cardiomyopathy-causing E244D mutation in troponin T (TnT). We examined native thin filaments (NTF) from a bovine heart, reconstituted thin filaments containing human cardiac wild-type Tn (WTF), and filaments containing the E244D mutant of Tn (DTF), in the absence and presence of Ca2+. Analysis by model calculation showed that upon Ca2+-activation, tropomyosin (Tm) and Tn in the WTF and NTF moved together in a direction to expose myosin-binding sites on actin. On the other hand, Tm and Tn of the DTF moved in the opposite directions to each other upon Ca2+-activation. These movements caused Tm to expose more myosin-binding sites on actin than the WTF, suggesting that the affinity of myosin for actin is higher for the DTF. Thus, the mutation-induced structural changes in thin filaments would increase the number of myosin molecules bound to actin compared with the WTF, resulting in the force enhancement observed for the E244D mutation.
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Affiliation(s)
- Tatsuhito Matsuo
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Naka-Gun, Ibaraki 319-1106, Japan
| | - Fumiaki Kono
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Naka-Gun, Ibaraki 319-1106, Japan
| | - Satoru Fujiwara
- Quantum Beam Science Research Directorate, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Naka-Gun, Ibaraki 319-1106, Japan.
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247
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Programmable design of orthogonal protein heterodimers. Nature 2018; 565:106-111. [PMID: 30568301 DOI: 10.1038/s41586-018-0802-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 11/08/2018] [Indexed: 11/09/2022]
Abstract
Specificity of interactions between two DNA strands, or between protein and DNA, is often achieved by varying bases or side chains coming off the DNA or protein backbone-for example, the bases participating in Watson-Crick pairing in the double helix, or the side chains contacting DNA in TALEN-DNA complexes. By contrast, specificity of protein-protein interactions usually involves backbone shape complementarity1, which is less modular and hence harder to generalize. Coiled-coil heterodimers are an exception, but the restricted geometry of interactions across the heterodimer interface (primarily at the heptad a and d positions2) limits the number of orthogonal pairs that can be created simply by varying side-chain interactions3,4. Here we show that protein-protein interaction specificity can be achieved using extensive and modular side-chain hydrogen-bond networks. We used the Crick generating equations5 to produce millions of four-helix backbones with varying degrees of supercoiling around a central axis, identified those accommodating extensive hydrogen-bond networks, and used Rosetta to connect pairs of helices with short loops and to optimize the remainder of the sequence. Of 97 such designs expressed in Escherichia coli, 65 formed constitutive heterodimers, and the crystal structures of four designs were in close agreement with the computational models and confirmed the designed hydrogen-bond networks. In cells, six heterodimers were fully orthogonal, and in vitro-following mixing of 32 chains from 16 heterodimer designs, denaturation in 5 M guanidine hydrochloride and reannealing-almost all of the interactions observed by native mass spectrometry were between the designed cognate pairs. The ability to design orthogonal protein heterodimers should enable sophisticated protein-based control logic for synthetic biology, and illustrates that nature has not fully explored the possibilities for programmable biomolecular interaction modalities.
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248
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De-la-Torre P, Choudhary D, Araya-Secchi R, Narui Y, Sotomayor M. A Mechanically Weak Extracellular Membrane-Adjacent Domain Induces Dimerization of Protocadherin-15. Biophys J 2018; 115:2368-2385. [PMID: 30527337 PMCID: PMC6302040 DOI: 10.1016/j.bpj.2018.11.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/01/2018] [Accepted: 11/05/2018] [Indexed: 10/27/2022] Open
Abstract
The cadherin superfamily of proteins is defined by the presence of extracellular cadherin (EC) "repeats" that engage in protein-protein interactions to mediate cell-cell adhesion, cell signaling, and mechanotransduction. The extracellular domains of nonclassical cadherins often have a large number of EC repeats along with other subdomains of various folds. Protocadherin-15 (PCDH15), a protein component of the inner-ear tip link filament essential for mechanotransduction, has 11 EC repeats and a membrane adjacent domain (MAD12) of atypical fold. Here we report the crystal structure of a pig PCDH15 fragment including EC10, EC11, and MAD12 in a parallel dimeric arrangement. MAD12 has a unique molecular architecture and folds as a ferredoxin-like domain similar to that found in the nucleoporin protein Nup54. Analytical ultracentrifugation experiments along with size-exclusion chromatography coupled to multiangle laser light scattering and small-angle x-ray scattering corroborate the crystallographic dimer and show that MAD12 induces parallel dimerization of PCDH15 near its membrane insertion point. In addition, steered molecular dynamics simulations suggest that MAD12 is mechanically weak and may unfold before tip-link rupture. Sequence analyses and structural modeling predict the existence of similar domains in cadherin-23, protocadherin-24, and the "giant" FAT and CELSR cadherins, indicating that some of them may also exhibit MAD-induced parallel dimerization.
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Affiliation(s)
- Pedro De-la-Torre
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Deepanshu Choudhary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Raul Araya-Secchi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Structural Biophysics, Section for Neutron and X-ray Science, Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yoshie Narui
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.
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249
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Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L, Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K, Wiedemann N, Schanda P. Structural Basis of Membrane Protein Chaperoning through the Mitochondrial Intermembrane Space. Cell 2018; 175:1365-1379.e25. [PMID: 30445040 PMCID: PMC6242696 DOI: 10.1016/j.cell.2018.10.039] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/16/2018] [Accepted: 10/15/2018] [Indexed: 12/04/2022]
Abstract
The exchange of metabolites between the mitochondrial matrix and the cytosol depends on β-barrel channels in the outer membrane and α-helical carrier proteins in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones escort these proteins through the intermembrane space, but the structural and mechanistic details remain elusive. We have used an integrated structural biology approach to reveal the functional principle of TIM chaperones. Multiple clamp-like binding sites hold the mitochondrial membrane proteins in a translocation-competent elongated form, thus mimicking characteristics of co-translational membrane insertion. The bound preprotein undergoes conformational dynamics within the chaperone binding clefts, pointing to a multitude of dynamic local binding events. Mutations in these binding sites cause cell death or growth defects associated with impairment of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial "transfer-chaperone" system is able to guide α-helical and β-barrel membrane proteins in a "nascent chain-like" conformation through a ribosome-free compartment.
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Affiliation(s)
- Katharina Weinhäupl
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Caroline Lindau
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Audrey Hessel
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Yong Wang
- Structural Biology and NMR Laboratory, the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Conny Schütze
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Tobias Jores
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Laura Melchionda
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Birgit Schönfisch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Hubert Kalbacher
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Beate Bersch
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Martha Brennich
- European Molecular Biology Laboratory, 38042 Grenoble, France
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nils Wiedemann
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Paul Schanda
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 71 Avenue des Martyrs, 38000 Grenoble, France.
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250
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Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun 2018; 9:4542. [PMID: 30382099 PMCID: PMC6208384 DOI: 10.1038/s41467-018-06942-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 12/24/2022] Open
Abstract
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. The DIR2s RNA aptamer activates the fluorescence of cyanine dyes allowing detection of two well-resolved emission colors. Here authors solve the crystal structures of the apo and OTB-SO3 fluorophore-bound DIR2s and show how the fluorophore ligand is bound.
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Affiliation(s)
- Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Artur Laski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaohong Tan
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Tudor P Constantin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Alan S Waggoner
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bruce A Armitage
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
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