1
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Chen Z, Antoni FA. Human adenylyl cyclase 9 is auto-stimulated by its isoform-specific C-terminal domain. Life Sci Alliance 2023; 6:e202201791. [PMID: 36657828 PMCID: PMC9873982 DOI: 10.26508/lsa.202201791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
Human transmembrane adenylyl cyclase 9 (AC9) is not regulated by heterotrimeric G proteins. Key to the resistance to stimulation by Gs-coupled receptors (GsRs) is auto-inhibition by the COOH-terminal domain (C2b). The present study investigated the role of the C2b domain in the regulation of cyclic AMP production by AC9 in HEK293FT cells expressing the GloSensor22F cyclic AMP-reporter protein. Surprisingly, we found C2b to be essential for sustaining the basal output of cyclic AMP by AC9. A human mutation (E326D) in the parallel coiled-coil formed by the signalling helices of AC9 dramatically increased basal activity, which was also dependent on the C2b domain. Intriguingly, the same mutation enabled stimulation of AC9 by GsRs. In summary, auto-regulation by the C2b domain of AC9 sustains its basal activity and quenches activation by GsR. Thus, AC9 appears to be tailored to support constitutive activation of cyclic AMP effector systems. A switch from this paradigm to stimulation by GsRs may be occasioned by conformational changes at the coiled-coil or removal of the C2b domain.
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Affiliation(s)
- Zhihao Chen
- Centre for Discovery Brain Sciences, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
| | - Ferenc A Antoni
- Centre for Discovery Brain Sciences, Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh, UK
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2
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Qing R, Hao S, Smorodina E, Jin D, Zalevsky A, Zhang S. Protein Design: From the Aspect of Water Solubility and Stability. Chem Rev 2022; 122:14085-14179. [PMID: 35921495 PMCID: PMC9523718 DOI: 10.1021/acs.chemrev.1c00757] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Indexed: 12/13/2022]
Abstract
Water solubility and structural stability are key merits for proteins defined by the primary sequence and 3D-conformation. Their manipulation represents important aspects of the protein design field that relies on the accurate placement of amino acids and molecular interactions, guided by underlying physiochemical principles. Emulated designer proteins with well-defined properties both fuel the knowledge-base for more precise computational design models and are used in various biomedical and nanotechnological applications. The continuous developments in protein science, increasing computing power, new algorithms, and characterization techniques provide sophisticated toolkits for solubility design beyond guess work. In this review, we summarize recent advances in the protein design field with respect to water solubility and structural stability. After introducing fundamental design rules, we discuss the transmembrane protein solubilization and de novo transmembrane protein design. Traditional strategies to enhance protein solubility and structural stability are introduced. The designs of stable protein complexes and high-order assemblies are covered. Computational methodologies behind these endeavors, including structure prediction programs, machine learning algorithms, and specialty software dedicated to the evaluation of protein solubility and aggregation, are discussed. The findings and opportunities for Cryo-EM are presented. This review provides an overview of significant progress and prospects in accurate protein design for solubility and stability.
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Affiliation(s)
- Rui Qing
- State
Key Laboratory of Microbial Metabolism, School of Life Sciences and
Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shilei Hao
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Key
Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400030, China
| | - Eva Smorodina
- Department
of Immunology, University of Oslo and Oslo
University Hospital, Oslo 0424, Norway
| | - David Jin
- Avalon GloboCare
Corp., Freehold, New Jersey 07728, United States
| | - Arthur Zalevsky
- Laboratory
of Bioinformatics Approaches in Combinatorial Chemistry and Biology, Shemyakin−Ovchinnikov Institute of Bioorganic
Chemistry RAS, Moscow 117997, Russia
| | - Shuguang Zhang
- Media
Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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3
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Cohesin ATPase activities regulate DNA binding and coiled-coil configuration. Proc Natl Acad Sci U S A 2022; 119:e2208004119. [PMID: 35939705 PMCID: PMC9388089 DOI: 10.1073/pnas.2208004119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Cohesin is a heteropentameric protein complex consisting of two structural maintenance of chromosomes (SMC) subunits and three non-SMC subunits. The two SMC subunits form a heterodimer with an ATPase head and hinge that are connected by long coiled coils. Isolation of ATPase mutants followed by comprehensive identification of suppressor mutations in SMC subunits that can bypass ATPase defects was performed. Locations and properties of mutant alleles reflect how ATPase activities could be compromised by structural adaptation. ATP-driven conformational changes may enhance DNA anchoring by the head, alter interactions of coiled coils at the head with other subunits for DNA to go through, and fold/extend coiled coils near break sites around midpoint to bring together DNA elements far from each other. The cohesin complex is required for sister chromatid cohesion and genome compaction. Cohesin coiled coils (CCs) can fold at break sites near midpoints to bring head and hinge domains, located at opposite ends of coiled coils, into proximity. Whether ATPase activities in the head play a role in this conformational change is yet to be known. Here, we dissected functions of cohesin ATPase activities in cohesin dynamics in Schizosaccharomyces pombe. Isolation and characterization of cohesin ATPase temperature-sensitive (ts) mutants indicate that both ATPase domains are required for proper chromosome segregation. Unbiased screening of spontaneous suppressor mutations rescuing the temperature lethality of cohesin ATPase mutants identified several suppressor hotspots in cohesin that located outside of ATPase domains. Then, we performed comprehensive saturation mutagenesis targeted to these suppressor hotspots. Large numbers of the identified suppressor mutations indicated several different ways to compensate for the ATPase mutants: 1) Substitutions to amino acids with smaller side chains in coiled coils at break sites around midpoints may enable folding and extension of coiled coils more easily; 2) substitutions to arginine in the DNA binding region of the head may enhance DNA binding; or 3) substitutions to hydrophobic amino acids in coiled coils, connecting the head and interacting with other subunits, may alter conformation of coiled coils close to the head. These results reflect serial structural changes in cohesin driven by its ATPase activities potentially for packaging DNAs.
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4
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Aurora-B phosphorylates the myosin II heavy chain to promote cytokinesis. J Biol Chem 2021; 297:101024. [PMID: 34343568 PMCID: PMC8385403 DOI: 10.1016/j.jbc.2021.101024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 07/21/2021] [Accepted: 07/29/2021] [Indexed: 12/22/2022] Open
Abstract
Cytokinesis, the final step of mitosis, is mediated by an actomyosin contractile ring, the formation of which is temporally and spatially regulated following anaphase onset. Aurora-B is a member of the chromosomal passenger complex, which regulates various processes during mitosis; it is not understood, however, how Aurora-B is involved in cytokinesis. Here, we show that Aurora-B and myosin-IIB form a complex in vivo during telophase. Aurora-B phosphorylates the myosin-IIB rod domain at threonine 1847 (T1847), abrogating the ability of myosin-IIB monomers to form filaments. Furthermore, phosphorylation of myosin-IIB filaments by Aurora-B also promotes filament disassembly. We show that myosin-IIB possessing a phosphomimetic mutation at T1847 was unable to rescue cytokinesis failure caused by myosin-IIB depletion. Cells expressing a phosphoresistant mutation at T1847 had significantly longer intercellular bridges, implying that Aurora-B-mediated phosphorylation of myosin-IIB is important for abscission. We propose that myosin-IIB is a substrate of Aurora-B and reveal a new mechanism of myosin-IIB regulation by Aurora-B in the late stages of mitosis.
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5
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Ma X, Chen T, Peng Z, Wang Z, Liu J, Yang T, Wu L, Liu G, Zhou M, Tong M, Guan Y, Zhang X, Lin Y, Tang X, Li L, Tang Z, Pan T, Zhang H. Histone chaperone CAF-1 promotes HIV-1 latency by leading the formation of phase-separated suppressive nuclear bodies. EMBO J 2021; 40:e106632. [PMID: 33739466 PMCID: PMC8126954 DOI: 10.15252/embj.2020106632] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/11/2021] [Accepted: 02/19/2021] [Indexed: 01/08/2023] Open
Abstract
HIV-1 latency is a major obstacle to achieving a functional cure for AIDS. Reactivation of HIV-1-infected cells followed by their elimination via immune surveillance is one proposed strategy for eradicating the viral reservoir. However, current latency-reversing agents (LRAs) show high toxicity and low efficiency, and new targets are needed to develop more promising LRAs. Here, we found that the histone chaperone CAF-1 (chromatin assembly factor 1) is enriched on the HIV-1 long terminal repeat (LTR) and forms nuclear bodies with liquid-liquid phase separation (LLPS) properties. CAF-1 recruits epigenetic modifiers and histone chaperones to the nuclear bodies to establish and maintain HIV-1 latency in different latency models and primary CD4+ T cells. Three disordered regions of the CHAF1A subunit are important for phase-separated CAF-1 nuclear body formation and play a key role in maintaining HIV-1 latency. Disruption of phase-separated CAF-1 bodies could be a potential strategy to reactivate latent HIV-1.
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Affiliation(s)
- Xiancai Ma
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Chen
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Zhilin Peng
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ziwen Wang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Jun Liu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Tao Yang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Liyang Wu
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Guangyan Liu
- College of Basic Medical SciencesShenyang Medical CollegeShenyangLiaoningChina
| | - Mo Zhou
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Muye Tong
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yuanjun Guan
- Core Laboratory Platform for Medical ScienceZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xu Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Yingtong Lin
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Xiaoping Tang
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Linghua Li
- Department of Infectious DiseasesGuangzhou 8th People’s HospitalGuangzhouGuangdongChina
| | - Zhonghui Tang
- Department of BioinformaticsZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
| | - Ting Pan
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Center for Infection and Immunity StudySchool of MedicineSun Yat‐sen UniversityShenzhenGuangdongChina
| | - Hui Zhang
- Institute of Human VirologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
- Key Laboratory of Tropical Disease Control of Ministry of EducationZhongshan School of MedicineSun Yat‐sen UniversityGuangzhouGuangdongChina
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6
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The chilling of adenylyl cyclase 9 and its translational potential. Cell Signal 2020; 70:109589. [PMID: 32105777 DOI: 10.1016/j.cellsig.2020.109589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/21/2020] [Accepted: 02/23/2020] [Indexed: 12/26/2022]
Abstract
A recent break-through paper has revealed for the first time the high-resolution, three-dimensional structure of a mammalian trans-membrane adenylyl cyclase (tmAC) obtained by cryo-electronmicroscopy (cryo-EM). Reporting the structure of adenylyl cyclase 9 (AC9) in complex with activated Gsα, the cryo-EM study revealed that AC9 has three functionally interlinked, yet structurally distinct domains. The array of the twelve transmembrane helices is connected to the cytosolic catalytic core by two helical segments that are stabilized through the formation of a parallel coiled-coil. Surprisingly, in the presence of Gsα, the isoform-specific carboxyl-terminal tail of AC9 occludes the forskolin- as well as the active substrate-sites, resulting in marked autoinhibition of the enzyme. As AC9 has the lowest primary sequence homology with the eight further mammalian tmAC paralogues, it appears to be the best candidate for selective pharmacologic targeting. This is now closer to reality as the structural insight provided by the cryo-EM study indicates that all of the three structural domains are potential targets for bioactive agents. The present paper summarizes for molecular physiologists and pharmacologists what is known about the biological role of AC9, considers the potential modes of physiologic regulation, as well as pharmacologic targeting on the basis of the high-resolution cryo-EM structure. The translational potential of AC9 is considered upon highlighting the current state of genome-wide association screens, and the corresponding experimental evidence. Overall, whilst the high- resolution structure presents unique opportunities for the full understanding of the control of AC9, the data on the biological role of the enzyme and its translational potential are far from complete, and require extensive further study.
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7
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Babkoff A, Cohen-Kfir E, Aharon H, Ronen D, Rosenberg M, Wiener R, Ravid S. A direct interaction between survivin and myosin II is required for cytokinesis. J Cell Sci 2019; 132:132/14/jcs233130. [PMID: 31315909 DOI: 10.1242/jcs.233130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/14/2019] [Indexed: 02/05/2023] Open
Abstract
An acto-myosin contractile ring, which forms after anaphase onset and is highly regulated in time and space, mediates cytokinesis, the final step of mitosis. The chromosomal passenger complex (CPC), composed of Aurora-B kinase, INCENP, borealin and survivin (also known as BIRC5), regulates various processes during mitosis, including cytokinesis. It is not understood, however, how CPC regulates cytokinesis. We show that survivin binds to non-muscle myosin II (NMII), regulating its filament assembly. Survivin and NMII interact mainly in telophase, and Cdk1 regulates their interaction in a mitotic-phase-specific manner, revealing the mechanism for the specific timing of survivin-NMII interaction during mitosis. The survivin-NMII interaction is indispensable for cytokinesis, and its disruption leads to multiple mitotic defects. We further show that only the survivin homodimer binds to NMII, attesting to the biological importance for survivin homodimerization. We suggest a novel function for survivin in regulating the spatio-temporal formation of the acto-NMII contractile ring during cytokinesis and we elucidate the role of Cdk1 in regulating this process.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Aryeh Babkoff
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Einav Cohen-Kfir
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Hananel Aharon
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Daniel Ronen
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Michael Rosenberg
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Reuven Wiener
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shoshana Ravid
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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8
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Spencer RK, Hochbaum AI. The Phe-Ile Zipper: A Specific Interaction Motif Drives Antiparallel Coiled-Coil Hexamer Formation. Biochemistry 2017; 56:5300-5308. [DOI: 10.1021/acs.biochem.7b00756] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
| | - Allon I. Hochbaum
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
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9
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Cahill J, Rajaure M, O'Leary C, Sloan J, Marrufo A, Holt A, Kulkarni A, Hernandez O, Young R. Genetic Analysis of the Lambda Spanins Rz and Rz1: Identification of Functional Domains. G3 (BETHESDA, MD.) 2017; 7:741-753. [PMID: 28040784 PMCID: PMC5295617 DOI: 10.1534/g3.116.037192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/26/2016] [Indexed: 11/18/2022]
Abstract
Coliphage lambda proteins Rz and Rz1 are the inner membrane and outer membrane subunits of the spanin complex-a heterotetramer that bridges the periplasm and is essential for the disruption of the outer membrane during phage lysis. Recent evidence suggests the spanin complex functions by fusing the inner and outer membrane. Here, we use a genetics approach to investigate and characterize determinants of spanin function. Because Rz1 is entirely embedded in the +1 reading frame of Rz, the genes were disembedded before using random mutagenesis to construct a library of lysis-defective alleles for both genes. Surprisingly, most of the lysis-defective missense mutants exhibited normal accumulation or localization in vivo, and also were found to be normal for complex formation in vitro Analysis of the distribution and nature of single missense mutations revealed subdomains that resemble key motifs in established membrane-fusion systems, i.e., two coiled-coil domains in Rz, a proline-rich region of Rz1, and flexible linkers in both proteins. When coding sequences are aligned respective to the embedded genetic architecture of Rz1 within Rz, genetically silent domains of Rz1 correspond to mutationally sensitive domains in Rz, and vice versa, suggesting that the modular structure of the two subunits facilitated the evolutionary compression that resulted in the unique embedded gene architecture.
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Affiliation(s)
- Jesse Cahill
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Manoj Rajaure
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Chandler O'Leary
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Jordan Sloan
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Armando Marrufo
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Ashley Holt
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Aneesha Kulkarni
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Oscar Hernandez
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
| | - Ry Young
- Center for Phage Technology and Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843
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10
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Spencer RK, Hochbaum AI. X-ray Crystallographic Structure and Solution Behavior of an Antiparallel Coiled-Coil Hexamer Formed by de Novo Peptides. Biochemistry 2016; 55:3214-23. [DOI: 10.1021/acs.biochem.6b00201] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
| | - Allon I. Hochbaum
- Department of Chemistry and Department of Chemical Engineering & Materials Science, University of California, Irvine, Irvine, California 92697-2575, United States
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11
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Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly. PLoS One 2015; 10:e0132706. [PMID: 26181054 PMCID: PMC4504709 DOI: 10.1371/journal.pone.0132706] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 06/17/2015] [Indexed: 01/05/2023] Open
Abstract
Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general.
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12
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Lun AS, Chen J, Lange S. Probing muscle ankyrin-repeat protein (MARP) structure and function. Anat Rec (Hoboken) 2015; 297:1615-29. [PMID: 25125175 DOI: 10.1002/ar.22968] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/02/2014] [Indexed: 12/20/2022]
Abstract
Muscle ankyrin-repeat proteins (MARPs) have been shown to serve diverse functions within cardiac and skeletal muscle cells. Apart from their interactions with sarcomeric proteins like titin or myopalladin that locate them along myofilaments, MARPs are able to shuttle to the nucleus where they act as modulators for a variety of transcription factors. The deregulation of MARPs in many cardiac and skeletal myopathies contributes to their use as biomarkers for these diseases. Many of their functions are attributed to their domain composition. MARPs consist of an N-terminal coiled-coil domain responsible for their dimerization. The C-terminus contains a series of ankyrin repeats, whose best-characterized function is to bind to the N2A region of the giant sarcomeric protein titin. Here we investigate the nature of their dimerization and their interaction with titin more closely. We demonstrate that the coiled-coil domain in all MARPs enables their homo- and hetero-dimerization in antiparallel fashion. Protein complementation experiments indicate further antiparallel binding of the ankyrin repeats to titin's N2A region. Binding of MARP to titin also affects its PKA mediated phosphorylation. We demonstrate further that MARPs themselves are phosphorylated by PKA and PKC, potentially altering their structure or function. These studies elucidate structural relationships within the stretch-responsive MARP/titin complex in cross-striated muscle cells, and may relate to disease relevant posttranslational modifications of MARPs and titin that alter muscle compliance.
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13
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Negron C, Keating AE. A set of computationally designed orthogonal antiparallel homodimers that expands the synthetic coiled-coil toolkit. J Am Chem Soc 2014; 136:16544-56. [PMID: 25337788 PMCID: PMC4277747 DOI: 10.1021/ja507847t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Indexed: 12/11/2022]
Abstract
Molecular engineering of protein assemblies, including the fabrication of nanostructures and synthetic signaling pathways, relies on the availability of modular parts that can be combined to give different structures and functions. Currently, a limited number of well-characterized protein interaction components are available. Coiled-coil interaction modules have been demonstrated to be useful for biomolecular design, and many parallel homodimers and heterodimers are available in the coiled-coil toolkit. In this work, we sought to design a set of orthogonal antiparallel homodimeric coiled coils using a computational approach. There are very few antiparallel homodimers described in the literature, and none have been measured for cross-reactivity. We tested the ability of the distance-dependent statistical potential DFIRE to predict orientation preferences for coiled-coil dimers of known structure. The DFIRE model was then combined with the CLASSY multistate protein design framework to engineer sets of three orthogonal antiparallel homodimeric coiled coils. Experimental measurements confirmed the successful design of three peptides that preferentially formed antiparallel homodimers that, furthermore, did not interact with one additional previously reported antiparallel homodimer. Two designed peptides that formed higher-order structures suggest how future design protocols could be improved. The successful designs represent a significant expansion of the existing protein-interaction toolbox for molecular engineers.
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Affiliation(s)
- Christopher Negron
- Program
in Computational and Systems Biology and Departments of Biology and Biological
Engineering, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 021393, United States
| | - Amy E. Keating
- Program
in Computational and Systems Biology and Departments of Biology and Biological
Engineering, Massachusetts Institute of
Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 021393, United States
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14
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Moore JR, Li X, Nirody J, Fischer S, Lehman W. Structural implications of conserved aspartate residues located in tropomyosin's coiled-coil core. BIOARCHITECTURE 2014; 1:250-255. [PMID: 22754618 PMCID: PMC3384579 DOI: 10.4161/bioa.18117] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polar residues lying between adjacent α-helical chains of coiled-coils often contribute to coiled-coil curvature and flexibility, while more typical core hydrophobic residues anneal the chains together. In tropomyosins, ranging from smooth and skeletal muscle to cytoplasmic isoforms, a highly conserved Asp at residue 137 places negative charges within the tropomyosin coiled-coil core in a position which may affect the conformation needed for tropomyosin binding and regulatory movements on actin. Proteolytic susceptibility suggested that substituting a canonical Leu for the naturally occurring Asp at residue 137 increases inter-chain rigidity by stabilizing the tropomyosin coiled-coil. Using molecular dynamics, we now directly assess changes in coiled-coil curvature and flexibility caused by such mutants. Although the coiled-coil flexibility is modestly diminished near the residue 137 mutation site, as expected, a delocalized increase in flexibility along the overall coiled-coil is observed. Even though the average shape of the D137L tropomyosin is straighter than that of wild-type tropomyosin, it is still capable of binding actin due to this increase in flexibility. We conclude that the conserved, non-canonical Asp-137 destabilizes the local structure resulting in a local flexible region in the middle of tropomyosin that normally is important for tropomyosin steady-state equilibrium position on actin.
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15
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Acidic pH triggers conformational changes at the NH2-terminal propeptide of the precursor of pulmonary surfactant protein B to form a coiled coil structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1738-51. [DOI: 10.1016/j.bbamem.2014.03.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/19/2014] [Accepted: 03/24/2014] [Indexed: 11/21/2022]
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16
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Dahan I, Petrov D, Cohen-Kfir E, Ravid S. The tumor suppressor Lgl1 forms discrete complexes with NMII-A and Par6α-aPKCζ that are affected by Lgl1 phosphorylation. J Cell Sci 2013; 127:295-304. [PMID: 24213535 DOI: 10.1242/jcs.127357] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Non-muscle myosin IIA (NMII-A) and the tumor suppressor lethal giant larvae 1 (Lgl1) play a central role in the polarization of migrating cells. Mammalian Lgl1 interacts directly with NMII-A, inhibiting its ability to assemble into filaments in vitro. Lgl1 also regulates the cellular localization of NMII-A, the maturation of focal adhesions and cell migration. In Drosophila, phosphorylation of Lgl affects its association with the cytoskeleton. Here we show that phosphorylation of mammalian Lgl1 by aPKCζ prevents its interaction with NMII-A both in vitro and in vivo, and affects its inhibition of NMII-A filament assembly. Phosphorylation of Lgl1 affects its cellular localization and is important for the cellular organization of the acto-NMII cytoskeleton. We further show that Lgl1 forms two distinct complexes in vivo, Lgl1-NMIIA and Lgl1-Par6α-aPKCζ, and that the formation of these complexes is affected by the phosphorylation state of Lgl1. The complex Lgl1-Par6α-aPKCζ resides in the leading edge of the cell. Finally, we show that aPKCζ and NMII-A compete to bind directly to Lgl1 at the same domain. These results provide new insights into the mechanism regulating the interaction between Lgl1, NMII-A, Par6α and aPKCζ in polarized migrating cells.
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Affiliation(s)
- Inbal Dahan
- Department of Biochemistry and Molecular Biology, The Institute of Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem 91120, Israel
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17
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Yar S, Chowdhury SAK, Davis RT, Kobayashi M, Monasky MM, Rajan S, Wolska BM, Gaponenko V, Kobayashi T, Wieczorek DF, Solaro RJ. Conserved Asp-137 is important for both structure and regulatory functions of cardiac α-tropomyosin (α-TM) in a novel transgenic mouse model expressing α-TM-D137L. J Biol Chem 2013; 288:16235-16246. [PMID: 23609439 DOI: 10.1074/jbc.m113.458695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
α-Tropomyosin (α-TM) has a conserved, charged Asp-137 residue located in the hydrophobic core of its coiled-coil structure, which is unusual in that the residue is found at a position typically occupied by a hydrophobic residue. Asp-137 is thought to destabilize the coiled-coil and so impart structural flexibility to the molecule, which is believed to be crucial for its function in the heart. A previous in vitro study indicated that the conversion of Asp-137 to a more typical canonical Leu alters flexibility of TM and affects its in vitro regulatory functions. However, the physiological importance of the residue Asp-137 and altered TM flexibility is unknown. In this study, we further analyzed structural properties of the α-TM-D137L variant and addressed the physiological importance of TM flexibility in cardiac function in studies with a novel transgenic mouse model expressing α-TM-D137L in the heart. Our NMR spectroscopy data indicated that the presence of D137L introduced long range rearrangements in TM structure. Differential scanning calorimetry measurements demonstrated that α-TM-D137L has higher thermal stability compared with α-TM, which correlated with decreased flexibility. Hearts of transgenic mice expressing α-TM-D137L showed systolic and diastolic dysfunction with decreased myofilament Ca(2+) sensitivity and cardiomyocyte contractility without changes in intracellular Ca(2+) transients or post-translational modifications of major myofilament proteins. We conclude that conversion of the highly conserved Asp-137 to Leu results in loss of flexibility of TM that is important for its regulatory functions in mouse hearts. Thus, our results provide insight into the link between flexibility of TM and its function in ejecting hearts.
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Affiliation(s)
- Sumeyye Yar
- Departments of Biochemistry and Molecular Genetics, Chicago, Illinois 60612; Physiology and Biophysics, Chicago, Illinois 60612
| | | | | | | | | | - Sudarsan Rajan
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - Beata M Wolska
- Physiology and Biophysics, Chicago, Illinois 60612; Medicine, Chicago, Illinois 60612; Center for Cardiovascular Research, University of Illinois, Chicago, Illinois 60612
| | - Vadim Gaponenko
- Departments of Biochemistry and Molecular Genetics, Chicago, Illinois 60612
| | - Tomoyoshi Kobayashi
- Physiology and Biophysics, Chicago, Illinois 60612; Center for Cardiovascular Research, University of Illinois, Chicago, Illinois 60612
| | - David F Wieczorek
- Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - R John Solaro
- Physiology and Biophysics, Chicago, Illinois 60612; Center for Cardiovascular Research, University of Illinois, Chicago, Illinois 60612.
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18
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Rosenberg MM, Ronen D, Lahav N, Nazirov E, Ravid S, Friedler A. High resolution characterization of myosin IIC protein tailpiece and its effect on filament assembly. J Biol Chem 2013; 288:9779-9789. [PMID: 23426373 DOI: 10.1074/jbc.m112.430173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The motor protein nonmuscle myosin II (NMII) must undergo dynamic oligomerization into filaments to perform its cellular functions. A small nonhelical region at the tail of the long coiled-coil region (tailpiece) is a common feature of all dynamically assembling myosin II proteins. This tailpiece is a key regulatory domain affecting NMII filament assembly properties and is subject to phosphorylation in vivo. We previously demonstrated that the positively charged region of the tailpiece binds to assembly-incompetent NMII-C fragments, inducing filament assembly. In the current study, we investigated the molecular mechanisms by which the tailpiece regulates NMII-C self-assembly. Using alanine scan, we found that specific positive and aromatic residues within the positively charged region of the tailpiece are important for inducing NMII-C filament assembly and for filament elongation. Combining peptide arrays with deletion studies allowed us to identify the tailpiece binding sites in the coiled-coil rod. Elucidation of the mechanism by which the tailpiece induces filament assembly permitted us further investigation into the role of tailpiece phosphorylation. Sedimentation and CD spectroscopy identified that phosphorylation of Thr(1957) or Thr(1960) inhibited the ability of the tailpiece to bind the coiled-coil rod and to induce NMII-C filament formation. This study provides molecular insight into the role of specific residues within the NMII-C tailpiece that are responsible for shifting the oligomeric equilibrium of NMII-C toward filament assembly and determining its morphology.
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Affiliation(s)
- Masha M Rosenberg
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904
| | - Daniel Ronen
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Noa Lahav
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904
| | - Elvira Nazirov
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
| | - Shoshana Ravid
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus Givat Ram, Jerusalem 91904.
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19
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Nisbet DR, Williams RJ. Self-Assembled Peptides: Characterisation and In Vivo Response. Biointerphases 2012; 7:2. [DOI: 10.1007/s13758-011-0002-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 11/09/2011] [Indexed: 11/25/2022] Open
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20
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Sunitha MS, Nair AG, Charya A, Jadhav K, Mukhopadhyay S, Sowdhamini R. Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins. BMC Res Notes 2012; 5:530. [PMID: 23009691 PMCID: PMC3542152 DOI: 10.1186/1756-0500-5-530] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coiled-coils are found in different proteins like transcription factors, myosin tail domain, tropomyosin, leucine zippers and kinesins. Analysis of various structures containing coiled-coils has revealed the importance of electrostatic and hydrophobic interactions. In such domains, regions of different strength of interactions need to be identified since they could be biologically relevant. FINDINGS We have updated our coiled-coil validation webserver, now called COILCHECK+, where new features were added to efficiently identify the strength of interaction at the interface region and measure the density of charged residues and hydrophobic residues. We have examined charged residues and hydrophobic ladders, using a new algorithm called CHAHO, which is incorporated within COILCHECK + server. CHAHO permits the identification of spatial charged residue patches and the continuity of hydrophobic ladder which stabilizes and destabilizes the coiled-coil structure. CONCLUSIONS The availability of such computational tools should be useful to understand the importance of spatial clustering of charged residues and the continuity of hydrophobic residues at the interface region of coiled-coil dimers. COILCHECK + is a structure based tool to validate coiled-coil stability; it can be accessed at http://caps.ncbs.res.in/coilcheckplus.
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Affiliation(s)
- Margaret S Sunitha
- National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
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21
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Dahan I, Yearim A, Touboul Y, Ravid S. The tumor suppressor Lgl1 regulates NMII-A cellular distribution and focal adhesion morphology to optimize cell migration. Mol Biol Cell 2012; 23:591-601. [PMID: 22219375 PMCID: PMC3279388 DOI: 10.1091/mbc.e11-01-0015] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The Drosophila tumor suppressor Lethal (2) giant larvae (Lgl) regulates the apical-basal polarity in epithelia and asymmetric cell division. However, little is known about the role of Lgl in cell polarity in migrating cells. In this study we show direct physiological interactions between the mammalian homologue of Lgl (Lgl1) and the nonmuscle myosin II isoform A (NMII-A). We demonstrate that Lgl1 and NMII-A form a complex in vivo and provide data that Lgl1 inhibits NMII-A filament assembly in vitro. Furthermore, depletion of Lgl1 results in the unexpected presence of NMII-A in the cell leading edge, a region that is not usually occupied by this protein, suggesting that Lgl1 regulates the cellular localization of NMII-A. Finally, we show that depletion of Lgl1 affects the size and number of focal adhesions, as well as cell polarity, membrane dynamics, and the rate of migrating cells. Collectively these findings indicate that Lgl1 regulates the polarity of migrating cells by controlling the assembly state of NMII-A, its cellular localization, and focal adhesion assembly.
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Affiliation(s)
- Inbal Dahan
- Department of Biochemistry and Molecular Biology, Institute of Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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22
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Croasdale R, Ivins FJ, Muskett F, Daviter T, Scott DJ, Hardy T, Smerdon SJ, Fry AM, Pfuhl M. An undecided coiled coil: the leucine zipper of Nek2 kinase exhibits atypical conformational exchange dynamics. J Biol Chem 2011; 286:27537-47. [PMID: 21669869 PMCID: PMC3149346 DOI: 10.1074/jbc.m110.196972] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 05/14/2011] [Indexed: 01/09/2023] Open
Abstract
Leucine zippers are oligomerization domains used in a wide range of proteins. Their structure is based on a highly conserved heptad repeat sequence in which two key positions are occupied by leucines. The leucine zipper of the cell cycle-regulated Nek2 kinase is important for its dimerization and activation. However, the sequence of this leucine zipper is most unusual in that leucines occupy only one of the two hydrophobic positions. The other position, depending on the register of the heptad repeat, is occupied by either acidic or basic residues. Using NMR spectroscopy, we show that this leucine zipper exists in two conformations of almost equal population that exchange with a rate of 17 s(-1). We propose that the two conformations correspond to the two possible registers of the heptad repeat. This hypothesis is supported by a cysteine mutant that locks the protein in one of the two conformations. NMR spectra of this mutant showed the predicted 2-fold reduction of peaks in the (15)N HSQC spectrum and the complete removal of cross peaks in exchange spectra. It is possible that interconversion of these two conformations may be triggered by external signals in a manner similar to that proposed recently for the microtubule binding domain of dynein and the HAMP domain. As a result, the leucine zipper of Nek2 kinase is the first example where the frameshift of coiled-coil heptad repeats has been directly observed experimentally.
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Affiliation(s)
- Rebecca Croasdale
- From the Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Frank J. Ivins
- the Medical Research Council, National Institute of Medical Research, Division of Molecular Structure, Mill Hill, London NW7 1AA, United Kingdom
| | - Fred Muskett
- From the Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Tina Daviter
- the ISMB Biophysics Centre, Birkbeck, University of London, London WC1E 7HX, United Kingdom, and
| | - David J. Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, United Kingdom
| | - Tara Hardy
- From the Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Steven J. Smerdon
- the Medical Research Council, National Institute of Medical Research, Division of Molecular Structure, Mill Hill, London NW7 1AA, United Kingdom
| | - Andrew M. Fry
- From the Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Mark Pfuhl
- From the Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
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23
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Lau WL, Degrado WF, Roder H. The effects of pK(a) tuning on the thermodynamics and kinetics of folding: design of a solvent-shielded carboxylate pair at the a-position of a coiled-coil. Biophys J 2011; 99:2299-308. [PMID: 20923665 DOI: 10.1016/j.bpj.2010.07.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 07/26/2010] [Accepted: 07/29/2010] [Indexed: 10/19/2022] Open
Abstract
The tuning of the pK(a) of ionizable residues plays a critical role in various protein functions, such as ligand-binding, catalysis, and allostery. Proteins harness the free energy of folding to position ionizable groups in highly specific environments that strongly affect their pK(a) values. To investigate the interplay among protein folding kinetics, thermodynamics, and pK(a) modulation, we introduced a pair of Asp residues at neighboring interior positions of a coiled-coil. A single Asp residue was replaced for an Asn side chain at the a-position of the coiled-coil from GCN4, which was also crosslinked at the C-terminus via a flexible disulfide bond. The thermodynamic and kinetic stability of the system was measured by circular dichroism and stopped-flow fluorescence as a function of pH and concentration of guanidine HCl. Both sets of data are consistent with a two-state equilibrium between fully folded and unfolded forms. Distinct pK(a) values of 6.3 and 5.35 are assigned to the first and second protonation of the Asp pair; together they represent an energetic difference of 5 kcal/mol relative to the protonation of two Asp residues with unperturbed pK(a) values. Analysis of the rate data as a function of pH and denaturant concentration allowed calculation of the kinetic constants for the conformational transitions of the peptide with the Asp residues in the doubly protonated, singly protonated, and unprotonated forms. The doubly and singly protonated forms fold rapidly, and a ϕ-value analysis shows that their contribution to folding occurs subsequent to the transition state ensemble for folding. By contrast, the doubly charged state shows a reduced rate of folding and a ϕ-value near 0.5 indicative of a repulsive interaction, and possibly also heterogeneity in the transition state ensemble.
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Affiliation(s)
- Wai Leung Lau
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
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24
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Ronen D, Rosenberg MM, Shalev DE, Rosenberg M, Rotem S, Friedler A, Ravid S. The positively charged region of the myosin IIC non-helical tailpiece promotes filament assembly. J Biol Chem 2009; 285:7079-86. [PMID: 19959848 DOI: 10.1074/jbc.m109.049221] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The motor protein, non-muscle myosin II (NMII), must undergo dynamic oligomerization into filaments to participate in cellular processes such as cell migration and cytokinesis. A small non-helical region at the tail of the long coiled-coil region (tailpiece) is a common feature of all dynamically assembling myosin II proteins. In this study, we investigated the role of the tailpiece in NMII-C self-assembly. We show that the tailpiece is natively unfolded, as seen by circular dichroism and NMR experiments, and is divided into two regions of opposite charge. The positively charged region (Tailpiece(1946-1967)) starts at residue 1946 and is extended by seven amino acids at its N terminus from the traditional coiled-coil ending proline (Tailpiece(1953-1967)). Pull-down and sedimentation assays showed that the positive Tailpiece(1946-1967) binds to assembly incompetent NMII-C fragments inducing filament assembly. The negative region, residues 1968-2000, is responsible for NMII paracrystal morphology as determined by chimeras in which the negative region was swapped between the NMII isoforms. Mixing the positive and negative peptides had no effect on the ability of the positive peptide to bind and induce filament assembly. This study provides molecular insight into the role of the structurally disordered tailpiece of NMII-C in shifting the oligomeric equilibrium of NMII-C toward filament assembly and determining its morphology.
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Affiliation(s)
- Daniel Ronen
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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25
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Ghosh TS, Chaitanya SK, Sankararamakrishnan R. End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1032-41. [PMID: 19770500 DOI: 10.1107/s0907444909027012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Accepted: 07/09/2009] [Indexed: 11/10/2022]
Abstract
Helix-helix interactions are important for the structure, stability and function of alpha-helical proteins. Helices that either cross in the middle or show extensive contacts between each other, such as coiled coils, have been investigated in previous studies. Interactions between two helices can also occur only at the terminal regions or between the terminal region of one helix and the middle region of another helix. Examples of such helix pairs are found in aquaporin, H(+)/Cl(-) transporter and Bcl-2 proteins. The frequency of the occurrence of such ;end-to-end' (EE) and ;end-to-middle' (EM) helix pairs in protein structures is not known. Questions regarding the residue preferences in the interface and the mode of interhelical interactions in such helix pairs also remain unanswered. In this study, high-resolution structures of all-alpha proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N-N, N-C, C-C, N-MID and C-MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their preferences for occurring in the interface of EE and EM helix pairs. In contrast to interacting non-EE/EM helix pairs, helices in EE and EM pairs are farther apart. In these helix pairs, residues with large surface area/volume and longer side chains are preferred in the interfacial region.
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Affiliation(s)
- Tarini Shankar Ghosh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
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26
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Ronen D, Ravid S. Myosin II tailpiece determines its paracrystal structure, filament assembly properties, and cellular localization. J Biol Chem 2009; 284:24948-57. [PMID: 19553683 DOI: 10.1074/jbc.m109.023754] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Non muscle myosin II (NMII) is a major motor protein present in all cell types. The three known vertebrate NMII isoforms share high sequence homology but play different cellular roles. The main difference in sequence resides in the C-terminal non-helical tailpiece (tailpiece). In this study we demonstrate that the tailpiece is crucial for proper filament size, overcoming the intrinsic properties of the coiled-coil rod. Furthermore, we show that the tailpiece by itself determines the NMII filament structure in an isoform-specific manner, thus providing a possible mechanism by which each NMII isoform carries out its unique cellular functions. We further show that the tailpiece determines the cellular localization of NMII-A and NMII-B and is important for NMII-C role in focal adhesion complexes. We mapped NMII-C sites phosphorylated by protein kinase C and casein kinase II and showed that these phosphorylations affect its solubility properties and cellular localization. Thus phosphorylation fine-tunes the tailpiece effects on the coiled-coil rod, enabling dynamic regulation of NMII-C assembly. We thus show that the small tailpiece of NMII is a distinct domain playing a role in isoform-specific filament assembly and cellular functions.
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Affiliation(s)
- Daniel Ronen
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research, Israel-Canada, the Hebrew University, Hadassah Medical School, Jerusalem 91220, Israel
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27
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Pant K, Watt J, Greenberg M, Jones M, Szczesna-Cordary D, Moore JR. Removal of the cardiac myosin regulatory light chain increases isometric force production. FASEB J 2009; 23:3571-80. [PMID: 19470801 DOI: 10.1096/fj.08-126672] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The myosin neck, which is supported by the interactions between light chains and the underlying alpha-helical heavy chain, is thought to act as a lever arm to amplify movements originating in the globular motor domain. Here, we studied the role of the cardiac myosin regulatory light chains (RLCs) in the capacity of myosin to produce force using a novel optical-trap-based isometric force in vitro motility assay. We measured the isometric force and actin filament velocity for native porcine cardiac (PC) myosin, RLC-depleted PC (PC(depl)) myosin, and PC myosin reconstituted with recombinant bacterially expressed human cardiac RLC (PC(recon)). RLC depletion reduced unloaded actin filament velocity by 58% and enhanced the myosin-based isometric force approximately 2-fold. No significant change between PC and PC(depl) preparations was observed in the maximal rate of actin-activated myosin ATPase activity. Reconstitution of PC(depl) myosin with human RLC partially restored the velocity and force levels to near untreated values. The reduction in unloaded velocity after RLC extraction is consistent with the myosin neck acting as a lever, while the enhancement in isometric force can be directly related to enhancement of unitary force. The force data are consistent with a model in which the neck region behaves as a cantilevered beam.
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Affiliation(s)
- Kiran Pant
- Boston University School of Medicine, Department of Physiology and Biophysics, 72 E. Concord St., Boston, MA 02118, USA
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28
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Gaida A, Hagemann UB, Mattay D, Räuber C, Müller KM, Arndt KM. Selection of peptides interfering with protein-protein interaction. Methods Mol Biol 2009; 535:263-291. [PMID: 19377990 DOI: 10.1007/978-1-59745-557-2_16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Cell physiology depends on a fine-tuned network of protein-protein interactions, and misguided interactions are often associated with various diseases. Consequently, peptides, which are able to specifically interfere with such adventitious interactions, are of high interest for analytical as well as medical purposes. One of the most abundant protein interaction domains is the coiled-coil motif, and thus provides a premier target. Coiled coils, which consist of two or more alpha-helices wrapped around each other, have one of the simplest interaction interfaces, yet they are able to confer highly specific homo- and heterotypic interactions involved in virtually any cellular process. While there are several ways to generate interfering peptides, the combination of library design with a powerful selection system seems to be one of the most effective and promising approaches. This chapter guides through all steps of such a process, starting with library options and cloning, detailing suitable selection techniques and ending with purification for further down-stream characterization. Such generated peptides will function as versatile tools to interfere with the natural function of their targets thereby illuminating their down-stream signaling and, in general, promoting understanding of factors leading to specificity and stability in protein-protein interactions. Furthermore, peptides interfering with medically relevant proteins might become important diagnostics and therapeutics.
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Affiliation(s)
- Annette Gaida
- Albert-Ludwigs-University of Freiburg, Institute of Biology III, Freiburg, Germany
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29
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Lu S, Horowits R. Role of nonmuscle myosin IIB and N-RAP in cell spreading and myofibril assembly in primary mouse cardiomyocytes. ACTA ACUST UNITED AC 2008; 65:747-61. [PMID: 18615632 DOI: 10.1002/cm.20299] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We investigated the role of nonmuscle myosin heavy chain (NMHC) IIB in cultured embryonic mouse cardiomyocytes by specific knockdown using RNA interference. NMHC IIB protein levels decreased 90% compared with mock-transfected cells by 3 days post transfection. NMHC IIB knockdown resulted in a slow decrease in N-RAP protein levels over 6 days with no change in N-RAP transcript levels. N-RAP is a scaffold for alpha-actinin and actin assembly during myofibrillogenesis, and we quantitated myofibril accumulation by morphometric analysis of alpha-actinin organization. Between 3 and 6 days, NMHC IIB knockdown was accompanied by the abolishment of cardiomyocyte spreading. During this period the rate of myofibril accumulation steadily decreased, correlating with the slowly decreasing levels of N-RAP. Between 6 and 8 days NMHC IIB and N-RAP protein levels recovered, and cardiomyocyte spreading and myofibril accumulation resumed. Inhibition of proteasome function using MG132 led to accumulation of excess N-RAP, and the secondary decrease in N-RAP that otherwise accompanied NMHC IIB knockdown was abolished. The results show that NMHC IIB knockdown led to decreased N-RAP levels through proteasome-mediated degradation. Furthermore, these proteins have distinct functional roles, with NMHC IIB playing a role in cardiomyocyte spreading and N-RAP functioning in myofibril assembly.
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Affiliation(s)
- Shajia Lu
- Department of Health and Human Services, Laboratory of Muscle Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda 20892-8024, Maryland, USA
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Diss ML, Kennan AJ. Simultaneous directed assembly of three distinct heterodimeric coiled coils. Org Lett 2008; 10:3797-800. [PMID: 18693746 DOI: 10.1021/ol801461a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe simultaneous formation of three distinct heterodimeric coiled coils from a mixture of six different peptides. The choice among electrostatically viable complexes is governed by alignment of buried core residues, including a fundamentally new interaction that exploits urea-terminated side chains. Buried urea/urea contacts lead to extremely stable dimeric coiled coils, with T(m) values between 63 and 79 degrees C. Core ureas can also form stable complexes with a variety of other polar groups, including guanidines, acids, and amides.
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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Grigoryan G, Keating AE. Structural specificity in coiled-coil interactions. Curr Opin Struct Biol 2008; 18:477-83. [PMID: 18555680 DOI: 10.1016/j.sbi.2008.04.008] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Revised: 04/14/2008] [Accepted: 04/29/2008] [Indexed: 10/22/2022]
Abstract
Coiled coils have a rich history in the field of protein design and engineering. Novel structures, such as the first seven-helix coiled coil, continue to provide surprises and insights. Large-scale datasets quantifying the influence of systematic mutations on coiled-coil stability are a valuable new asset to the area. Scoring methods based on sequence and/or structure can predict interaction preferences in coiled-coil-mediated bZIP transcription factor dimerization. Experimental and computational methods for dealing with the near-degeneracy of many coiled-coil structures appear promising for future design applications.
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Rosenberg M, Straussman R, Ben-Ya'acov A, Ronen D, Ravid S. MHC-IIB filament assembly and cellular localization are governed by the rod net charge. PLoS One 2008; 3:e1496. [PMID: 18231583 PMCID: PMC2204051 DOI: 10.1371/journal.pone.0001496] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2007] [Accepted: 12/26/2007] [Indexed: 12/23/2022] Open
Abstract
Background Actin-dependent myosin II molecular motors form an integral part of the cell cytoskeleton. Myosin II molecules contain a long coiled-coil rod that mediates filament assembly required for myosin II to exert its full activity. The exact mechanisms orchestrating filament assembly are not fully understood. Methodology/Principal Findings Here we examine mechanisms controlling filament assembly of non-muscle myosin IIB heavy chain (MHC-IIB). We show that in vitro the entire C-terminus region of net positive charge, found in myosin II rods, is important for self-assembly of MHC-IIB fragments. In contrast, no particular sequences in the rod region with net negative charge were identified as important for self-assembly, yet a minimal area from this region is necessary. Proper paracrystal formation by MHC-IIB fragments requires the 196aa charge periodicity along the entire coiled-coil region. In vivo, in contrast to self-assembly in vitro, negatively-charged regions of the coiled-coil were found to play an important role by controlling the intracellular localization of native MHC-IIB. The entire positively-charged region is also important for intracellular localization of native MHC-IIB. Conclusions/Significance A correct distribution of positive and negative charges along myosin II rod is a necessary component in proper filament assembly and intracellular localization of MHC-IIB.
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Affiliation(s)
- Michael Rosenberg
- Department of Biochemistry, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Ravid Straussman
- Department of Biochemistry, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Ami Ben-Ya'acov
- Department of Biochemistry, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Daniel Ronen
- Department of Biochemistry, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Shoshana Ravid
- Department of Biochemistry, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
- * To whom correspondence should be addressed. E-mail:
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Diss ML, Kennan AJ. Orthogonal recognition in dimeric coiled coils via buried polar-group modulation. J Am Chem Soc 2008; 130:1321-7. [PMID: 18171063 DOI: 10.1021/ja076265w] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe the design and exploration of new buried polar groups to control coiled-coil dimerization. Employing our recently described method for on-resin guanidinylation, we have prepared coiled-coil peptides with a single core guanidine, spaced from the backbone by 1-3 methylene groups. Heterodimeric mixtures of these sequences with guanidine, amide, and carboxylic acid binding partners form a large number of reasonably stable coiled coils (T(m) > or = 60 degrees C). A detailed stability trend examination reveals that asparagine/acid pairs are sharply sensitive to acid residue chain length (Asn/Asp much worse than Asn/Glu), while guanidine/acid pairs are largely insensitive. This has been exploited to create orthogonal recognition pairs which establish the capacity to form two distinct heterodimeric coiled coils by simple mixing of four different peptides. One dimer has buried core asparagines, while the other pairs aspartic acid with any of three guanidinylated side chains. Specificity of this behavior is underscored by failure of glutamic acid substituted sequences to perform accordingly. The successful alternate pairs are further characterized by various biophysical methods (circular dichroism, ultracentrifugation, thermal and chemical denaturation, affinity tags).
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Affiliation(s)
- Maria L Diss
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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Sumida JP, Wu E, Lehrer SS. Conserved Asp-137 imparts flexibility to tropomyosin and affects function. J Biol Chem 2007; 283:6728-34. [PMID: 18165684 DOI: 10.1074/jbc.m707485200] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tropomyosin (Tm) is an alpha-helical coiled-coil that controls muscle contraction by sterically regulating the myosin-actin interaction. Tm moves between three states on F-actin as either a uniform or a non-uniform semi-flexible rod. Tm is stabilized by hydrophobic residues in the "a" and "d" positions of the heptad repeat. The highly conserved Asp-137 is unusual in that it introduces a negative charge on each chain in a position typically occupied by hydrophobic residues. The occurrence of two charged residues in the hydrophobic region is expected to destabilize the region and impart flexibility. To determine whether this region is unstable, we have substituted hydrophobic Leu for Asp-137 and studied changes in Tm susceptibility to limited proteolysis by trypsin and changes in regulation. We found that native and Tm controls that contain Asp-137 were readily cleaved at Arg-133 with t 1/2 of 5 min. In contrast, the Leu-137 mutant was not cleaved under the same conditions. Actin stabilized Tm, causing a 10-fold reduction in the rate of cleavage at Arg-133. The actin-myosin subfragment S1 ATPase activity was greater for the Leu mutant compared with controls in the absence of troponin and in the presence of troponin and Ca2+. We conclude that the highly conserved Asp-137 destabilizes the middle of Tm, resulting in a more flexible region that is important for the cooperative activation of the thin filament by myosin. We thus have shown a link between the dynamic properties of Tm and its function.
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Affiliation(s)
- John P Sumida
- Cardiovascular Program, Boston Biomedical Research Institute, Watertown, Massachusetts 02472, USA
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