1
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Singh SK, Siegler N, Pandey H, Yanir N, Popov M, Goldstein-Levitin A, Sadan M, Debs G, Zarivach R, Frank GA, Kass I, Sindelar CV, Zalk R, Gheber L. Noncanonical interaction with microtubules via the N-terminal nonmotor domain is critical for the functions of a bidirectional kinesin. Sci Adv 2024; 10:eadi1367. [PMID: 38324691 PMCID: PMC10849588 DOI: 10.1126/sciadv.adi1367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
Abstract
Several kinesin-5 motors (kinesin-5s) exhibit bidirectional motility. The mechanism of such motility remains unknown. Bidirectional kinesin-5s share a long N-terminal nonmotor domain (NTnmd), absent in exclusively plus-end-directed kinesins. Here, we combined in vivo, in vitro, and cryo-electron microscopy (cryo-EM) studies to examine the impact of NTnmd mutations on the motor functions of the bidirectional kinesin-5, Cin8. We found that NTnmd deletion mutants exhibited cell viability and spindle localization defects. Using cryo-EM, we examined the structure of a microtubule (MT)-bound motor domain of Cin8, containing part of its NTnmd. Modeling and molecular dynamic simulations based on the cryo-EM map suggested that the NTnmd of Cin8 interacts with the C-terminal tail of β-tubulin. In vitro experiments on subtilisin-treated MTs confirmed this notion. Last, we showed that NTnmd mutants are defective in plus-end-directed motility in single-molecule and antiparallel MT sliding assays. These findings demonstrate that the NTnmd, common to bidirectional kinesin-5s, is critical for their bidirectional motility and intracellular functions.
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Affiliation(s)
- Sudhir K. Singh
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Nurit Siegler
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Himanshu Pandey
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Neta Yanir
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Mary Popov
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | | | - Mayan Sadan
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Garrett Debs
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Raz Zarivach
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Gabriel A. Frank
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Itamar Kass
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Charles V. Sindelar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06510, USA
| | - Ran Zalk
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Larisa Gheber
- 1Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
- Ilse Katz Institute for Nanoscale Science & Technology, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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2
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Webb CT, Yang W, Riley BT, Hayes BK, Sivaraman KK, Malcolm TR, Harrop S, Atkinson SC, Kass I, Buckle AM, Drinkwater N, McGowan S. A metal ion-dependent conformational switch modulates activity of the Plasmodium M17 aminopeptidase. J Biol Chem 2022; 298:102119. [PMID: 35691342 PMCID: PMC9270245 DOI: 10.1016/j.jbc.2022.102119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/12/2022] Open
Abstract
The metal-dependent M17 aminopeptidases are conserved throughout all kingdoms of life. This large enzyme family is characterized by a conserved binuclear metal center and a distinctive homohexameric arrangement. Recently, we showed that hexamer formation in Plasmodium M17 aminopeptidases was controlled by the metal ion environment, although the functional necessity for hexamer formation is still unclear. To further understand the mechanistic role of the hexameric assembly, here we undertook an investigation of the structure and dynamics of the M17 aminopeptidase from Plasmodium falciparum, PfA-M17. We describe a novel structure of PfA-M17, which shows that the active sites of each trimer are linked by a dynamic loop, and loop movement is coupled with a drastic rearrangement of the binuclear metal center and substrate-binding pocket, rendering the protein inactive. Molecular dynamics simulations and biochemical analyses of PfA-M17 variants demonstrated that this rearrangement is inherent to PfA-M17, and that the transition between the active and inactive states is metal dependent and part of a dynamic regulatory mechanism. Key to the mechanism is a remodeling of the binuclear metal center, which occurs in response to a signal from the neighboring active site and serves to moderate the rate of proteolysis under different environmental conditions. In conclusion, this work identifies a precise mechanism by which oligomerization contributes to PfA-M17 function. Furthermore, it describes a novel role for metal cofactors in the regulation of enzymes, with implications for the wide range of metalloenzymes that operate via a two-metal ion catalytic center, including DNA processing enzymes and metalloproteases.
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Affiliation(s)
- Chaille T Webb
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Wei Yang
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia; Current address Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen, 518172, China
| | - Blake T Riley
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Brooke K Hayes
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Komagal Kannan Sivaraman
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Tess R Malcolm
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Stephen Harrop
- Australian Synchrotron. 800 Blackburn Road, Clayton, VIC, 3168, Australia
| | - Sarah C Atkinson
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Itamar Kass
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton Melbourne, VIC 3800, Australia; Victorian Life Sciences Computation Center, Monash University, Clayton 3800, Victoria, Australia; Current address InterX LTD, Ramat-Gan, Israel
| | - Ashley M Buckle
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Nyssa Drinkwater
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton Melbourne, VIC 3800, Australia.
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3
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Goldstein-Levitin A, Pandey H, Allhuzaeel K, Kass I, Gheber L. Intracellular functions and motile properties of bi-directional kinesin-5 Cin8 are regulated by neck linker docking. eLife 2021; 10:71036. [PMID: 34387192 PMCID: PMC8456603 DOI: 10.7554/elife.71036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 07/13/2021] [Indexed: 12/03/2022] Open
Abstract
In this study, we analyzed intracellular functions and motile properties of neck-linker (NL) variants of the bi-directional S. cerevisiae kinesin-5 motor, Cin8. We also examined – by modeling – the configuration of H-bonds during NL docking. Decreasing the number of stabilizing H-bonds resulted in partially functional variants, as long as a conserved backbone H-bond at the N-latch position (proposed to stabilize the docked conformation of the NL) remained intact. Elimination of this conserved H-bond resulted in production of a non-functional Cin8 variant. Surprisingly, additional H-bond stabilization of the N-latch position, generated by replacement of the NL of Cin8 by sequences of the plus-end directed kinesin-5 Eg5, also produced a nonfunctional variant. In that variant, a single replacement of N-latch asparagine with glycine, as present in Cin8, eliminated the additional H-bond stabilization and rescued the functional defects. We conclude that exact N-latch stabilization during NL docking is critical for the function of bi-directional kinesin-5 Cin8.
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Affiliation(s)
| | - Himanshu Pandey
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Kanary Allhuzaeel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Itamar Kass
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel.,InterX LTD, Ramat-Gan, Israel
| | - Larisa Gheber
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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4
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Fodor J, Riley BT, Kass I, Buckle AM, Borg NA. The Role of Conformational Dynamics in Abacavir-Induced Hypersensitivity Syndrome. Sci Rep 2019; 9:10523. [PMID: 31324847 PMCID: PMC6642150 DOI: 10.1038/s41598-019-47001-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/04/2019] [Indexed: 02/06/2023] Open
Abstract
Abacavir is an antiretroviral drug used to reduce human immunodeficiency virus (HIV) replication and decrease the risk of developing acquired immune deficiency syndrome (AIDS). However, its therapeutic value is diminished by the fact that it is associated with drug hypersensitivity reactions in up to 8% of treated patients. This hypersensitivity is strongly associated with patients carrying human leukocyte antigen (HLA)-B*57:01, but not patients carrying closely related alleles. Abacavir’s specificity to HLA-B*57:01 is attributed to its binding site within the peptide-binding cleft and subsequent influence of the repertoire of peptides that can bind HLA-B*57:01. To further our understanding of abacavir-induced hypersensitivity we used molecular dynamics (MD) to analyze the dynamics of three different peptides bound to HLA-B*57:01 in the presence and absence of abacavir or abacavir analogues. We found that abacavir and associated peptides bind to HLA-B*57:01 in a highly diverse range of conformations that are not apparent from static crystallographic snapshots, but observed no difference in either the conformations, nor degree of flexibility when compared to abacavir-unbound systems. Our results support hypersensitivity models in which abacavir-binding alters the conformational ensemble of neopeptides, so as to favour exposed peptide surfaces that are no longer recognized as self by circulating CD8+ T cells, and are conducive to TCR binding. Our findings highlight the need to also consider the role of dynamics in understanding drug-induced hypersensitivities at the molecular and mechanistic level. This additional insight can help inform the chemical modification of abacavir to prevent hypersensitivity reactions in HLA-B*57:01+ HIV patients whilst retaining potent antiretroviral activity.
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Affiliation(s)
- James Fodor
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
| | - Natalie A Borg
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, 3800, Australia.
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5
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Barber‐Zucker S, Hall J, Mangapuram SV, Kass I, Kolusheva S, MacMillan F, Zarivach R, Henn A. Metal binding to the dynamic cytoplasmic domain of the cation diffusion facilitator (CDF) protein MamM induces a ‘locked‐in’ configuration. FEBS J 2019; 286:2193-2215. [DOI: 10.1111/febs.14795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/02/2019] [Accepted: 02/25/2019] [Indexed: 01/03/2023]
Affiliation(s)
- Shiran Barber‐Zucker
- Department of Life Sciences Ben‐Gurion University of the Negev Beer Sheva Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer Sheva Israel
- Ilse Katz Institute for Nanoscale Science and Technology Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Jenny Hall
- School of Chemistry University of East Anglia Norwich Research Park UK
| | | | - Itamar Kass
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Sofiya Kolusheva
- Ilse Katz Institute for Nanoscale Science and Technology Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Fraser MacMillan
- School of Chemistry University of East Anglia Norwich Research Park UK
| | - Raz Zarivach
- Department of Life Sciences Ben‐Gurion University of the Negev Beer Sheva Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer Sheva Israel
- Ilse Katz Institute for Nanoscale Science and Technology Ben‐Gurion University of the Negev Beer Sheva Israel
| | - Arnon Henn
- Faculty of Biology Technion‐ Israel Institute of Technology Haifa Israel
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6
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Yang W, Riley BT, Lei X, Porebski BT, Kass I, Buckle AM, McGowan S. Cover Feature: Mapping the Pathway and Dynamics of Bestatin Inhibition of the
Plasmodium falciparum
M1 Aminopeptidase
Pf
A‐M1 (ChemMedChem 23/2018). ChemMedChem 2018. [DOI: 10.1002/cmdc.201800741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wei Yang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Blake T. Riley
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Xiangyun Lei
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta GA USA
| | - Benjamin T. Porebski
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
- Current address: Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Itamar Kass
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
- Victorian Life Sciences Computation CentreMonash University Clayton VIC 3800 Australia
| | - Ashley M. Buckle
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Sheena McGowan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
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7
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Yang W, Riley BT, Lei X, Porebski BT, Kass I, Buckle AM, McGowan S. Mapping the Pathway and Dynamics of Bestatin Inhibition of the
Plasmodium falciparum
M1 Aminopeptidase
Pf
A‐M1. ChemMedChem 2018; 13:2504-2513. [DOI: 10.1002/cmdc.201800563] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/04/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Wei Yang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Blake T. Riley
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Xiangyun Lei
- School of Chemical and Biomolecular EngineeringGeorgia Institute of Technology Atlanta GA USA
| | - Benjamin T. Porebski
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
- Current address: Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Itamar Kass
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
- Victorian Life Sciences Computation CentreMonash University Clayton VIC 3800 Australia
| | - Ashley M. Buckle
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
| | - Sheena McGowan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery InstituteMonash University Clayton VIC 3800 Australia
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8
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Li C, Clark LVT, Zhang R, Porebski BT, McCoey JM, Borg NA, Webb GI, Kass I, Buckle M, Song J, Woolfson A, Buckle AM. Structural Capacitance in Protein Evolution and Human Diseases. J Mol Biol 2018; 430:3200-3217. [PMID: 30111491 DOI: 10.1016/j.jmb.2018.06.051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/18/2018] [Accepted: 06/29/2018] [Indexed: 10/28/2022]
Abstract
Canonical mechanisms of protein evolution include the duplication and diversification of pre-existing folds through genetic alterations that include point mutations, insertions, deletions, and copy number amplifications, as well as post-translational modifications that modify processes such as folding efficiency and cellular localization. Following a survey of the human mutation database, we have identified an additional mechanism that we term "structural capacitance," which results in the de novo generation of microstructure in previously disordered regions. We suggest that the potential for structural capacitance confers select proteins with the capacity to evolve over rapid timescales, facilitating saltatory evolution as opposed to gradualistic canonical Darwinian mechanisms. Our results implicate the elements of protein microstructure generated by this distinct mechanism in the pathogenesis of a wide variety of human diseases. The benefits of rapidly furnishing the potential for evolutionary change conferred by structural capacitance are consequently counterbalanced by this accompanying risk. The phenomenon of structural capacitance has implications ranging from the ancestral diversification of protein folds to the engineering of synthetic proteins with enhanced evolvability.
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Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Liah V T Clark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Rory Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Julia M McCoey
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia; Amai Proteins, Prof. A. D. Bergman 2B, Suite 212, Rehovot 7670504, Israel
| | - Malcolm Buckle
- LBPA, ENS Cachan, CNRS, Université Paris-Saclay, F-94235 Cachan, France
| | - Jiangning Song
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | | | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.
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9
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Yang W, Riley BT, Lei X, Porebski BT, Kass I, Buckle AM, McGowan S. Generation of AMBER force field parameters for zinc centres of M1 and M17 family aminopeptidases. J Biomol Struct Dyn 2017; 36:2595-2604. [DOI: 10.1080/07391102.2017.1364669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wei Yang
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Blake T. Riley
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Xiangyun Lei
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive N.W., Atlanta, GA, 30332-0100, USA
| | - Benjamin T. Porebski
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Itamar Kass
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Victorian Life Sciences Computation Centre, Monash University, Clayton 3800, Victoria, Australia
| | - Ashley M. Buckle
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Sheena McGowan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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10
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Riley BT, Ilyichova O, Costa MGS, Porebski BT, de Veer SJ, Swedberg JE, Kass I, Harris JM, Hoke DE, Buckle AM. Direct and indirect mechanisms of KLK4 inhibition revealed by structure and dynamics. Sci Rep 2016; 6:35385. [PMID: 27767076 PMCID: PMC5073354 DOI: 10.1038/srep35385] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 09/28/2016] [Indexed: 11/09/2022] Open
Abstract
The kallikrein-related peptidase (KLK) family of proteases is involved in many aspects of human health and disease. One member of this family, KLK4, has been implicated in cancer development and metastasis. Understanding mechanisms of inactivation are critical to developing selective KLK4 inhibitors. We have determined the X-ray crystal structures of KLK4 in complex with both sunflower trypsin inhibitor-1 (SFTI-1) and a rationally designed SFTI-1 derivative to atomic (~1 Å) resolution, as well as with bound nickel. These structures offer a structural rationalization for the potency and selectivity of these inhibitors, and together with MD simulation and computational analysis, reveal a dynamic pathway between the metal binding exosite and the active site, providing key details of a previously proposed allosteric mode of inhibition. Collectively, this work provides insight into both direct and indirect mechanisms of inhibition for KLK4 that have broad implications for the enzymology of the serine protease superfamily, and may potentially be exploited for the design of therapeutic inhibitors.
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Affiliation(s)
- Blake T Riley
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Olga Ilyichova
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland 4059, Australia
| | - David E Hoke
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
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11
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Porebski BT, Keleher S, Hollins JJ, Nickson AA, Marijanovic EM, Borg NA, Costa MGS, Pearce MA, Dai W, Zhu L, Irving JA, Hoke DE, Kass I, Whisstock JC, Bottomley SP, Webb GI, McGowan S, Buckle AM. Smoothing a rugged protein folding landscape by sequence-based redesign. Sci Rep 2016; 6:33958. [PMID: 27667094 PMCID: PMC5036219 DOI: 10.1038/srep33958] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/01/2016] [Indexed: 11/09/2022] Open
Abstract
The rugged folding landscapes of functional proteins puts them at risk of misfolding and aggregation. Serine protease inhibitors, or serpins, are paradigms for this delicate balance between function and misfolding. Serpins exist in a metastable state that undergoes a major conformational change in order to inhibit proteases. However, conformational labiality of the native serpin fold renders them susceptible to misfolding, which underlies misfolding diseases such as α1-antitrypsin deficiency. To investigate how serpins balance function and folding, we used consensus design to create conserpin, a synthetic serpin that folds reversibly, is functional, thermostable, and polymerization resistant. Characterization of its structure, folding and dynamics suggest that consensus design has remodeled the folding landscape to reconcile competing requirements for stability and function. This approach may offer general benefits for engineering functional proteins that have risky folding landscapes, including the removal of aggregation-prone intermediates, and modifying scaffolds for use as protein therapeutics.
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Affiliation(s)
- Benjamin T Porebski
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom
| | - Shani Keleher
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Jeffrey J Hollins
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Adrian A Nickson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Emilia M Marijanovic
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Natalie A Borg
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Mauricio G S Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, 21949900 Rio de Janeiro, Brazil
| | - Mary A Pearce
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Weiwen Dai
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Liguang Zhu
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - James A Irving
- Wolfson Institute for Biomedical Research, University College London, Gower Street, London, WC1E 6BT, United Kingdom
| | - David E Hoke
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - James C Whisstock
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, Australia
| | - Stephen P Bottomley
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Geoffrey I Webb
- Faculty of Information Technology, Monash University, Clayton, Victoria 3800, Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.,Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M Buckle
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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12
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Barber-Zucker S, Uebe R, Davidov G, Navon Y, Sherf D, Chill JH, Kass I, Bitton R, Schüler D, Zarivach R. Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance. Sci Rep 2016; 6:31933. [PMID: 27550551 PMCID: PMC4994047 DOI: 10.1038/srep31933] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/29/2016] [Indexed: 11/08/2022] Open
Abstract
Cation diffusion facilitators (CDF) are highly conserved, metal ion efflux transporters that maintain divalent transition metal cation homeostasis. Most CDF proteins contain two domains, the cation transporting transmembrane domain and the regulatory cytoplasmic C-terminal domain (CTD). MamM is a magnetosome-associated CDF protein essential for the biomineralization of magnetic iron-oxide particles in magnetotactic bacteria. To investigate the structure-function relationship of CDF cytoplasmic domains, we characterized a MamM M250P mutation that is synonymous with the disease-related mutation L349P of the human CDF protein ZnT-10. Our results show that the M250P exchange in MamM causes severe structural changes in its CTD resulting in abnormal reduced function. Our in vivo, in vitro and in silico studies indicate that the CTD fold is critical for CDF proteins' proper function and support the previously suggested role of the CDF cytoplasmic domain as a CDF regulatory element. Based on our results, we also suggest a mechanism for the effects of the ZnT-10 L349P mutation in human.
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Affiliation(s)
- Shiran Barber-Zucker
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - René Uebe
- Department of Microbiology, University of Bayreuth, Bayreuth, 95447, Germany
| | - Geula Davidov
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Yotam Navon
- Department of Chemical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Dror Sherf
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Jordan H. Chill
- Department of Chemistry, Bar-Ilan University, Ramat-Gan, 5290002, Israel
| | - Itamar Kass
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ronit Bitton
- Department of Chemical Engineering and Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, Bayreuth, 95447, Germany
| | - Raz Zarivach
- Department of Life Sciences and The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
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13
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Le SN, Porebski BT, McCoey J, Fodor J, Riley B, Godlewska M, Góra M, Czarnocka B, Banga JP, Hoke DE, Kass I, Buckle AM. Modelling of Thyroid Peroxidase Reveals Insights into Its Enzyme Function and Autoantigenicity. PLoS One 2015; 10:e0142615. [PMID: 26623656 PMCID: PMC4666655 DOI: 10.1371/journal.pone.0142615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 10/23/2015] [Indexed: 11/18/2022] Open
Abstract
Thyroid peroxidase (TPO) catalyses the biosynthesis of thyroid hormones and is a major autoantigen in Hashimoto's disease--the most common organ-specific autoimmune disease. Epitope mapping studies have shown that the autoimmune response to TPO is directed mainly at two surface regions on the molecule: immunodominant regions A and B (IDR-A, and IDR-B). TPO has been a major target for structural studies for over 20 years; however, to date, the structure of TPO remains to be determined. We have used a molecular modelling approach to investigate plausible modes of TPO structure and dimer organisation. Sequence features of the C-terminus are consistent with a coiled-coil dimerization motif that most likely anchors the TPO dimer in the apical membrane of thyroid follicular cells. Two contrasting models of TPO were produced, differing in the orientation and exposure of their active sites relative to the membrane. Both models are equally plausible based upon the known enzymatic function of TPO. The "trans" model places IDR-B on the membrane-facing side of the myeloperoxidase (MPO)-like domain, potentially hindering access of autoantibodies, necessitating considerable conformational change, and perhaps even dissociation of the dimer into monomers. IDR-A spans MPO- and CCP-like domains and is relatively fragmented compared to IDR-B, therefore most likely requiring domain rearrangements in order to coalesce into one compact epitope. Less epitope fragmentation and higher solvent accessibility of the "cis" model favours it slightly over the "trans" model. Here, IDR-B clusters towards the surface of the MPO-like domain facing the thyroid follicular lumen preventing steric hindrance of autoantibodies. However, conformational rearrangements may still be necessary to allow full engagement with autoantibodies, with IDR-B on both models being close to the dimer interface. Taken together, the modelling highlights the need to consider the oligomeric state of TPO, its conformational properties, and its proximity to the membrane, when interpreting epitope-mapping data.
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Affiliation(s)
- Sarah N. Le
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Benjamin T. Porebski
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Julia McCoey
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - James Fodor
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Blake Riley
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Marlena Godlewska
- The Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Warsaw, Poland
| | - Monika Góra
- Institute of Biochemistry and Biophysics PAS, Department of Genetics, Warsaw, Poland
| | - Barbara Czarnocka
- The Centre of Postgraduate Medical Education, Department of Biochemistry and Molecular Biology, Warsaw, Poland
| | - J Paul Banga
- King's College London School of Medicine, Division of Diabetes and Nutrition Sciences, London, United Kingdom
| | - David E. Hoke
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Itamar Kass
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- * E-mail: (AMB); (IK)
| | - Ashley M. Buckle
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- * E-mail: (AMB); (IK)
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14
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Riley BT, Broendum SS, Reboul CF, Cowieson NP, Costa MGS, Kass I, Jackson C, Perahia D, Buckle AM, McGowan S. Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC. PLoS One 2015; 10:e0140219. [PMID: 26470022 PMCID: PMC4607406 DOI: 10.1371/journal.pone.0140219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 09/23/2015] [Indexed: 11/26/2022] Open
Abstract
The growing problem of antibiotic resistance underlies the critical need to develop new treatments to prevent and control resistant bacterial infection. Exogenous application of bacteriophage lysins results in rapid and specific destruction of Gram-positive bacteria and therefore lysins represent novel antibacterial agents. The PlyC phage lysin is the most potent lysin characterized to date and can rapidly lyse Group A, C and E streptococci. Previously, we have determined the X-ray crystal structure of PlyC, revealing a complicated and unique arrangement of nine proteins. The scaffold features a multimeric cell-wall docking assembly bound to two catalytic domains that communicate and work synergistically. However, the crystal structure appeared to be auto-inhibited and raised important questions as to the mechanism underlying its extreme potency. Here we use small angle X-ray scattering (SAXS) and reveal that the conformational ensemble of PlyC in solution is different to that in the crystal structure. We also investigated the flexibility of the enzyme using both normal mode (NM) analysis and molecular dynamics (MD) simulations. Consistent with our SAXS data, MD simulations show rotational dynamics of both catalytic domains, and implicate inter-domain communication in achieving a substrate-ready conformation required for enzyme function. Our studies therefore provide insights into how the domains in the PlyC holoenzyme may act together to achieve its extraordinary potency.
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Affiliation(s)
- Blake T. Riley
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Sebastian S. Broendum
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Cyril F. Reboul
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Australia
| | | | - Mauricio G. S. Costa
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Itamar Kass
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Victorian Life Sciences Computation Initiative Life Sciences Computation Centre, Monash University, Clayton, Australia
| | - Colin Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, Cachan, France
| | - Ashley M. Buckle
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- * E-mail: (AMB); (SM)
| | - Sheena McGowan
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
- Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- * E-mail: (AMB); (SM)
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15
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Lim SS, Yang W, Krishnarjuna B, Kannan Sivaraman K, Chandrashekaran IR, Kass I, MacRaild CA, Devine SM, Debono CO, Anders RF, Scanlon MJ, Scammells PJ, Norton RS, McGowan S. Structure and dynamics of apical membrane antigen 1 from Plasmodium falciparum FVO. Biochemistry 2014; 53:7310-20. [PMID: 25360546 DOI: 10.1021/bi5012089] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Apical membrane antigen 1 (AMA1) interacts with RON2 to form a protein complex that plays a key role in the invasion of host cells by malaria parasites. Blocking this protein-protein interaction represents a potential route to controlling malaria and related parasitic diseases, but the polymorphic nature of AMA1 has proven to be a major challenge to vaccine-induced antibodies and peptide inhibitors exerting strain-transcending inhibitory effects. Here we present the X-ray crystal structure of AMA1 domains I and II from Plasmodium falciparum strain FVO. We compare our new structure to those of AMA1 from P. falciparum 3D7 and Plasmodium vivax. A combination of normalized B factor analysis and computational methods has been used to investigate the flexibility of the domain I loops and how this correlates with their roles in determining the strain specificity of human antibody responses and inhibitory peptides. We also investigated the domain II loop, a key region involved in inhibitor binding, by comparison of multiple AMA1 crystal structures. Collectively, these results provide valuable insights that should contribute to the design of strain-transcending agents targeting P. falciparum AMA1.
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Affiliation(s)
- San Sui Lim
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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16
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Samson AL, Knaupp AS, Kass I, Kleifeld O, Marijanovic EM, Hughes VA, Lupton CJ, Buckle AM, Bottomley SP, Medcalf RL. Oxidation of an exposed methionine instigates the aggregation of glyceraldehyde-3-phosphate dehydrogenase. J Biol Chem 2014; 289:26922-26936. [PMID: 25086035 DOI: 10.1074/jbc.m114.570275] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is a ubiquitous and abundant protein that participates in cellular energy production. GAPDH normally exists in a soluble form; however, following necrosis, GAPDH and numerous other intracellular proteins convert into an insoluble disulfide-cross-linked state via the process of "nucleocytoplasmic coagulation." Here, free radical-induced aggregation of GAPDH was studied as an in vitro model of nucleocytoplasmic coagulation. Despite the fact that disulfide cross-linking is a prominent feature of GAPDH aggregation, our data show that it is not a primary rate-determining step. To identify the true instigating event of GAPDH misfolding, we mapped the post-translational modifications that arise during its aggregation. Solvent accessibility and energy calculations of the mapped modifications within the context of the high resolution native GAPDH structure suggested that oxidation of methionine 46 may instigate aggregation. We confirmed this by mutating methionine 46 to leucine, which rendered GAPDH highly resistant to free radical-induced aggregation. Molecular dynamics simulations suggest that oxidation of methionine 46 triggers a local increase in the conformational plasticity of GAPDH that likely promotes further oxidation and eventual aggregation. Hence, methionine 46 represents a "linchpin" whereby its oxidation is a primary event permissive for the subsequent misfolding, aggregation, and disulfide cross-linking of GAPDH. A critical role for linchpin residues in nucleocytoplasmic coagulation and other forms of free radical-induced protein misfolding should now be investigated. Furthermore, because disulfide-cross-linked aggregates of GAPDH arise in many disorders and because methionine 46 is irrelevant to native GAPDH function, mutation of methionine 46 in models of disease should allow the unequivocal assessment of whether GAPDH aggregation influences disease progression.
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Affiliation(s)
- Andre L Samson
- Australian Centre for Blood Diseases, Monash University, Melbourne 3004, Victoria, Australia and; Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia.
| | - Anja S Knaupp
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia; Australian Regenerative Medicine Institute and Department of Anatomy and Developmental Biology, and Monash University, Clayton 3800, Victoria, Australia
| | - Itamar Kass
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia; Victorian Life Sciences Computation Centre, Monash University, Clayton 3800, Victoria, Australia
| | - Oded Kleifeld
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Emilia M Marijanovic
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Victoria A Hughes
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Chris J Lupton
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Stephen P Bottomley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton 3800, Victoria, Australia
| | - Robert L Medcalf
- Australian Centre for Blood Diseases, Monash University, Melbourne 3004, Victoria, Australia and.
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17
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Wijeyewickrema LC, Yongqing T, Tran TP, Thompson PE, Viljoen JE, Coetzer TH, Duncan RC, Kass I, Buckle AM, Pike RN. Molecular determinants of the substrate specificity of the complement-initiating protease, C1r. J Biol Chem 2013; 288:15571-80. [PMID: 23589288 PMCID: PMC3668718 DOI: 10.1074/jbc.m113.451757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 03/21/2013] [Indexed: 12/31/2022] Open
Abstract
The serine protease, C1r, initiates activation of the classical pathway of complement, which is a crucial innate defense mechanism against pathogens and altered-self cells. C1r both autoactivates and subsequently cleaves and activates C1s. Because complement is implicated in many inflammatory diseases, an understanding of the interaction between C1r and its target substrates is required for the design of effective inhibitors of complement activation. Examination of the active site specificity of C1r using phage library technology revealed clear specificity for Gln at P2 and Ile at P1', which are found in these positions in physiological substrates of C1r. Removal of one or both of the Gln at P2 and Ile at P1' in the C1s substrate reduced the rate of C1r activation. Substituting a Gln residue into the P2 of the activation site of MASP-3, a protein with similar domain structure to C1s that is not normally cleaved by C1r, enabled efficient activation of this enzyme. Molecular dynamics simulations and structural modeling of the interaction of the C1s activation peptide with the active site of C1r revealed the molecular mechanisms that particularly underpin the specificity of the enzyme for the P2 Gln residue. The complement control protein domains of C1r also made important contributions to efficient activation of C1s by this enzyme, indicating that exosite interactions were also important. These data show that C1r specificity is well suited to its cleavage targets and that efficient cleavage of C1s is achieved through both active site and exosite contributions.
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Affiliation(s)
- Lakshmi C. Wijeyewickrema
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Tang Yongqing
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Thuy P. Tran
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Phillip E. Thompson
- the Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia, and
| | - Jacqueline E. Viljoen
- the Department of Biochemistry, School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville 3209, South Africa
| | - Theresa H. Coetzer
- the Department of Biochemistry, School of Life Sciences, University of KwaZulu-Natal (Pietermaritzburg Campus), Private Bag X01, Scottsville 3209, South Africa
| | - Renee C. Duncan
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Itamar Kass
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Ashley M. Buckle
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Robert N. Pike
- From the Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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18
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Kass I, Knaupp AS, Bottomley SP, Buckle AM. Conformational properties of the disease-causing Z variant of α1-antitrypsin revealed by theory and experiment. Biophys J 2012; 102:2856-65. [PMID: 22735536 DOI: 10.1016/j.bpj.2012.05.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 05/09/2012] [Accepted: 05/16/2012] [Indexed: 11/24/2022] Open
Abstract
The human serine protease inhibitor (serpin) α-1 antitrypsin (α1-AT) protects tissues from proteases of inflammatory cells. The most common disease-causing mutation in α1-AT is the Z-mutation (E342K) that results in an increased propensity of α1-AT to polymerize in the ER of hepatocytes, leading to a lack of secretion into the circulation. The structural consequences of this mutation, however, remain elusive. We report a comparative molecular dynamics investigation of the native states of wild-type and Z α1-AT, revealing a striking contrast between their structures and dynamics in the breach region at the top of β-sheet A, which is closed in the wild-type simulations but open in the Z form. Our findings are consistent with experimental observations, notably the increased solvent exposure of buried residues in the breach region in Z, as well as polymerization via domain swapping, whereby the reactive center loop is rapidly inserted into an open A-sheet before proper folding of the C-terminal β-strands, allowing C-terminal domain swapping with a neighboring molecule. Taken together, our experimental and simulation data imply that mutations at residue 342 that either stabilize an open form of the top of β-sheet A or increase the local flexibility in this region, may favor polymerization and hence aggregation.
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Affiliation(s)
- Itamar Kass
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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19
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Abstract
Currently, over a hundred high-resolution structures of serpins are available, exhibiting a wide range of conformations. However, our understanding of serpin dynamics and conformational change is still limited, mainly due to challenges of monitoring structural changes and characterizing transient conformations using experimental methods. Insight can be provided, however, by employing theoretical and computational approaches. In this chapter, we present an overview of such methods, focusing on molecular dynamics and simulation. As serpin conformational dynamics span a wide range of timescales, we discuss the relative merits of each method and suggest which method is suited to specific conformational phenomena.
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Affiliation(s)
- Itamar Kass
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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20
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Kwan AH, Macindoe I, Vukasin PV, Morris VK, Kass I, Gupte R, Mark AE, Templeton MD, Mackay JP, Sunde M. The Cys3-Cys4 loop of the hydrophobin EAS is not required for rodlet formation and surface activity. J Mol Biol 2008; 382:708-20. [PMID: 18674544 DOI: 10.1016/j.jmb.2008.07.034] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 07/08/2008] [Accepted: 07/11/2008] [Indexed: 10/21/2022]
Abstract
Class I hydrophobins are fungal proteins that self-assemble into robust amphipathic rodlet monolayers on the surface of aerial structures such as spores and fruiting bodies. These layers share many structural characteristics with amyloid fibrils and belong to the growing family of functional amyloid-like materials produced by microorganisms. Although the three-dimensional structure of the soluble monomeric form of a class I hydrophobin has been determined, little is known about the molecular structure of the rodlets or their assembly mechanism. Several models have been proposed, some of which suggest that the Cys3-Cys4 loop has a critical role in the initiation of assembly or in the polymeric structure. In order to provide insight into the relationship between hydrophobin sequence and rodlet assembly, we investigated the role of the Cys3-Cys4 loop in EAS, a class I hydrophobin from Neurospora crassa. Remarkably, deletion of up to 15 residues from this 25-residue loop does not impair rodlet formation or reduce the surface activity of the protein, and the physicochemical properties of rodlets formed by this mutant are indistinguishable from those of its full-length counterpart. In addition, the core structure of the truncation mutant is essentially unchanged. Molecular dynamics simulations carried out on the full-length protein and this truncation mutant binding to an air-water interface show that, although it is hydrophobic, the loop does not play a role in positioning the protein at the surface. These results demonstrate that the Cys3-Cys4 loop does not have an integral role in the formation or structure of the rodlets and that the major determinant of the unique properties of these proteins is the amphipathic core structure, which is likely to be preserved in all hydrophobins despite the high degree of sequence variation across the family.
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Affiliation(s)
- Ann H Kwan
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, New South Wales 2006, Australia
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21
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Mukherjee P, Kass I, Arkin IT, Zanni MT. Structural disorder of the CD3zeta transmembrane domain studied with 2D IR spectroscopy and molecular dynamics simulations. J Phys Chem B 2006; 110:24740-9. [PMID: 17134238 PMCID: PMC2722928 DOI: 10.1021/jp0640530] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In a recently reported study [Mukherjee, et al. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 3528] we used 2D IR spectroscopy and 1-(13)C=(18)O isotope labeling to measure the vibrational dynamics of 11 amide I modes in the CD3zeta transmembrane domain. We found that the homogeneous line widths and population relaxation times were all nearly identical, but that the amount of inhomogeneous broadening correlated with the position of the amide group inside the membrane. In this study, we use molecular dynamics simulations to investigate the structural and dynamical origins of these experimental observations. We use two models to convert the simulations to frequency trajectories from which the mean frequencies, standard deviations, frequency correlation functions, and 2D IR spectra are calculated. Model 1 correlates the hydrogen-bond length to the amide I frequency, whereas model 2 uses an ab initio-based electrostatic model. We find that the structural distributions of the peptidic groups and their environment are reflected in the vibrational dynamics of the amide I modes. Environmental forces from the water and lipid headgroups partially denature the helices, shifting the infrared frequencies and creating larger inhomogeneous distributions for residues near the ends. The least inhomogeneously broadened residues are those located in the middle of the membrane where environmental electrostatic forces are weakest and the helices are most ordered. Comparison of the simulations to experiment confirms that the amide I modes near the C-terminal are larger than at the N-terminal because of the asymmetric structure of the peptide bundle in the membrane. The comparison also reveals that residues at a kink in the alpha-helices have broader line widths than more helical parts of the peptide because the peptide backbone at the kink exhibits a larger amount of structural disorder. Taken together, the simulations and experiments reveal that infrared line shapes are sensitive probes of membrane protein structural and environmental heterogeneity.
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Affiliation(s)
- Prabuddha Mukherjee
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
| | - Itamar Kass
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem 91904, Israel
| | - Isaiah T. Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem 91904, Israel
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin – Madison, Madison, Wisconsin 53706
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Arbely E, Granot Z, Kass I, Orly J, Arkin IT. A trimerizing GxxxG motif is uniquely inserted in the severe acute respiratory syndrome (SARS) coronavirus spike protein transmembrane domain. Biochemistry 2006; 45:11349-56. [PMID: 16981695 DOI: 10.1021/bi060953v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In an attempt to understand what distinguishes severe acute respiratory syndrome (SARS) coronavirus (SCoV) from other members of the coronaviridae, we searched for elements that are unique to its proteins and not present in any other family member. We identified an insertion of two glycine residues, forming the GxxxG motif, in the SCoV spike protein transmembrane domain (TMD), which is not found in any other coronavirus. This surprising finding raises an "oligomerization riddle": the GxxxG motif is a known dimerization signal, while the SCoV spike protein is known to be trimeric. Using an in vivo assay, we found that the SCoV spike protein TMD is oligomeric and that this oligomerization is driven by the GxxxG motif. We also found that the GxxxG motif contributes toward the trimerization of the entire spike protein; in that, mutations in the GxxxG motif decrease trimerization of the full-length protein expressed in mammalian cells. Using molecular modeling, we show that the SCoV spike protein TMD adopts a distinct and unique structure as opposed to all other coronaviruses. In this unique structure, the glycine residues of the GxxxG motif are facing each other, enhancing helix-helix interactions by allowing for the close positioning of the helices. This unique orientation of the glycine residues also stabilizes the trimeric bundle during multi-nanosecond molecular dynamics simulation in a hydrated lipid bilayer. To the best of our knowledge, this is the first demonstration that the GxxxG motif can potentiate other oligomeric forms beside a dimer. Finally, according to recent studies, the stabilization of the trimeric bundle is linked to a higher fusion activity of the spike protein, and the possible influence of the GxxxG motif on this feature is discussed.
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Affiliation(s)
- Eyal Arbely
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel
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Mukherjee P, Krummel AT, Fulmer EC, Kass I, Arkin IT, Zanni MT. Site-specific vibrational dynamics of the CD3zeta membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy. J Chem Phys 2006; 120:10215-24. [PMID: 15268045 DOI: 10.1063/1.1718332] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Heterodyned two-dimensional infrared (2D IR) spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3zeta. Using 1-(13)C[Double Bond](18)O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm(-1), respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm(-1) to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3zeta peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.
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Affiliation(s)
- Prabuddha Mukherjee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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24
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Abstract
Fast protein dynamics can be missed with techniques that have relatively slow observation times. Using 2D IR spectroscopy and isotope labeling, we have probed the rapid, picosecond dynamics of a membrane protein in its native environment. By measuring the homogeneous and inhomogeneous IR linewidths of 11 amide I modes (backbone carbonyl stretch), we have captured the structural distributions and dynamics of the CD3zeta protein along its transmembrane segment that are lost with slower time-scale techniques. We find that the homogeneous lifetimes and population relaxation times are the same for almost all of the residues. In contrast, the inhomogeneous linewidths vary significantly with the largest inhomogeneous distribution occurring for residues near the N terminus and the narrowest near the center. This behavior is highly consistent with a recently reported experimental model of the protein and water accessibility as observed by molecular dynamics simulations. The data support the proposed CD3zeta peptide structure, and the simulations point to the structural disorder of water and lipid head-groups as the main source of inhomogeneous broadening. Taken together, this rigorous analysis of the vibrational dynamics of a membrane peptide provides experimental insight into a time regime of motions that has so far been largely unexplored.
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Affiliation(s)
- Prabuddha Mukherjee
- Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396; and
| | - Itamar Kass
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, Hebrew University of Jerusalem, Edmund Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Isaiah T. Arkin
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, Hebrew University of Jerusalem, Edmund Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396; and
- To whom correspondence should be addressed. E-mail:
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25
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Kass I, Arkin IT. How pH opens a H+ channel: the gating mechanism of influenza A M2. Structure 2006; 13:1789-98. [PMID: 16338407 DOI: 10.1016/j.str.2005.08.022] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2005] [Revised: 07/14/2005] [Accepted: 08/14/2005] [Indexed: 11/26/2022]
Abstract
The tetrameric M2 protein from influenza A is one of the simplest pH-gated H+ channels known, offering the potential of structurally characterizing its gating mechanism. Since the only ionizable groups in the pore are four histidines, we investigated the stability and dynamics of all six possible protonation states of the protein by using molecular dynamics. We show that while all channel protonation states are surprisingly stable, only systems with two or more charged histidines are appreciably conductive. The structural switch, from a uniprotonated to a biprotonated channel, causes an electrostatic repulsion between the charged histidines that pushes the helices apart. This results in the formation of a continuous water file that conducts protons via a H+ wire. pKa calculations place this transition at a pH of 5.6, in remarkable agreement with the experimental value. Since the conversion from uniprotonation to biprotonation occurs during endosome acidification, this explains how M2 is activated in vivo.
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Affiliation(s)
- Itamar Kass
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem, 91904, Israel
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26
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Abstract
Site-specific infrared dichroism is an emerging method capable of proposing a model for the backbone structure of a transmembrane alpha-helix within a helical bundle. Dichroism measurements of single, isotopically enhanced vibrational modes (e.g., Amide I 13C=18O or Gly CD2 stretching modes) can yield precise orientational restraints for the monomer helix protomer that can be used as refinement constraints in model building of the entire helical bundle. Essential, however, for the interpretation of the dichroism measurements, is an accurate modeling of the sample disorder. In this study we derive an enhanced and more realistic modeling of the sample disorder based on a Gaussian distribution of the chromophore around a particular angle. The enhanced utility of the Gaussian model is exemplified by the comparative data analysis based on the aforementioned model to previously employed models.
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Affiliation(s)
- Itamar Kass
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Jerusalem, Israel
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27
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Abstract
Effective antivirals are few and far between, and as such, the appearance of resistance toward such treatments is an obvious medical concern. In this article, we analyze the mechanism by which influenza attains resistance toward amantadine, a blocker of the viral M2 H(+) channel. Binding analyses of amantadine to M2 peptides from different viral strains showed that the virus has developed two alternate routes to avoid blockage of its channel: (1) a conventional route, in which the channel no longer binds the blocker and, hence, the blocker cannot exert its inhibitory function; and (2) a novel mechanism, in which binding of the blocker is retained, yet the function of the protein is unaffected. Pore diameter profiles revealed the molecular mechanism by which the virus may attain this novel type of resistance: an increase in the size of the channel. Thus, despite the drug binding the channel, it may not be able to block the pore, since the channel diameter has increased. Our findings may have broad ramifications in the design of new antivirals, and of novel blockers against malfunctioning human channels implicated in disease.
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Affiliation(s)
- Peleg Astrahan
- Department of Biological Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University, Jerusalem, Israel
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28
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Abstract
Infrared spectroscopy has long been used to examine the average secondary structure and orientation of membrane proteins. With the recent utilization of site-specific isotope labeling (e.g., peptidic 1-(13)C = (18)O) it is now possible to examine localized properties, rather than global averages. The technique of site-specific infrared dichroism (SSID) capitalized on this fact, and derives site-specific orientational restraints for the labeled amino acids. These restraints can then be used to solve the backbone structure of simple alpha-helical bundles, emphasizing the capabilities of this approach. So far SSID has been carried out in attenuated total internal reflection optical mode, with all of the respective caveats of attenuated total internal reflection. In this report we extend SSID through the use of transmission infrared spectroscopy tilt series. We develop the corresponding theory and demonstrate that accurate site-specific orientational restraints can be derived from a simple transmission experiment.
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Affiliation(s)
- Eyal Arbely
- The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem, Israel
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29
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Abstract
An interesting example of an allosteric protein is the chaperonin GroEL. It undergoes adenosine 5'-triphosphate-induced conformational changes that are reflected in binding of adenosine 5'-triphosphate with positive cooperativity within rings and negative cooperativity between rings. Herein, correlated mutations in chaperonins are analyzed to unravel routes of allosteric communication in GroEL and in its complex with its co-chaperonin GroES. It is shown that analysis of correlated mutations in the chaperonin family can provide information about pathways of allosteric communication within GroEL and between GroEL and GroES. The results are discussed in the context of available structural, genetic, and biochemical data concerning short- and long-range interactions in the GroE system.
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Affiliation(s)
- Itamar Kass
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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Daughton DM, Kass I, Fix AJ, Ahrens K, Rennard SI. Smoking intervention: combination therapy using nicotine chewing gum and the American Lung Association's "Freedom from Smoking" manuals. Prev Med 1986; 15:432-5. [PMID: 3763565 DOI: 10.1016/0091-7435(86)90010-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The smoking cessation efficacy of a two-session group program using the American Lung Association's "Freedom from Smoking" self-help manuals, nicotine gum, and brief, repeated professional supervision was estimated in an uncontrolled clinical trial. Of the 39 participants, 12 (31%) remained cigarette free for 1 year, and 4 others (10%) had not smoked during the 3 months prior to the 1-year follow-up. Claims of cessation were verified by expired-air carbon monoxide measurement. Nearly all successful abstainers were able to achieve 48-hr cessation during their first week using the gum. This finding suggests that nicotine gum is best used to help the smoker quit abruptly, rather than as an aid in a tapering-off strategy. This study's smoking intervention program appears to provide a relatively low-cost method of improving the success rates among smokers who wish to quit.
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31
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Fix AJ, Daughton D, Kass I, Bell CW, Golden CJ. Cognitive functioning and survival among patients with chronic obstructive pulmonary disease. Int J Neurosci 1985; 27:13-7. [PMID: 3926683 DOI: 10.3109/00207458509149131] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An earlier study by the authors had demonstrated neuropsychological impairment among 66 clinically stable patients suffering from chronic obstructive pulmonary disease (COPD), and had found that the deficits were directly associated with the amount of oxygen available to body tissue. We were able to follow 62 of the patients for three years when retrospective analyses were performed to determine the relationship of the neuropsychological test scores with the patients' three-year survival status. Patients who survived had scored significantly (p less than 0.01) higher on the neuropsychological tests than those who had died. Individual analyses of variance indicated that the significant relationship between the neuropsychological tests and survival status was attributable primarily to the Benton Visual Motor Retention Test and the digit symbol subtest of the Wechsler Adult Intelligence Scale. The latter test had, in the earlier study, shown the strongest relationship with partial pressure of oxygen and with a pulmonary function test. These findings suggest that certain neuropsychological tests may reflect both the progress of COPD and three-year survival probability among the patients.
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Abstract
Long-term effects of ipratropium bromide (IB) were evaluated using a double-blind cross-over design in 23 adult chronic bronchitic participants. Two 20-micrograms doses of either IB or placebo were administered as an inhalant four times a day for a period of seven weeks. Sputum volume expectorated during a 24-hour period decreased significantly (p less than 0.05) over the entire length of the study, but sputum viscosity or its dry weight were not affected. Although total number of inflammatory cells in sputum was decreased by the use of IB (p less than 0.05), macrophages increased slightly. Subjects coughed less while receiving IB, and their cough was less severe (p less than 0.05). Ipratropium bromide caused a significant improvement (p less than 0.05) in the mechanics of breathing primarily in the subjects between 46 to 55 years of age. No major adverse reaction to IB was recorded.
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33
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Daughton DM, James Fix A, Kass I, Patil KD. Three-year survival rates of pulmonary rehabilitation patients with chronic obstructive pulmonary disease. J Natl Med Assoc 1984; 76:265-8. [PMID: 6425508 PMCID: PMC2561620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A retrospective study analyzed medical and psychosocial factors associated with the three-year survival rates of clinically stable chronic obstructive pulmonary disease patients enrolled in a pulmonary rehabilitation program. The 69 percent three-year survival rate was similar to rates reported in previous studies. Neither continued cigarette smoking nor psychological variables were significantly associated with patient longevity. Discriminant analysis revealed that the combination of arterial O(2) and CO(2) tensions or its simple approximation (PaO(2) - PaCO(2)) was the best predictor of patient survival at three years.
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34
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Repsher LH, Anderson JA, Bush RK, Falliers CJ, Kass I, Kemp JP, Reed C, Siegel S, Webb DR. Assessment of tachyphylaxis following prolonged therapy of asthma with inhaled albuterol aerosol. Chest 1984; 85:34-8. [PMID: 6360573 DOI: 10.1378/chest.85.1.34] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Controversy exists concerning possible tachyphylaxis of the acute bronchodilating effect of albuterol, especially with regard to the duration of its acute bronchodilating action. We evaluated 140 patients with bronchial asthma in a prospective double-blind controlled study of possible tachyphylaxis to albuterol aerosol as compared to isoproterenol aerosol. We demonstrated statistically significant tachyphylaxis with regard to duration of acute bronchodilating effect. We believe that this tachyphylaxis is not clinically significant because there was no tachyphylaxis with regard to peak bronchodilating effect and because the duration of bronchodilating effect remains significantly greater, both quantitatively and statistically, when compared to isoproterenol aerosol. Moreover, it appeared that most of the tachyphylaxis was present at four weeks of therapy. There was a small increment of tachyphylaxis after eight weeks of therapy, but no further increase in tachyphylaxis was demonstrated after 13 weeks of inhaled albuterol therapy. We therefore feel that clinically significant tachyphylaxis to inhaled albuterol aerosol must be quite unusual and that chronic therapy with inhaled albuterol aerosol is probably both safe and efficacious for bronchospastic disorders.
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35
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Daughton D, Fix AJ, Kass I, McDonald T, Stevens C. Relationship between a pulmonary function test (FEV1) and the ADAPT quality-of-life scale. Percept Mot Skills 1983; 57:359-62. [PMID: 6634316 DOI: 10.2466/pms.1983.57.2.359] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In a previous study the Additive Daily Activities Profile Test (ADAPT) correlated .83 with maximum oxygen consumption among pulmonary rehabilitation patients. The present study expanded the pulmonary population base and compared the ADAPT scores of 41 patients at two independent centers with a more readily available parameter, the forced expiratory volume in the first second of forced exhalation (FEV1). The relationships between the two major ADAPT subscales and FEV1 were significant but lower in magnitude than that found with maximum oxygen consumption. The ADAPT continues to be sensitive to physical impairment and in translating the effect of impairment upon daily physical activity.
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Abstract
Previous studies have shown that large doses of a urinary alkalinizing agent reduced cigarette consumption spontaneously among smokers. After establishing a safe daily dose of an alkalinizing agent, sodium bicarbonate, its effect upon smoking cessation rates among 72 enrollees in a smoking cessation program was studied. In the first study, we determined that sodium bicarbonate (3900 mg per day) significantly increased urinary pH (from 6.0 to 6.7) and lowered titratable acidity. Ascorbic acid (1500 mg per day) had no effect of pH or acidity. In a second study, a group given sodium bicarbonate surpassed a placebo control group (who were given 1500 mg per day ascorbic acid) in total daily cigarette reduction after 5 weeks and in week-to-week smoking reduction. The groups did not, however, differ in the number who achieved total abstinence.
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37
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Daughton DM, Fix AJ, Kass I, Bell CW, Patil KD. Maximum oxygen consumption and the ADAPT quality-of-life scale. Arch Phys Med Rehabil 1982; 63:620-2. [PMID: 7149948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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38
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Abstract
Sixty-six patients with chronic obstructive pulmonary disease (COPD) were evaluated for neuropsychological functioning. While the patients showed normal skills on broad intellectual tasks, they displayed mild cerebral deficits on several neuropsychological tests. Multiple regression analyses revealed that the neuropsychological test battery scores were significantly related to partial pressure of arterial oxygen (PaO2), and to degree of pulmonary impairment. Although the cognitive deficits were real, they were generally small. This result may explain why the widely assumed link between chronic lung disorders and cognitive deficit has been difficult to demonstrate. The general pattern was similar to deficits produced by chronic alcoholism and childhood asthma, with complex skills suffering the greatest insult. Because the cognitive deficits among COPD patients in stable condition are small, it is uncertain whether they have importance clinically or for accomplishing daily activities.
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39
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Bell CW, Drehsen SF, Kass I, Burgher LW. A COMPARISON OF VERTICAL AND HORIZONTAL POSITION EXERCISE ON ARTERIAL OXYGEN SATURATION IN PULMONARY PATIENTS. Med Sci Sports Exerc 1982. [DOI: 10.1249/00005768-198202000-00142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Hodgkin JE, Farrell MJ, Gibson SR, Kanner RE, Kass I, Lampton LM, Nield M, Petty TL. American Thoracic Society. Medical Section of the American Lung Association. Pulmonary rehabilitation. Am Rev Respir Dis 1981; 124:663-6. [PMID: 7305126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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41
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Bell CW, Rohe DA, Patil K, Kass I. 1: 45 p.m.: ENERGETICS OF CRUTCH WALKING IN CHILDREN KITH MYELOMENINGOCELE. Med Sci Sports Exerc 1981. [DOI: 10.1249/00005768-198101320-00317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Abstract
Bitolterol mesylate (WIN 37284) is alpha-[tert-butylaminomethyl]-3,4-dihydroxybenzyl alcohol 3,4-di(p-toluate) methanesulfonate, a diester sympathomimetic amine bronchodilator. Bitolterol mesylate represents a new concept in sympathomimetic amine therapy. It is "prodrug" which is inactive until altered in the body. The intact 3,4-diester molecule is metabolized by esterase hydrolysis to release the active catecholamine, N-t-butylarterenol. Because the level of esterase is greater in the pulmonary tissue than in the heart, bitolterol mesylate aerosol was shown to be an effective bronchodilator drug, without any significant cardic side effects. The onset of action was rapid and lasted more than six hours. The improvement over baseline values in the forced expiratory volume in the first second and the mean forced expiratory flow during the middle half of the forced vital capacity was greater than 15 percent and 30 percent, respectively.
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Fix AJ, Daughton D, Kass I, Bell CW, Golden CJ. Emotional, intellectual and physiological predictors of vocational outcome of pulmonary rehabilitation patients. Psychol Rep 1980; 46:379-82. [PMID: 7384347 DOI: 10.2466/pr0.1980.46.2.379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Previous researchers have independently shown that pulmonary function measures, intelligence test scores, and a recently developed MMPI-derived scale can predict post-hospital employment among rehabilitation patients with chronic obstructive pulmonary disease. This study compared the effectiveness of the three variables in predicting employment among a group of vocational rehabilitation candidates with chronic obstructive pulmonary disease. Only the MMPI-derived scale (COPD-VR) identified the non-working patients significantly above base rate. While this finding does not necessarily mean that personality, or attitudinal, factors are more important than physiological or intellectual variables in vocational rehabilitation success among such patients, it gives further support to the validity of the COPD-VR scale.
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45
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Abstract
A woman developed peripheral neuropathy and optic neuritis while receiving ethambutol in the retreatment of drug-resistant pulmonary tuberculosis. There was prompt improvement in peripheral neuropathy and the ocular symptoms following the withdrawal of the drug. The clinical events in this case suggest that occasionally symptoms of peripheral neuropathy may precede the development of optic neuritis by several months, and thus serve as a warning for the subsequent development of the more serious visual toxicity.
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47
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Abstract
Because carbon monoxide (CO) is an easily understood danger of cigarette smoking, new breath CO analyzers may be useful in cessation programs. Self-reported cigarette consumption and breath CO correlated .70 using a 90-sec. CO-determination method. Smokers averaging 17 daily cigarettes had average breath CO of 24 parts per million (ppm), falling to 7.71 ppm for smokers claiming at least 24-hr. abstinence. Corresponding carboxyhemoglobin (COHb) estimates were 4.34% (slightly above World Health Organization 4% safety limit) and 1.39%. Smoking clinics can use CO-monitoring devices for feedback or surveillance, although feedback would provide the most benefits for participants.
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48
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Daughton DM, Fix AJ, Kass I, Patil KD, Bell CW. Physiological-intellectual components of rehabilitation success in patients with chronic obstructive pulmonary disease (COPD). J Chronic Dis 1979; 32:405-9. [PMID: 447791 DOI: 10.1016/0021-9681(79)90081-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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49
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Fix AJ, Daughton D, Kass I, Patil KD, Kass M, Polenz D. Personality traits affecting vocational rehabilitation success in patients with chronic obstructive pulmonary disease. Psychol Rep 1978; 43:939-44. [PMID: 740836 DOI: 10.2466/pr0.1978.43.3.939] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Item analysis of the Minnesota Multiphasic Personality Inventory responses of 147 patients with chronic obstructive pulmonary disease produced 48 items associated with three levels of post-hospital vocational adjustment, and with death. A subgroup of vocational rehabilitation candidates provided insights to the psychological processes underlying successful outcome. Those who worked more than six months following hospitalization were more gregarious and used more denial than other patients. Those who did not work at all were more anxious and had lower self-confidence. Patients who died within a year had shown a charitable philosophical orientation'.
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50
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Kass I, Vijayachandra Nair S, Patil KD. Beclomethasone dipropionate aerosol in the treatment of steroid-dependent asthmatic patients. An assessment of 18 months of therapy. Chest 1977; 71:703-7. [PMID: 405181 DOI: 10.1378/chest.71.6.703] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Twenty-nine of 33 steroid-dependent asthmatic patients received 18 months of therapy with beclomethasone dipropionate. Only four of 29 subjects required concurrent oral therapy with steroids. Twenty-six of 29 patients noted a marked improvement in their asthma; three of 29 described an indeterminate response. A statistically significant improvement in many of the symptoms, the plasma cortisol level, the first-second forced expiratory volume, and the forced expiratory flow at 50 percent of the observed forced vital capacity was present only at the end of three months of therapy with beclomethasone dipropionate. Steroid-withdrawal symptoms, particularly those related to the nose and sinuses, were initially troublesome but decreased with the passage of time. No oropharyngeal fungal infections were observed. At a dose below the hypothalamic-pituitary-adrenal suppressive level, therapy with beclomethasone dipropionate appears to be safe and effective for treating patients with steroid-dependent asthma.
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