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Watterson JG. The cluster model of energy transduction in biological systems. Biosystems 2024; 240:105213. [PMID: 38616011 DOI: 10.1016/j.biosystems.2024.105213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 04/16/2024]
Abstract
The central problem in transduction is to explain how the energy caught from sunlight by chloroplasts becomes biological work. Or to express it in different terms: how does the energy remain trapped in the biological network and not get lost through thermalization into the environment? The pathway consists of an immensely large number of steps crossing hierarchical levels - some upwards, to larger assemblies, others downwards into energy rich molecules - before fuelling an action potential or a contracting cell. Accepting the assumption that steps are executed by protein domains, we expect that transduction mechanisms are the result of conformational changes, which in turn involve rearrangements of the bonds responsible for the protein fold. But why are these essential changes so difficult to detect? In this presentation, the metabolic pathway is viewed as equivalent to an energy conduit composed of equally sized units - the protein domains - rather than a row of catalysts. The flow of energy through them occurs by the same mechanism as through the cytoplasmic medium (water). This mechanism is based on the cluster-wave model of water structure, which successfully explains the transfer of energy through the liquid medium responsible for the build up of osmotic pressure. The analogy to the line of balls called "Newton's cradle" provides a useful comparison, since there the transfer is also invisible to us because the intermediate balls are motionless. It is further proposed that the spatial arrangements of the H-bonds of the α and β secondary structures support wave motion, with the linear and lateral forms of the groups of bonds belonging to the helices and sheets executing the longitudinal and transverse modes, respectively.
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2
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Sasmal S, Pal T, Hocky GM, McCullagh M. Quantifying Unbiased Conformational Ensembles from Biased Simulations Using ShapeGMM. J Chem Theory Comput 2024; 20:3492-3502. [PMID: 38662196 PMCID: PMC11104435 DOI: 10.1021/acs.jctc.4c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/26/2024]
Abstract
Quantifying the conformational ensembles of biomolecules is fundamental to describing mechanisms of processes such as protein folding, interconversion between folded states, ligand binding, and allosteric regulation. Accurate quantification of these ensembles remains a challenge for conventional molecular simulations of all but the simplest molecules due to insufficient sampling. Enhanced sampling approaches, such as metadynamics, were designed to overcome this challenge; however, the nonuniform frame weights that result from many of these approaches present an additional challenge to ensemble quantification techniques such as Markov State Modeling or structural clustering. Here, we present rigorous inclusion of nonuniform frame weights into a structural clustering method entitled shapeGMM. The result of frame-weighted shapeGMM is a high dimensional probability density and generative model for the unbiased system from which we can compute important thermodynamic properties such as relative free energies and configurational entropy. The accuracy of this approach is demonstrated by the quantitative agreement between GMMs computed by Hamiltonian reweighting and direct simulation of a coarse-grained helix model system. Furthermore, the relative free energy computed from a shapeGMM probability density of alanine dipeptide reweighted from a metadynamics simulation quantitatively reproduces the underlying free energy in the basins. Finally, the method identifies hidden structures along the actin globular to filamentous-like structural transition from a metadynamics simulation on a linear discriminant analysis coordinate trained on GMM states, illustrating how structural clustering of biased data can lead to biophysical insight. Combined, these results demonstrate that frame-weighted shapeGMM is a powerful approach to quantifying biomolecular ensembles from biased simulations.
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Affiliation(s)
- Subarna Sasmal
- Department of Chemistry, New York
University, New York, New York 10003, United
States
| | - Triasha Pal
- Department of Chemistry, New York
University, New York, New York 10003, United
States
| | - Glen M. Hocky
- Department of Chemistry, New York
University, New York, New York 10003, United
States
- Simons Center for Computational Physical Chemistry,
New York University, New York, New York 10003,
United States
| | - Martin McCullagh
- Department of Chemistry, Oklahoma State
University, Stillwater, Oklahoma 74078, United
States
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3
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Li T, Du J, Ren M. Structural Significance of His73 in F-Actin Dynamics: Insights from Ab Initio Study. Int J Mol Sci 2022; 23:ijms231810447. [PMID: 36142357 PMCID: PMC9499316 DOI: 10.3390/ijms231810447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/01/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
F-actin dynamics (polymerization and depolymerization) are associated with nucleotide exchange, providing the driving forces for dynamic cellular activities. As an important residue in the nucleotide state-sensing region in actin, His73 is often found to be methylated in natural actin and directly participates in F-actin dynamics by regulating nucleotide exchange. The interaction between His73 and its neighboring residue, Gly158, has significance for F-actin dynamics. However, this weak chemical interaction is difficult to characterize using classic molecular modeling methods. In this study, ab initio modeling was employed to explore the binding energy between His73 and Gly158. The results confirm that the methyl group on the His73 side chain contributes to the structural stability of atomistic networks in the nucleotide state-sensing region of actin monomers and confines the material exchange (Pi release) pathway within F-actin dynamics. Further binding energy analyses of actin structures under different nucleotide states showed that the potential model of His73/Gly158 hydrogen bond breaking in the material exchange mechanism is not obligatory within F-actin dynamics.
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Affiliation(s)
- Tong Li
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Juan Du
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
| | - Mingfa Ren
- Department of Engineering Mechanics, Dalian University of Technology, Dalian 116024, China
- State Key Laboratory of Structural Analysis for Industrial Equipment, Dalian University of Technology, Dalian 116024, China
- Correspondence: ; Tel.: +86-411-8479161
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4
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Karlsson R, Dráber P. Profilin-A master coordinator of actin and microtubule organization in mammalian cells. J Cell Physiol 2021; 236:7256-7265. [PMID: 33821475 DOI: 10.1002/jcp.30379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
The last two decades have witnessed a tremendous increase in cell biology data. Not least is this true for studies of the dynamic organization of the microfilament and microtubule systems in animal cells where analyses of the molecular components and their interaction patterns have deepened our understanding of these complex force-generating machineries. Previous observations of a molecular cross-talk between the two systems have now led to the realization of the existence of several intricate mechanisms operating to maintain their coordinated cellular organization. In this short review, we relate to this development by discussing new results concerning the function of the actin regulator profilin 1 as a control component of microfilament-microtubule cross-talk.
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Affiliation(s)
- Roger Karlsson
- Department of Molecular Biosciences, WGI, Stockholm University, Stockholm, Sweden
| | - Pavel Dráber
- Department of Biology of Cytoskeleton, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
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Merino F, Pospich S, Raunser S. Towards a structural understanding of the remodeling of the actin cytoskeleton. Semin Cell Dev Biol 2019; 102:51-64. [PMID: 31836290 PMCID: PMC7221352 DOI: 10.1016/j.semcdb.2019.11.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/03/2022]
Abstract
Actin filaments (F-actin) are a key component of eukaryotic cells. Whether serving as a scaffold for myosin or using their polymerization to push onto cellular components, their function is always related to force generation. To control and fine-tune force production, cells have a large array of actin-binding proteins (ABPs) dedicated to control every aspect of actin polymerization, filament localization, and their overall mechanical properties. Although great advances have been made in our biochemical understanding of the remodeling of the actin cytoskeleton, the structural basis of this process is still being deciphered. In this review, we summarize our current understanding of this process. We outline how ABPs control the nucleation and disassembly, and how these processes are affected by the nucleotide state of the filaments. In addition, we highlight recent advances in the understanding of actomyosin force generation, and describe recent advances brought forward by the developments of electron cryomicroscopy.
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Affiliation(s)
- Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Sabrina Pospich
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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6
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Oda T, Takeda S, Narita A, Maéda Y. Structural Polymorphism of Actin. J Mol Biol 2019; 431:3217-3228. [DOI: 10.1016/j.jmb.2019.05.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/17/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
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Chruszcz M, Kapingidza AB, Dolamore C, Kowal K. A robust method for the estimation and visualization of IgE cross-reactivity likelihood between allergens belonging to the same protein family. PLoS One 2018; 13:e0208276. [PMID: 30496313 PMCID: PMC6264518 DOI: 10.1371/journal.pone.0208276] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/14/2018] [Indexed: 12/11/2022] Open
Abstract
Among the vast number of identified protein families, allergens emanate from relatively few families which translates to only a small fraction of identified protein families. In allergy diagnostics and immunotherapy, interactions between immunoglobulin E and allergens are crucial because the formation of an allergen-antibody complex is necessary for triggering an allergic reaction. In allergic diseases, there is a phenomenon known as cross-reactivity. Cross-reactivity describes a situation where an individual has produced antibodies against a particular allergenic protein, but said antibodies fail to discriminate between the original sensitizer and other similar proteins that usually belong to the same family. To expound the concept of cross-reactivity, this study examines ten protein families that include allergens selected specifically for the analysis of cross-reactivity. The selected allergen families had at least 13 representative proteins, overall folds that differ significantly between families, and include relevant allergens with various potencies. The selected allergens were analyzed using information on sequence similarities and identities between members of the families as well as reports on clinically relevant cross-reactivities. Based on our analysis, we propose to introduce a new A-RISC index (Allergens’–Relative Identity, Similarity and Cross-reactivity) which describes homology between two allergens belonging to the same protein family and is used to predict the likelihood of cross-reactivity between them. Information on sequence similarities and identities, as well as on the values of the proposed A-RISC index is used to introduce four categories describing a risk of a cross-reactive reaction, namely: high, medium-high, medium-low and low. The proposed approach can facilitate analysis in component-resolved allergy diagnostics, generation of avoidance guidelines for allergic individuals, and help with the design of immunotherapy.
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Affiliation(s)
- Maksymilian Chruszcz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
- * E-mail:
| | - A. Brenda Kapingidza
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Coleman Dolamore
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina, United States of America
| | - Krzysztof Kowal
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
- Department of Experimental Allergology and Immunology, Medical University of Bialystok, Bialystok, Poland
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Sandestig A, Green A, Jonasson J, Vogt H, Wahlström J, Pepler A, Ellnebo K, Biskup S, Stefanova M. Could Dissimilar Phenotypic Effects of ACTB Missense Mutations Reflect the Actin Conformational Change? Two Novel Mutations and Literature Review. Mol Syndromol 2018; 9:259-265. [PMID: 30733661 DOI: 10.1159/000492267] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2018] [Indexed: 02/03/2023] Open
Abstract
The beta-actin gene encodes 1 of 6 different actin proteins. De novo heterozygous missense mutations in ACTB have been identified in patients with Baraitser-Winter syndrome (BRWS) and also in patients with developmental disorders other than BRWS, such as deafness, dystonia, and neutrophil dysfunction. We describe 2 different novel de novo missense ACTB mutations, c.208C>G (p.Pro70Ala) and c.511C>T (p.Leu171Phe), found by trio exome sequencing analysis of 2 unrelated patients: an 8-year-old boy with a suspected BRWS and a 4-year-old girl with unclear developmental disorder. The mutated residue in the first case is situated in the actin H-loop, which is involved in actin polymerization. The mutated residue in the second case (p.Leu171Phe) is found at the actin barbed end in the W-loop, important for binding to profilin and other actin-binding molecules. While the boy presented with a typical BRWS facial appearance, the girl showed facial features not recognizable as a BRWS gestalt as well as ventricular arrhythmia, cleft palate, thrombocytopenia, and gray matter heterotopia. We reviewed previously published ACTB missense mutations and ascertained that a number of them do not cause typical BRWS. By comparing clinical and molecular data, we speculate that the phenotypic differences found in ACTB missense mutation carriers might supposedly be dependent on the conformational change of ACTB.
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Affiliation(s)
- Anna Sandestig
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Anna Green
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Jon Jonasson
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | - Hartmut Vogt
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | - Johan Wahlström
- Department of Pediatrics, Linköping University Hospital, Linköping, Sweden
| | | | - Katarina Ellnebo
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
| | | | - Margarita Stefanova
- Department of Clinical Genetics, Linköping University Hospital, Linköping, Sweden
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9
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Wang Y, Rezey AC, Wang R, Tang DD. Role and regulation of Abelson tyrosine kinase in Crk-associated substrate/profilin-1 interaction and airway smooth muscle contraction. Respir Res 2018; 19:4. [PMID: 29304860 PMCID: PMC5756382 DOI: 10.1186/s12931-017-0709-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Airway smooth muscle contraction is critical for maintenance of appropriate airway tone, and has been implicated in asthma pathogenesis. Smooth muscle contraction requires an "engine" (myosin activation) and a "transmission system" (actin cytoskeletal remodeling). However, the mechanisms that control actin remodeling in smooth muscle are not fully elucidated. The adapter protein Crk-associated substrate (CAS) regulates actin dynamics and the contraction in smooth muscle. In addition, profilin-1 (Pfn-1) and Abelson tyrosine kinase (c-Abl) are also involved in smooth muscle contraction. The interplays among CAS, Pfn-1 and c-Abl in smooth muscle have not been previously investigated. METHODS The association of CAS with Pfn-1 in mouse tracheal rings was evaluated by co-immunoprecipitation. Tracheal rings from c-Abl conditional knockout mice were used to assess the roles of c-Abl in the protein-protein interaction and smooth muscle contraction. Decoy peptides were utilized to evaluate the importance of CAS/Pfn-1 coupling in smooth muscle contraction. RESULTS Stimulation with acetylcholine (ACh) increased the interaction of CAS with Pfn-1 in smooth muscle, which was regulated by CAS tyrosine phosphorylation and c-Abl. The CAS/Pfn-1 coupling was also modified by the phosphorylation of cortactin (a protein implicated in Pfn-1 activation). In addition, ACh activation promoted the spatial redistribution of CAS and Pfn-1 in smooth muscle cells, which was reduced by c-Abl knockdown. Inhibition of CAS/Pfn-1 interaction by a decoy peptide attenuated the ACh-induced actin polymerization and contraction without affecting myosin light chain phosphorylation. Furthermore, treatment with the Src inhibitor PP2 and the actin polymerization inhibitor latrunculin A attenuated the ACh-induced c-Abl tyrosine phosphorylation (an indication of c-Abl activation). CONCLUSIONS Our results suggest a novel activation loop in airway smooth muscle: c-Abl promotes the CAS/Pfn-1 coupling and actin polymerization, which conversely facilitates c-Abl activation. The positive feedback may render c-Abl in active state after contractile stimulation.
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Affiliation(s)
- Yinna Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Alyssa C Rezey
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Ruping Wang
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA
| | - Dale D Tang
- Department of Molecular and Cellular Physiology, Albany Medical College, 47 New Scotland Avenue, MC-8, Albany, NY, 12208, USA.
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10
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Porta J, Lovelace J, Borgstahl GEO. How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal. J Appl Crystallogr 2017; 50:1200-1207. [PMID: 28808437 PMCID: PMC5541356 DOI: 10.1107/s1600576717007294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/17/2017] [Indexed: 11/21/2022] Open
Abstract
Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal.
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Affiliation(s)
- Jason Porta
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jeff Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
| | - Gloria E. O. Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198, USA
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11
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Kudryashov DS, Reisler E. ATP and ADP actin states. Biopolymers 2016; 99:245-56. [PMID: 23348672 DOI: 10.1002/bip.22155] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/07/2012] [Indexed: 11/06/2022]
Abstract
This minireview is dedicated to the memory of Henryk Eisenberg and honors his major contributions to many areas of biophysics and to the analysis of macromolecular states and interactions in particular. This work reviews the ATP and ADP states of a ubiquitous protein, actins, and considers the present evidence for and against unique, nucleotide-dependent conformations of this protein. The effects of ATP and ADP on specific structural elements of actins, its loops and clefts, as revealed by mutational, crosslinking, spectroscopic, and EPR methods are discussed. It is concluded that the existing evidence points to dynamic equilibria of these structural elements among various conformational states in both ATP- and ADP-actins, with the nucleotides impacting the equilibria distributions.
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Affiliation(s)
- Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, the Ohio State University, Columbus, OH 43210.
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12
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Hepler PK. The Cytoskeleton and Its Regulation by Calcium and Protons. PLANT PHYSIOLOGY 2016; 170:3-22. [PMID: 26722019 PMCID: PMC4704593 DOI: 10.1104/pp.15.01506] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/28/2015] [Indexed: 05/18/2023]
Abstract
Calcium and protons exert control over the formation and activity of the cytoskeleton, usually by modulating an associated motor protein or one that affects the structural organization of the polymer.
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Affiliation(s)
- Peter K Hepler
- Biology Department, University of Massachusetts, Amherst, Massachusetts 01003
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13
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Boopathy S, Silvas TV, Tischbein M, Jansen S, Shandilya SM, Zitzewitz JA, Landers JE, Goode BL, Schiffer CA, Bosco DA. Structural basis for mutation-induced destabilization of profilin 1 in ALS. Proc Natl Acad Sci U S A 2015; 112:7984-9. [PMID: 26056300 PMCID: PMC4491777 DOI: 10.1073/pnas.1424108112] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutations in profilin 1 (PFN1) are associated with amyotrophic lateral sclerosis (ALS); however, the pathological mechanism of PFN1 in this fatal disease is unknown. We demonstrate that ALS-linked mutations severely destabilize the native conformation of PFN1 in vitro and cause accelerated turnover of the PFN1 protein in cells. This mutation-induced destabilization can account for the high propensity of ALS-linked variants to aggregate and also provides rationale for their reported loss-of-function phenotypes in cell-based assays. The source of this destabilization is illuminated by the X-ray crystal structures of several PFN1 proteins, revealing an expanded cavity near the protein core of the destabilized M114T variant. In contrast, the E117G mutation only modestly perturbs the structure and stability of PFN1, an observation that reconciles the occurrence of this mutation in the control population. These findings suggest that a destabilized form of PFN1 underlies PFN1-mediated ALS pathogenesis.
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Affiliation(s)
- Sivakumar Boopathy
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Tania V Silvas
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Maeve Tischbein
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Silvia Jansen
- Department of Biology, Brandeis University, Waltham, MA 02453
| | - Shivender M Shandilya
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jill A Zitzewitz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - John E Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02453
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Daryl A Bosco
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605;
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14
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Kumpula EP, Kursula I. Towards a molecular understanding of the apicomplexan actin motor: on a road to novel targets for malaria remedies? Acta Crystallogr F Struct Biol Commun 2015; 71:500-13. [PMID: 25945702 PMCID: PMC4427158 DOI: 10.1107/s2053230x1500391x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/25/2015] [Indexed: 11/10/2022] Open
Abstract
Apicomplexan parasites are the causative agents of notorious human and animal diseases that give rise to considerable human suffering and economic losses worldwide. The most prominent parasites of this phylum are the malaria-causing Plasmodium species, which are widespread in tropical and subtropical regions, and Toxoplasma gondii, which infects one third of the world's population. These parasites share a common form of gliding motility which relies on an actin-myosin motor. The components of this motor and the actin-regulatory proteins in Apicomplexa have unique features compared with all other eukaryotes. This, together with the crucial roles of these proteins, makes them attractive targets for structure-based drug design. In recent years, several structures of glideosome components, in particular of actins and actin regulators from apicomplexan parasites, have been determined, which will hopefully soon allow the creation of a complete molecular picture of the parasite actin-myosin motor and its regulatory machinery. Here, current knowledge of the function of this motor is reviewed from a structural perspective.
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Affiliation(s)
- Esa-Pekka Kumpula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 3000, 90014 Oulu, Finland
- Helmholtz Centre for Infection Research, Notkestrasse 85, 22607 Hamburg, Germany
- German Electron Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Inari Kursula
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 3000, 90014 Oulu, Finland
- Helmholtz Centre for Infection Research, Notkestrasse 85, 22607 Hamburg, Germany
- German Electron Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Biomedicine, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
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15
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Nucleotide regulation of the structure and dynamics of G-actin. Biophys J 2014; 106:1710-20. [PMID: 24739170 DOI: 10.1016/j.bpj.2014.03.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 02/17/2014] [Accepted: 03/06/2014] [Indexed: 11/24/2022] Open
Abstract
Actin, a highly conserved cytoskeletal protein found in all eukaryotic cells, facilitates cell motility and membrane remodeling via a directional polymerization cycle referred to as treadmilling. The nucleotide bound at the core of each actin subunit regulates this process. Although the biochemical kinetics of treadmilling has been well characterized, the atomistic details of how the nucleotide affects polymerization remain to be definitively determined. There is increasing evidence that the nucleotide regulation (and other characteristics) of actin cannot be fully described from the minimum energy structure, but rather depends on a dynamic equilibrium between conformations. In this work we explore the conformational mobility of the actin monomer (G-actin) in a coarse-grained subspace using umbrella sampling to bias all-atom molecular-dynamics simulations along the variables of interest. The results reveal that ADP-bound actin subunits are more conformationally mobile than ATP-bound subunits. We used a multiscale analysis method involving coarse-grained and atomistic representations of these simulations to characterize how the nucleotide affects the low-energy states of these systems. The interface between subdomains SD2-SD4, which is important for polymerization, is stabilized in an actin filament-like (F-actin) conformation in ATP-bound G-actin. Additionally, the nucleotide modulates the conformation of the SD1-SD3 interface, a region involved in the binding of several actin-binding proteins.
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Sevdali M, Kumar V, Peckham M, Sparrow J. Human congenital myopathy actin mutants cause myopathy and alter Z-disc structure in Drosophila flight muscle. Neuromuscul Disord 2013; 23:243-55. [PMID: 23294764 DOI: 10.1016/j.nmd.2012.11.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 10/23/2012] [Accepted: 11/29/2012] [Indexed: 01/05/2023]
Abstract
Over 190 mutations in the human skeletal muscle α-actin gene, ACTA1 cause congenital actin myopathies. We transgenically expressed six different mutant actins, G15R, I136M, D154N, V163L, V163M and D292V in Drosophila indirect flight muscles and investigated their effects in flies that express one wild type and one mutant actin copy. All the flies were flightless, and the IFMs showed incomplete Z-discs, disorganised actin filaments and 'zebra bodies'. No differences in levels of sarcomeric protein expression were observed, but tropomodulin staining was somewhat disrupted in D164N, V163L, G15R and V163M heterozygotes. A single copy of D292V mutant actin rescued the hypercontractile phenotypes caused by TnI and TnT mutants, suggesting that the D292V mutation interferes with thin filament regulation. Our results show that expression of actin mutations homologous to those in humans in the indirect flight muscles of Drosophila disrupt sarcomere organisation, with somewhat similar phenotypes to those observed in humans. Using Drosophila to study actin mutations may help aid our understanding of congential myopathies caused by actin mutations.
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Affiliation(s)
- Maria Sevdali
- Department of Biology (Area 10), University of York, York YO10 5DD, UK
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Pivovarova AV, Chebotareva NA, Kremneva EV, Lappalainen P, Levitsky DI. Effects of actin-binding proteins on the thermal stability of monomeric actin. Biochemistry 2012; 52:152-60. [PMID: 23231323 DOI: 10.1021/bi3012884] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Differential scanning calorimetry (DSC) was applied to investigate the thermal unfolding of rabbit skeletal muscle G-actin in its complexes with actin-binding proteins, cofilin, twinfilin, and profilin. The results show that the effects of these proteins on the thermal stability of G-actin depend on the nucleotide, ATP or ADP, bound in the nucleotide-binding cleft between actin subdomains 2 and 4. Interestingly, cofilin binding stabilizes both ATP-G-actin and ADP-G-actin, whereas twinfilin increases the thermal stability of the ADP-G-actin but not that of the ATP-G-actin. By contrast, profilin strongly decreases the thermal stability of the ATP-G-actin but has no appreciable effect on the ADP-G-actin. Comparison of these DSC results with literature data reveals a relationship between the effects of actin-binding proteins on the thermal unfolding of G-actin, stabilization or destabilization, and their effects on the rate of nucleotide exchange in the nucleotide-binding cleft, decrease or increase. These results suggest that the thermal stability of G-actin depends, at least partially, on the conformation of the nucleotide-binding cleft: the actin molecule is more stable when the cleft is closed, while an opening of the cleft leads to significant destabilization of G-actin. Thus, DSC studies of the thermal unfolding of G-actin can provide new valuable information about the conformational changes induced by actin-binding proteins in the actin molecule.
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Affiliation(s)
- Anastasia V Pivovarova
- A. N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071, Russian Federation
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Grantham J, Lassing I, Karlsson R. Controlling the cortical actin motor. PROTOPLASMA 2012; 249:1001-1015. [PMID: 22526202 PMCID: PMC3459087 DOI: 10.1007/s00709-012-0403-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 03/21/2012] [Indexed: 05/31/2023]
Abstract
Actin is the essential force-generating component of the microfilament system, which powers numerous motile processes in eukaryotic cells and undergoes dynamic remodeling in response to different internal and external signaling. The ability of actin to polymerize into asymmetric filaments is the inherent property behind the site-directed force-generating capacity that operates during various intracellular movements and in surface protrusions. Not surprisingly, a broad variety of signaling pathways and components are involved in controlling and coordinating the activities of the actin microfilament system in a myriad of different interactions. The characterization of these processes has stimulated cell biologists for decades and has, as a consequence, resulted in a huge body of data. The purpose here is to present a cellular perspective on recent advances in our understanding of the microfilament system with respect to actin polymerization, filament structure and specific folding requirements.
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Affiliation(s)
- Julie Grantham
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Ingrid Lassing
- Department of Cell Biology, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Roger Karlsson
- Department of Cell Biology, Wenner-Gren Institute, Stockholm University, SE-106 91 Stockholm, Sweden
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