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Protein mechanics probed using simple molecular models. Biochim Biophys Acta Gen Subj 2020; 1864:129613. [DOI: 10.1016/j.bbagen.2020.129613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 01/14/2023]
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Bureau HR, Quirk S, Hernandez R. The relative stability of trpzip1 and its mutants determined by computation and experiment. RSC Adv 2020; 10:6520-6535. [PMID: 35495997 PMCID: PMC9049704 DOI: 10.1039/d0ra00920b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/04/2020] [Indexed: 11/21/2022] Open
Abstract
The single-point mutations of tprzip1 are indicated at left, and their relative energetics are compared at right.
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3
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Wang WB, Zhu JZ, Li XY, Li CH, Su JG, Li JY. Enhancement of protein mechanical stability: Correlated deformations are handcuffed by ligand binding. J Chem Phys 2019; 150:155102. [PMID: 31005084 DOI: 10.1063/1.5054932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
As revealed by previous experiments, protein mechanical stability can be effectively regulated by ligand binding with the binding site distant from the force-bearing region. However, the mechanism for such long-range allosteric control of protein mechanics is still largely unknown. In this work, we use protein topology-based elastic network model (ENM) and all-atomic steered molecular dynamics (SMD) simulations to study the impact of ligand binding on protein mechanical stability in two systems, i.e., GB1 and CheY-binding P2-domain of CheA (CBDCheA). Both ENM and SMD results show that the ligand binding has considerable and negligible effects on the mechanical stability of these two proteins, respectively. These results are consistent with the experimental observations. A physical mechanism for the enhancement of protein mechanical stability was then proposed: the correlated deformations of the force-bearing region and the binding site are handcuffed by the binding of ligand. The handcuff effect suppresses the propagation of internal force in the force-bearing region, thus improving the resistance to the loading force. Our study indicates that ENM method can effectively identify the structure motifs allosterically related to the deformation in the force bearing region, as well as the force propagation pathway within the structure of the studied proteins. Hence, it should be helpful to understand the molecular origin of the different mechanical properties in response to ligand binding for GB1 and CBDCheA.
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Affiliation(s)
- Wei Bu Wang
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Jian Zhuo Zhu
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xing Yuan Li
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China
| | - Ji Guo Su
- Key Laboratory for Microstructural Material Physics of Hebei Province, College of Science, Yanshan University, Qinhuangdao 066004, China
| | - Jing Yuan Li
- Institute of Quantitative Biology and Department of Physics, Zhejiang University, Hangzhou 310027, China
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Hughes ML, Dougan L. The physics of pulling polyproteins: a review of single molecule force spectroscopy using the AFM to study protein unfolding. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:076601. [PMID: 27309041 DOI: 10.1088/0034-4885/79/7/076601] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the most exciting developments in the field of biological physics in recent years is the ability to manipulate single molecules and probe their properties and function. Since its emergence over two decades ago, single molecule force spectroscopy has become a powerful tool to explore the response of biological molecules, including proteins, DNA, RNA and their complexes, to the application of an applied force. The force versus extension response of molecules can provide valuable insight into its mechanical stability, as well as details of the underlying energy landscape. In this review we will introduce the technique of single molecule force spectroscopy using the atomic force microscope (AFM), with particular focus on its application to study proteins. We will review the models which have been developed and employed to extract information from single molecule force spectroscopy experiments. Finally, we will end with a discussion of future directions in this field.
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Affiliation(s)
- Megan L Hughes
- School of Physics and Astronomy, University of Leeds, LS2 9JT, UK. Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
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Hadi-Alijanvand H, Proctor EA, Ding F, Dokholyan NV, Moosavi-Movahedi AA. A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase. Proteins 2016; 84:611-23. [DOI: 10.1002/prot.25011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 02/05/2016] [Accepted: 02/08/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Hamid Hadi-Alijanvand
- Department of Biological Sciences; Institute for Advanced Studies in Basic Sciences (IASBS); Zanjan Iran
- Institute of Biochemistry and Biophysics (IBB), University of Tehran; Tehran Iran
| | - Elizabeth A. Proctor
- Department of Biological Engineering; Massachusetts Institute of Technology; Cambridge Massachusetts 02139
| | - Feng Ding
- Department of Biochemistry and Biophysics; University of North Carolina at Chapel Hill, School of Medicine; Chapel Hill North Carolina 27599
- Department of Physics and Astronomy; Clemson University; Clemson South Carolina 29634
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics; University of North Carolina at Chapel Hill, School of Medicine; Chapel Hill North Carolina 27599
- Curriculum in Bioinformatics and Computational Biology; University of North Carolina at Chapel Hill, School of Medicine; Chapel Hill North Carolina 27599
- Program in Molecular and Cellular Biophysics; University of North Carolina at Chapel Hill, School of Medicine; Chapel Hill North Carolina 27599
| | - Ali A. Moosavi-Movahedi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran; Tehran Iran
- Center of Excellence in Biothermodynamics, Institute of Biochemistry and Biophysics (IBB), University of Tehran; Tehran Iran
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Kravats AN, Tonddast-Navaei S, Stan G. Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines. PLoS Comput Biol 2016; 12:e1004675. [PMID: 26734937 PMCID: PMC4703411 DOI: 10.1371/journal.pcbi.1004675] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/25/2015] [Indexed: 01/30/2023] Open
Abstract
Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system, coupling the energy from ATP hydrolysis to threading substrate proteins (SP) through their narrow central pore. Repetitive cycles of sequential intra-ring ATP hydrolysis events induce axial excursions of diaphragm-forming central pore loops that effect the application of mechanical forces onto SPs to promote unfolding and translocation. We perform Langevin dynamics simulations of a coarse-grained model of the ClpY ATPase-SP system to elucidate the molecular details of unfolding and translocation of an α/β model protein. We contrast this mechanism with our previous studies which used an all-α SP. We find conserved aspects of unfolding and translocation mechanisms by allosteric ClpY, including unfolding initiated at the tagged C-terminus and translocation via a power stroke mechanism. Topology-specific aspects include the time scales, the rate limiting steps in the degradation pathway, the effect of force directionality, and the translocase efficacy. Mechanisms of ClpY-assisted unfolding and translocation are distinct from those resulting from non-allosteric mechanical pulling. Bulk unfolding simulations, which mimic Atomic Force Microscopy-type pulling, reveal multiple unfolding pathways initiated at the C-terminus, N-terminus, or simultaneously from both termini. In a non-allosteric ClpY ATPase pore, mechanical pulling with constant velocity yields larger effective forces for SP unfolding, while pulling with constant force results in simultaneous unfolding and translocation. Cell survival is critically dependent on tightly regulated protein quality control, which includes chaperone-mediated folding and degradation. In the degradation pathway, AAA+ nanomachines, such as bacterial Clp proteases, use ATP-driven mechanisms to mechanically unfold, translocate, and destroy excess or defective proteins. Understanding these remodeling mechanisms is of central importance for deciphering the details of essential cellular processes. We perform coarse-grained computer simulations to extensively probe the effect of substrate protein topology on unfolding and translocation actions of the ClpY ATPase nanomachine. We find that, independent of SP topology, unfolding proceeds from the tagged C-terminus, which is engaged by the ATPase, and translocation involves coordinated steps. Topology-specific aspects include more complex unfolding and translocation pathways of the α/β SP compared with the all-α SP due to high stability of β-hairpins and interplay of tertiary contacts. In addition, directionality of the mechanical force applied by the Clp ATPase gives rise to distinct unfolding pathways.
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Affiliation(s)
- Andrea N. Kravats
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Sam Tonddast-Navaei
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - George Stan
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
- * E-mail:
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Kumar A, Campitelli P, Thorpe MF, Ozkan SB. Partial unfolding and refolding for structure refinement: A unified approach of geometric simulations and molecular dynamics. Proteins 2015; 83:2279-92. [PMID: 26476100 DOI: 10.1002/prot.24947] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/11/2015] [Accepted: 09/29/2015] [Indexed: 12/26/2022]
Abstract
The most successful protein structure prediction methods to date have been template-based modeling (TBM) or homology modeling, which predicts protein structure based on experimental structures. These high accuracy predictions sometimes retain structural errors due to incorrect templates or a lack of accurate templates in the case of low sequence similarity, making these structures inadequate in drug-design studies or molecular dynamics simulations. We have developed a new physics based approach to the protein refinement problem by mimicking the mechanism of chaperons that rehabilitate misfolded proteins. The template structure is unfolded by selectively (targeted) pulling on different portions of the protein using the geometric based technique FRODA, and then refolded using hierarchically restrained replica exchange molecular dynamics simulations (hr-REMD). FRODA unfolding is used to create a diverse set of topologies for surveying near native-like structures from a template and to provide a set of persistent contacts to be employed during re-folding. We have tested our approach on 13 previous CASP targets and observed that this method of folding an ensemble of partially unfolded structures, through the hierarchical addition of contact restraints (that is, first local and then nonlocal interactions), leads to a refolding of the structure along with refinement in most cases (12/13). Although this approach yields refined models through advancement in sampling, the task of blind selection of the best refined models still needs to be solved. Overall, the method can be useful for improved sampling for low resolution models where certain of the portions of the structure are incorrectly modeled.
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Affiliation(s)
- Avishek Kumar
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
| | - M F Thorpe
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona.,Rudolf Peierls Center for Theoretical Physics, University of Oxford, Oxford, OX1 3NP, United Kingdom
| | - S Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State University, Tempe, Arizona
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Srivastava A, Granek R. Cooperativity in thermal and force-induced protein unfolding: integration of crack propagation and network elasticity models. PHYSICAL REVIEW LETTERS 2013; 110:138101. [PMID: 23581376 DOI: 10.1103/physrevlett.110.138101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Indexed: 06/02/2023]
Abstract
We investigate force-induced and temperature-induced unfolding of proteins using the combination of a gaussian network model and a crack propagation model based on "bond"-breaking independent events. We assume the existence of threshold values for the mean strain and strain fluctuations that dictate bond rupture. Surprisingly, we find that this stepwise process usually leads to a few cooperative, first-order-like, transitions in which several bonds break simultaneously, reminiscent of the "avalanches" seen in disordered networks.
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Affiliation(s)
- Amit Srivastava
- The Stella and Avram Goren-Goldstein Department of Biotechnology Engineering, Ben-Gurion University of The Negev, Beer Sheva 84105, Israel
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Schlesier T, Diezemann G. Performance of Different Force Fields in Force Probe Simulations. J Phys Chem B 2013; 117:1862-71. [DOI: 10.1021/jp3115644] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas Schlesier
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische
Chemie, Universität Mainz, Duesbergweg
10-14, 55128
Mainz, Germany
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Dastidar SG, Lane DP, Verma CS. Why is F19Ap53 unable to bind MDM2? Simulations suggest crack propagation modulates binding. Cell Cycle 2012; 11:2239-47. [PMID: 22617389 DOI: 10.4161/cc.20333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Why doesn't the F19A mutant of p53 bind to MDM2? Binding thermodynamics have suggested that the loss of packing interactions upon mutating Phe into Ala sidechain results in destabilizing the binding free energy between p53 and MDM2. Does this mutation also modulate the initial recognition between p53 and MDM2? We look at atomistic computer simulations of the process of the initial encounter between wild type p53 peptide and its F19A mutant with the N-terminal domain of MDM2. These simulations show that binding is characterized by a complex multistep process. It starts with the capture of F19 of wild type p53 by certain residues in the MDM2 binding pocket. This initial step anchors the peptide onto the surface of MDM2, and with the consequent reduction in the search space of the peptide, the peptide docks into the partially occluded surface of MDM2. This is similar to a crack forming in an otherwise occluded hydrophobic cavity in MDM2, and the peptide, docked through F19, modulates the propagation of this crack, which subsequently results in the stepwise docking of the rest of the peptide through insertions of W23 and L26. The lack of the bulky sidechain of F in the F19A mutant results in the absence of the initial "grasp" complex, and hence the mutant peptide diffuses randomly on the surface of MDM2 without binding. This is the first such demonstration of the possibility that a "kinetic" effect may partly underlie the destabilized thermodynamics of binding of F19A and is a feature that appears to be conserved in evolution. The observations by Wallace et al. (Mol Cell 2006; 23:251-63) that despite the inability of F19A to bind at the N-terminal domain of MDM2, it gets ubiquitinated, can now be partly understood based on a mechanism whereby the occupation of the binding pocket by ligands/peptides induces, via crack propagation and the dynamics of gatekeeper Y100, the ubiquitination signal for interactions between the acidic domain of MDM2 and the DNA binding domain of p53.
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