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Lopez DM, Castro CE, Sotomayor M. In-Silico Analyses of Molecular Force Sensors for Mechanical Characterization of Biological Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603923. [PMID: 39091752 PMCID: PMC11291006 DOI: 10.1101/2024.07.17.603923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Mechanical forces play key roles in biological processes such as cell migration and sensory perception. In recent years molecular force sensors have been developed as tools for in situ force measurements. Here we use all-atom steered molecular dynamics simulations to predict and study the relationship between design parameters and mechanical properties for three types of molecular force sensors commonly used in cellular biological research: two peptide- and one DNA-based. The peptide-based sensors consist of a pair of fluorescent proteins, which can undergo Förster resonance energy transfer (FRET), linked by spider silk (GPGGA)n or synthetic (GGSGGS)n disordered regions. The DNA-based sensor consists of two fluorophore-labeled strands of DNA that can be unzipped or sheared upon force application with a FRET signal as readout of dissociation. We simulated nine sensors, three of each kind. After equilibration, flexible peptide linkers of three different lengths were stretched by applying forces to their N- and C-terminal Cα atoms in opposite directions. Similarly, we equilibrated a DNA-based sensor and pulled on the phosphate atom of the terminal guanine of one strand and a selected phosphate atom on the other strand in the opposite direction. These simulations were performed at constant velocity (0.01 nm/ns - 10 nm/ns) and constant force (10 pN - 500 pN) for all versions of the sensors. Our results show how the force response of these sensors depends on their length, sequence, configuration and loading rate. Mechanistic insights gained from simulations analyses indicate that interpretation of experimental results should consider the influence of transient formation of secondary structure in peptide-based sensors and of overstretching in DNA-based sensors. These predictions can guide optimal fluorophore choice and facilitate the rational design of new sensors for use in protein, DNA, hybrid systems, and molecular devices.
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Affiliation(s)
- Diana M. Lopez
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Carlos E. Castro
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, Ohio 43210
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210
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2
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van der Sleen L, Stevens JA, Marrink SJ, Poolman B, Tych K. Probing the stability and interdomain interactions in the ABC transporter OpuA using single-molecule optical tweezers. Cell Rep 2024; 43:114110. [PMID: 38607912 DOI: 10.1016/j.celrep.2024.114110] [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: 09/01/2023] [Revised: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Transmembrane transporter proteins are essential for maintaining cellular homeostasis and, as such, are key drug targets. Many transmembrane transporter proteins are known to undergo large structural rearrangements during their functional cycles. Despite the wealth of detailed structural and functional data available for these systems, our understanding of their dynamics and, consequently, how they function is generally limited. We introduce an innovative approach that enables us to directly measure the dynamics and stability of interdomain interactions of transmembrane proteins using optical tweezers. Focusing on the osmoregulatory ATP-binding cassette transporter OpuA from Lactococcus lactis, we examine the mechanical properties and potential interactions of its substrate-binding domains. Our measurements are performed in lipid nanodiscs, providing a native-mimicking environment for the transmembrane protein. The technique provides high spatial and temporal resolution and allows us to study the functionally relevant motions and interdomain interactions of individual transmembrane transporter proteins in real time in a lipid bilayer.
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Affiliation(s)
- Lyan van der Sleen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Jan A Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Siewert J Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands.
| | - Kasia Tych
- Chemical Biology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands.
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3
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Stadlbauer P, Mlýnský V, Krepl M, Šponer J. Complexity of Guanine Quadruplex Unfolding Pathways Revealed by Atomistic Pulling Simulations. J Chem Inf Model 2023; 63:4716-4731. [PMID: 37458574 PMCID: PMC10428220 DOI: 10.1021/acs.jcim.3c00171] [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: 02/02/2023] [Indexed: 08/15/2023]
Abstract
Guanine quadruplexes (GQs) are non-canonical nucleic acid structures involved in many biological processes. GQs formed in single-stranded regions often need to be unwound by cellular machinery, so their mechanochemical properties are important. Here, we performed steered molecular dynamics simulations of human telomeric GQs to study their unfolding. We examined four pulling regimes, including a very slow setup with pulling velocity and force load accessible to high-speed atomic force microscopy. We identified multiple factors affecting the unfolding mechanism, i.e.,: (i) the more the direction of force was perpendicular to the GQ channel axis (determined by GQ topology), the more the base unzipping mechanism happened, (ii) the more parallel the direction of force was, GQ opening and cross-like GQs were more likely to occur, (iii) strand slippage mechanism was possible for GQs with an all-anti pattern in a strand, and (iv) slower pulling velocity led to richer structural dynamics with sampling of more intermediates and partial refolding events. We also identified that a GQ may eventually unfold after a force drop under forces smaller than those that the GQ withstood before the drop. Finally, we found out that different unfolding intermediates could have very similar chain end-to-end distances, which reveals some limitations of structural interpretations of single-molecule spectroscopic data.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech
Academy of Sciences, Královopolská 135, Brno 612 00, Czech Republic
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4
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Kav B, Weikl TR, Schneck E. Measuring pico-Newton Forces with Lipid Anchors as Force Sensors in Molecular Dynamics Simulations. J Phys Chem B 2023; 127:4081-4089. [PMID: 37127845 PMCID: PMC10184124 DOI: 10.1021/acs.jpcb.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Binding forces between biomolecules are ubiquitous in nature but sometimes as weak as a few pico-Newtons (pN). In many cases, the binding partners are attached to biomembranes with the help of a lipid anchor. One important example are glycolipids that promote membrane adhesion through weak carbohydrate-carbohydrate binding between adjacent membranes. Here, we use molecular dynamics (MD) simulations to quantify the forces generated by bonds involving membrane-anchored molecules. We introduce a method in which the protrusion of the lipid anchors from the membrane acts as the force sensor. Our results with two different glycolipids reveal binding forces of up to 20 pN and corroborate the recent notion that carbohydrate-carbohydrate interactions are generic rather than specific.
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Affiliation(s)
- Batuhan Kav
- Max Planck Institute of Colloids and Interfaces, 14467, Potsdam, Germany
- Institute of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Thomas R Weikl
- Max Planck Institute of Colloids and Interfaces, 14467, Potsdam, Germany
| | - Emanuel Schneck
- Max Planck Institute of Colloids and Interfaces, 14467, Potsdam, Germany
- Institute for Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
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5
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Materzok T, De Boer D, Gorb S, Müller-Plathe F. Gecko Adhesion on Flat and Rough Surfaces: Simulations with a Multi-Scale Molecular Model. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201674. [PMID: 35927024 DOI: 10.1002/smll.202201674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/07/2022] [Indexed: 06/15/2023]
Abstract
A multiscale modeling approach is used to develop a particle-based mesoscale gecko spatula model that is able to link atomistic simulations and mesoscale (0.44 µm) simulations. It is used to study the detachment of spatulae from flat as well as nanostructured surfaces. The spatula model is based on microscopical information about spatulae structure and on atomistic molecular simulation results. Target properties for the coarse-graining result from a united-atom model of gecko keratin in periodic boundary conditions (PBC), previously developed by the authors. Pull-off forces necessary to detach gecko keratin under 2D PBC parallel to the surface are previously overestimated when only a small region of a spatula is examined. It is shown here that this is due to the restricted geometry (i.e., missing peel-off mode) and not model parameters. The spatula model peels off when pulled away from a surface, both in the molecular picture of the pull-off process and in the force-extension curve of non-equilibrium simulations mimicking single-spatula detachment studied with atomic force microscopy equipment. The force field and spatula model can reproduce experimental pull-off forces. Inspired by experimental results, the underlying mechanism that causes pull-off forces to be at a minimum on surfaces of varying roughnesses is also investigated. A clear sigmoidal increase in the pull-off force of spatulae with surface roughness shows that adhesion is determined by the ratio between spatula pad area and the area between surface peaks. Experiments showed a correlation with root-mean-square roughness of the surface, but the results of this work indicate that this is not a causality but depends on the area accessible.
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Affiliation(s)
- Tobias Materzok
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
| | - Danna De Boer
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
| | - Stanislav Gorb
- Zoological Institute Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, D-24118, Kiel, Germany
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287, Darmstadt, Germany
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6
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Zhuang Y, Thota N, Quirk S, Hernandez R. Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics. J Chem Theory Comput 2022; 18:4649-4659. [PMID: 35830368 DOI: 10.1021/acs.jctc.2c00498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jarzynski's equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the required use of very large solvent boxes. We introduce telescoping box schemes within adaptive steered molecular dynamics (ASMD) in which we adjust the solvent box between stages and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long α-helical peptide, Ala30, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost.
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Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Nikhil Thota
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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7
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Neel BL, Nisler CR, Walujkar S, Araya-Secchi R, Sotomayor M. Elastic versus brittle mechanical responses predicted for dimeric cadherin complexes. Biophys J 2022; 121:1013-1028. [PMID: 35151631 PMCID: PMC8943749 DOI: 10.1016/j.bpj.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/02/2022] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Cadherins are a superfamily of adhesion proteins involved in a variety of biological processes that include the formation of intercellular contacts, the maintenance of tissue integrity, and the development of neuronal circuits. These transmembrane proteins are characterized by ectodomains composed of a variable number of extracellular cadherin (EC) repeats that are similar but not identical in sequence and fold. E-cadherin, along with desmoglein and desmocollin proteins, are three classical-type cadherins that have slightly curved ectodomains and engage in homophilic and heterophilic interactions through an exchange of conserved tryptophan residues in their N-terminal EC1 repeat. In contrast, clustered protocadherins are straighter than classical cadherins and interact through an antiparallel homophilic binding interface that involves overlapped EC1 to EC4 repeats. Here we present molecular dynamics simulations that model the adhesive domains of these cadherins using available crystal structures, with systems encompassing up to 2.8 million atoms. Simulations of complete classical cadherin ectodomain dimers predict a two-phased elastic response to force in which these complexes first softly unbend and then stiffen to unbind without unfolding. Simulated α, β, and γ clustered protocadherin homodimers lack a two-phased elastic response, are brittle and stiffer than classical cadherins and exhibit complex unbinding pathways that in some cases involve transient intermediates. We propose that these distinct mechanical responses are important for function, with classical cadherin ectodomains acting as molecular shock absorbers and with stiffer clustered protocadherin ectodomains facilitating overlap that favors binding specificity over mechanical resilience. Overall, our simulations provide insights into the molecular mechanics of single cadherin dimers relevant in the formation of cellular junctions essential for tissue function.
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Affiliation(s)
- Brandon L Neel
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
| | - Collin R Nisler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Sanket Walujkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Raul Araya-Secchi
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Santiago, Chile
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio; Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Chemical Physics Graduate Program, The Ohio State University, Columbus, Ohio.
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8
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Daday C, de Buhr S, Mercadante D, Gräter F. Mechanical force can enhance c-Src kinase activity by impairing autoinhibition. Biophys J 2022; 121:684-691. [PMID: 35120901 PMCID: PMC8943751 DOI: 10.1016/j.bpj.2022.01.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 12/21/2021] [Accepted: 01/28/2022] [Indexed: 11/25/2022] Open
Abstract
Cellular mechanosensing is pivotal for virtually all biological processes, and many molecular mechano-sensors and their way of function are being uncovered. In this work, we suggest that c-Src kinase acts as a direct mechano-sensor. c-Src is responsible for, among others, cell proliferation, and shows increased activity in stretched cells. In its native state, c-Src has little basal activity, because its kinase domain binds to an SH2 and SH3 domain. However, it is known that c-Src can bind to p130Cas, through which force can be transmitted to the membrane. Using molecular dynamics simulations, we show that force acting between the membrane-bound N-terminus of the SH3 domain and p130Cas induces partial SH3 unfolding, thereby impeding rebinding of the kinase domain onto SH2/SH3 and effectively enhancing kinase activity. Forces involved in this process are slightly lower or similar to the forces required to pull out c-Src from the membrane through the myristoyl linker, and key interactions involved in this anchoring are salt bridges between negative lipids and nearby basic residues in c-Src. Thus, c-Src appears to be a candidate for an intriguing mechanosensing mechanism of impaired kinase inhibition, which can be potentially tuned by membrane composition and other environmental factors.
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Affiliation(s)
- Csaba Daday
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Svenja de Buhr
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | | | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Mathematikon, Heidelberg, Germany.
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9
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Stirnemann G. Recent Advances and Emerging Challenges in the Molecular Modeling of Mechanobiological Processes. J Phys Chem B 2022; 126:1365-1374. [PMID: 35143190 DOI: 10.1021/acs.jpcb.1c10715] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many biological processes result from the effect of mechanical forces on macromolecular structures and on their interactions. In particular, the cell shape, motion, and differentiation directly depend on mechanical stimuli from the extracellular matrix or from neighboring cells. The development of experimental techniques that can measure and characterize the tiny forces acting at the cellular scale and down to the single-molecule, biomolecular level has enabled access to unprecedented details about the involved mechanisms. However, because the experimental observables often do not provide a direct atomistic picture of the corresponding phenomena, particle-based simulations performed at various scales are instrumental in complementing these experiments and in providing a molecular interpretation. Here, we will review the recent key achievements in the field, and we will highlight and discuss the many technical challenges these simulations are facing, as well as suggest future directions for improvement.
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Affiliation(s)
- Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France
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10
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Materzok T, Gorb S, Müller-Plathe F. Gecko adhesion: a molecular-simulation perspective on the effect of humidity. SOFT MATTER 2022; 18:1247-1263. [PMID: 35043818 DOI: 10.1039/d1sm01232k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gecko adhesion is investigated by molecular dynamics simulations. It is known, that the gecko adhesion system shows increased pull-off forces in humid environments. A coarse-grained model of gecko beta keratin, previously developed in our group, is extended and used to elucidate the molecular mechanisms involved in this humidity effect on adhesion. We show that neither the change of the elastic properties of gecko keratin, nor capillary forces, can solely explain the increased pull-off forces of wet gecko keratin. Instead, we establish a molecular picture of gecko adhesion where the interplay between capillary bridges and a mediator effect of water, enhances pull-off forces, consistent with observations in AFM experiments at high humidities. We find that water density is raised locally, in molecular scale asperities of the gecko keratin and that this increase in local water density smoothes the surface-spatula interface. Water, which is absorbed into the keratin, acts as a mediator, and leads during pull-off to the dominant contribution in the van der Waals energy, because the dispersion interactions between water and surface are primarily opposing the pull-off.
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Affiliation(s)
- Tobias Materzok
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287 Darmstadt, Germany.
| | - Stanislav Gorb
- Zoological Institute Functional Morphology and Biomechanics, Kiel University, Am Botanischen Garten 1-9, D-24118 Kiel, Germany.
| | - Florian Müller-Plathe
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie and Profile Area Thermofluids and Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 8, D-64287 Darmstadt, Germany.
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11
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Seifi B, Aina A, Wallin S. Structural fluctuations and mechanical stabilities of the metamorphic protein RfaH. Proteins 2020; 89:289-300. [PMID: 32996201 DOI: 10.1002/prot.26014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/17/2020] [Accepted: 08/31/2020] [Indexed: 01/08/2023]
Abstract
RfaH is a compact two-domain bacterial transcription factor that functions both as a regulator of transcription and an enhancer of translation. Underpinning the dual functional roles of RfaH is a partial but dramatic fold switch, which completely transforms the ~50-amino acid C-terminal domain (CTD) from an all-α state to an all-β state. The fold switch of the CTD occurs when RfaH binds to RNA polymerase (RNAP), however, the details of how this structural transformation is triggered is not well understood. Here we use all-atom Monte Carlo simulations to characterize structural fluctuations and mechanical stability properties of the full-length RfaH and the CTD as an isolated fragment. In agreement with experiments, we find that interdomain contacts are crucial for maintaining a stable, all-α CTD in free RfaH. To probe mechanical properties, we use pulling simulations to measure the work required to inflict local deformations at different positions along the chain. The resulting mechanical stability profile reveals that free RfaH can be divided into a "rigid" part and a "soft" part, with a boundary that nearly coincides with the boundary between the two domains. We discuss the potential role of this feature for how fold switching may be triggered by interaction with RNAP.
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Affiliation(s)
- Bahman Seifi
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
| | - Adekunle Aina
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
| | - Stefan Wallin
- Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St Johns, Newfoundland, Canada
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12
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Hartmann MJ, Singh Y, Vanden-Eijnden E, Hocky GM. Infinite switch simulated tempering in force (FISST). J Chem Phys 2020; 152:244120. [DOI: 10.1063/5.0009280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
| | - Yuvraj Singh
- Department of Chemistry, New York University, New York, New York 10003, USA
| | - Eric Vanden-Eijnden
- Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA
| | - Glen M. Hocky
- Department of Chemistry, New York University, New York, New York 10003, USA
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13
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Franz F, Daday C, Gräter F. Advances in molecular simulations of protein mechanical properties and function. Curr Opin Struct Biol 2020; 61:132-138. [PMID: 31954324 DOI: 10.1016/j.sbi.2019.12.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 01/05/2023]
Abstract
Single-molecule force spectroscopy and classical molecular dynamics are natural allies. Recent advances in both experiments and simulations have increasingly facilitated a direct comparison of SMFS and MD data, most importantly by closing the gap between time scales, which has been traditionally at least 5 orders of magnitudes wide. In this review, we will explore these advances chiefly on the computational side. We focus on protein dynamics under force and highlight recent studies that showcase how lower loading rates and more statistics help to better interpret previous experiments and to also motivate new ones. At the same time, steadily increasing system sizes are used to mimic more closely the mechanical environment in the biological context. We showcase some of these advances on atomistic and coarse-grained scale, from asymmetric membrane tension to larger (multidomain/multimeric) protein assemblies under force.
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Affiliation(s)
- Florian Franz
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, 69120 Heidelberg, Germany
| | - Csaba Daday
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Frauke Gräter
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, 69120 Heidelberg, Germany.
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14
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Baptista LA, Netz PA. Single molecule force spectroscopy of a streptomycin-binding RNA aptamer: An out-of-equilibrium molecular dynamics study. J Chem Phys 2019; 151:195102. [PMID: 31757139 DOI: 10.1063/1.5128126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Here, we investigate the unfolding behavior of a streptomycin-binding ribonucleic acid (RNA) aptamer under application of force in shear geometry. Using Langevin out-of-equilibrium simulations to emulate the single-molecule force spectroscopy (SMFS) experiment, we were able to understand the hierarchical unfolding process that occurs in the RNA molecule under application of stretching force and the influence of streptomycin modifying this unfolding. Subsequently, the application of the Jarzynski equality to the force profiles obtained in the pulling simulations shows that the free energies for individual systems and the difference of unfolding free energy upon streptomycin binding to the RNA free aptamer are in fair agreement with the experimental values, obtained through SMFS by Nick et al. [J. Phys. Chem. B 120, 6479 (2016)].
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Affiliation(s)
- Luis A Baptista
- Programa de Pós-Graduação em Química, Instituto de Química, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Paulo A Netz
- Department of Physical Chemistry, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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