1
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Walbrun A, Wang T, Matthies M, Šulc P, Simmel FC, Rief M. Single-molecule force spectroscopy of toehold-mediated strand displacement. Nat Commun 2024; 15:7564. [PMID: 39217165 PMCID: PMC11365964 DOI: 10.1038/s41467-024-51813-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024] Open
Abstract
Toehold-mediated strand displacement (TMSD) is extensively utilized in dynamic DNA nanotechnology and for a wide range of DNA or RNA-based reaction circuits. Investigation of TMSD kinetics typically relies on bulk fluorescence measurements providing effective, bulk-averaged reaction rates. Information on individual molecules or even base pairs is scarce. In this work, we explore the dynamics of strand displacement processes at the single-molecule level using single-molecule force spectroscopy with a microfluidics-enhanced optical trap supported by state-of-the-art coarse-grained simulations. By applying force, we can trigger and observe TMSD in real-time with microsecond and nanometer resolution. We find TMSD proceeds very rapidly under load with single step times of 1 µs. Tuning invasion efficiency by introducing mismatches allows studying thousands of forward/backward invasion events on a single molecule and analyze the kinetics of the invasion process. Extrapolation to zero force reveals single step times for DNA invading DNA four times faster than for RNA invading RNA. We also study the kinetics of DNA invading RNA, a process that in the absence of force would rarely occur. Our results reveal the importance of sequence effects for the TMSD process and have relevance for a wide range of applications in nucleic acid nanotechnology and synthetic biology.
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Affiliation(s)
- Andreas Walbrun
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Tianhe Wang
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Michael Matthies
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
| | - Petr Šulc
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany
- School of Molecular Sciences and Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Friedrich C Simmel
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Garching, Germany.
| | - Matthias Rief
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany.
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2
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Schanda P, Haran G. NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. Annu Rev Biophys 2024; 53:247-273. [PMID: 38346243 DOI: 10.1146/annurev-biophys-070323-022428] [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] [Indexed: 07/18/2024]
Abstract
Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.
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Affiliation(s)
- Paul Schanda
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria;
| | - Gilad Haran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel;
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3
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Zhou M, Zhou W, Yang H, Cao L, Li M, Yin P, Zhou Y. Molecular Modeling of Shockwave-Mediated Blood-Brain Barrier Opening for Targeted Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38622933 DOI: 10.1021/acsami.4c00812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Bubble-enhanced shock waves induce the transient opening of the blood-brain barrier (BBB) providing unique advantages for targeted drug delivery of brain tumor therapy, but little is known about the molecular details of this process. Based on our BBB model including 28 000 lipids and 280 tight junction proteins and coarse-grained dynamics simulations, we provided the molecular-level delivery mechanism of three typical drugs for the first time, including the lipophilic paclitaxel, hydrophilic gemcitabine, and siRNA encapsulated in liposome, across the BBB. The results show that the BBB is more difficult to be perforated by shock-induced jets than the human brain plasma membrane (PM), requiring higher shock wave speeds. For the pores formed, the BBB exhibits a greater ability to self-heal than PM. Hydrophobic paclitaxel can cross the BBB and be successfully absorbed, but the amount is only one-third of that of PM; however, the absorption of hydrophilic gemcitabine was almost negligible. Liposome-loaded siRNAs only stayed in the first layer of the BBB. The mechanism analysis shows that increasing the bubble size can promote drug absorption while reducing the risk of higher shock wave overpressure. An exponential function was proposed to describe the relation between bubble and overpressure, which can be extended to the experimental microbubble scale. The calculated overpressure is consistent with the experimental result. These molecular-scale details on shock-assisted BBB opening for targeted drug delivery would guide and assist experimental attempts to promote the application of this strategy in the clinical treatment of brain tumors.
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Affiliation(s)
- Mi Zhou
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
- School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Wenyu Zhou
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
| | - Hong Yang
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
| | - Luoxia Cao
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
| | - Ming Li
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
| | - Ping Yin
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
- School of Materials Science & Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Yang Zhou
- Institute of Chemical Materials, Chinese Academy of Engineering and Physics, Mianyang 621900, China
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4
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Mondal B, Chakraborty D, Hori N, Nguyen HT, Thirumalai D. Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences. J Chem Theory Comput 2024; 20:2934-2946. [PMID: 38498914 DOI: 10.1021/acs.jctc.3c01193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Interplay between divalent cations (Mg2+ and Ca2+) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30, with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the small-angle X-ray scattering profiles, which are in excellent agreement with experiments. Although ion-counting experiments mask the differences between Mg2+ and Ca2+, we find that Mg2+ binds to the minor grooves and phosphate groups, whereas Ca2+ binds specifically to the minor groove. Both Mg2+ and Ca2+ exhibit a tendency to bind to the minor groove of DNA as opposed to the major groove. The dA30 conformations are dominated by stacking interactions, resulting in structures with considerable helical order. The near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30 populating an ensemble of heterogeneous conformations. The successful applications of the TIS-ION model are poised to confront many problems in DNA biophysics.
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Affiliation(s)
- Balaka Mondal
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Debayan Chakraborty
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Naoto Hori
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Hung T Nguyen
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
- Department of Physics, The University of Texas, Austin, Texas 78712, United States
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5
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Yuan J, Tanaka H. Impact of Hydrodynamic Interactions on the Kinetic Pathway of Protein Folding. PHYSICAL REVIEW LETTERS 2024; 132:138402. [PMID: 38613272 DOI: 10.1103/physrevlett.132.138402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 02/29/2024] [Indexed: 04/14/2024]
Abstract
Protein folding is a fundamental process critical to cellular function and human health, but it remains a grand challenge in biophysics. Hydrodynamic interaction (HI) plays a vital role in the self-organization of soft and biological materials, yet its role in protein folding is not fully understood despite folding occurring in a fluid environment. Here, we use the fluid particle dynamics method to investigate many-body hydrodynamic couplings between amino acid residues and fluid motion in the folding kinetics of a coarse-grained four-α-helices bundle protein. Our results reveal that HI helps select fast folding pathways to the native state without being kinetically trapped, significantly speeding up the folding kinetics compared to its absence. First, the directional flow along the protein backbone expedites protein collapse. Then, the incompressibility-induced squeezing flow effects retard the accumulation of non-native hydrophobic contacts, thus preventing the protein from being trapped in local energy minima during the conformational search of the native structure. We also find that the significance of HI in folding kinetics depends on temperature, with a pronounced effect under biologically relevant conditions. Our findings suggest that HI, particularly the short-range squeezing effect, may be crucial in avoiding protein misfolding.
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Affiliation(s)
- Jiaxing Yuan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hajime Tanaka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Fundamental Engineering, Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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6
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. J Chem Theory Comput 2024; 20:1398-1413. [PMID: 38241144 DOI: 10.1021/acs.jctc.3c00833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription and gene expression to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse-grained Force Field for Energy Estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the self-organized polymer model with side-chains for proteins and the three interaction site model for DNA in a modular fashion, without recalibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a data set of high-resolution crystal structures. The only parameter in COFFEE is the strength (λDNAPRO) of the DNA-protein contact potential. For an optimal choice of λDNAPRO, the crystallographic B-factors for DNA-protein complexes with varying sizes and topologies are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts scattering profiles that are in quantitative agreement with small-angle X-ray scattering experiments, as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which do not alter the balance of electrostatic interactions but affect chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin 78712, Texas, United States
- Department of Physics, The University of Texas at Austin, 2515 Speedway, Austin 78712, Texas, United States
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7
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Li Z, Hu R, Li T, Zhu J, You H, Li Y, Liu BF, Li C, Li Y, Yang Y. A TeZla micromixer for interrogating the early and broad folding landscape of G-quadruplex via multistage velocity descending. Proc Natl Acad Sci U S A 2024; 121:e2315401121. [PMID: 38232280 PMCID: PMC10823215 DOI: 10.1073/pnas.2315401121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
Biomacromolecular folding kinetics involves fast folding events and broad timescales. Current techniques face limitations in either the required time resolution or the observation window. In this study, we developed the TeZla micromixer, integrating Tesla and Zigzag microstructures with a multistage velocity descending strategy. TeZla achieves a significant short mixing dead time (40 µs) and a wide time window covering four orders of magnitude (up to 300 ms). Using this unique micromixer, we explored the folding landscape of c-Myc G4 and its noncanonical-G4 derivatives with different loop lengths or G-vacancy sites. Our findings revealed that c-Myc can bypass folding intermediates and directly adopt a G4 structure in the cation-deficient buffer. Moreover, we found that the loop length and specific G-vacancy site could affect the folding pathway and significantly slow down the folding rates. These results were also cross-validated with real-time NMR and circular dichroism. In conclusion, TeZla represents a versatile tool for studying biomolecular folding kinetics, and our findings may ultimately contribute to the design of drugs targeting G4 structures.
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Affiliation(s)
- Zheyu Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Huijuan You
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics—Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics—Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan430074, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences—Wuhan National Laboratory for Optoelectronics, Wuhan430071, China
- Graduate University of Chinese Academy of Sciences, Beijing10049, China
- Optics Valley Laboratory, Hubei430074, China
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8
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Yuan J, Tanaka H. Hydrodynamic Effects on the Collapse Kinetics of Flexible Polyelectrolytes. PHYSICAL REVIEW LETTERS 2024; 132:038101. [PMID: 38307078 DOI: 10.1103/physrevlett.132.038101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 11/05/2023] [Accepted: 11/28/2023] [Indexed: 02/04/2024]
Abstract
Understanding the collapse kinetics of polyelectrolytes (PEs) is crucial for comprehending various biological and industrial phenomena. Despite occurring in an aqueous environment, previous computational studies have overlooked the influence of hydrodynamic interactions (HIs) facilitated by fluid motion. Here, we directly compute the Navier-Stokes equation to investigate the collapse kinetics of a highly charged flexible PE. Our findings reveal that HI accelerates PE collapse induced by hydrophobicity and multivalent salt. In the case of hydrophobicity, HI induces long-range collective motion of monomers, accelerating the coarsening of local clusters through either Brownian-coagulation-like or evaporation-condensation-like processes, depending on the strength of hydrophobicity with respect to electrostatic interaction. Regarding multivalent salt, HI does not affect the condensation dynamics of multivalent ions but facilitates quicker movement of local dipolar clusters along the PE, thereby expediting the collapse process. These results provide valuable insights into the underlying mechanisms of HI in PE collapse kinetics.
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Affiliation(s)
- Jiaxing Yuan
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hajime Tanaka
- Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Fundamental Engineering, Institute of Industrial Science, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8505, Japan
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9
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Airas J, Ding X, Zhang B. Transferable Implicit Solvation via Contrastive Learning of Graph Neural Networks. ACS CENTRAL SCIENCE 2023; 9:2286-2297. [PMID: 38161379 PMCID: PMC10755853 DOI: 10.1021/acscentsci.3c01160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/26/2023] [Accepted: 10/31/2023] [Indexed: 01/03/2024]
Abstract
Implicit solvent models are essential for molecular dynamics simulations of biomolecules, striking a balance between computational efficiency and biological realism. Efforts are underway to develop accurate and transferable implicit solvent models and coarse-grained (CG) force fields in general, guided by a bottom-up approach that matches the CG energy function with the potential of mean force (PMF) defined by the finer system. However, practical challenges arise due to the lack of analytical expressions for the PMF and algorithmic limitations in parameterizing CG force fields. To address these challenges, a machine learning-based approach is proposed, utilizing graph neural networks (GNNs) to represent the solvation free energy and potential contrasting for parameter optimization. We demonstrate the effectiveness of the approach by deriving a transferable GNN implicit solvent model using 600,000 atomistic configurations of six proteins obtained from explicit solvent simulations. The GNN model provides solvation free energy estimations much more accurately than state-of-the-art implicit solvent models, reproducing configurational distributions of explicit solvent simulations. We also demonstrate the reasonable transferability of the GNN model outside of the training data. Our study offers valuable insights for deriving systematically improvable implicit solvent models and CG force fields from a bottom-up perspective.
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Affiliation(s)
- Justin Airas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United
States
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United
States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, United
States
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10
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Airas J, Ding X, Zhang B. Transferable Coarse Graining via Contrastive Learning of Graph Neural Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556923. [PMID: 37745447 PMCID: PMC10515757 DOI: 10.1101/2023.09.08.556923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Coarse-grained (CG) force fields are essential for molecular dynamics simulations of biomolecules, striking a balance between computational efficiency and biological realism. These simulations employ simplified models grouping atoms into interaction sites, enabling the study of complex biomolecular systems over biologically relevant timescales. Efforts are underway to develop accurate and transferable CG force fields, guided by a bottom-up approach that matches the CG energy function with the potential of mean force (PMF) defined by the finer system. However, practical challenges arise due to many-body effects, lack of analytical expressions for the PMF, and limitations in parameterizing CG force fields. To address these challenges, a machine learning-based approach is proposed, utilizing graph neural networks (GNNs) to represent CG force fields and potential contrasting for parameterization from atomistic simulation data. We demonstrate the effectiveness of the approach by deriving a transferable GNN implicit solvent model using 600,000 atomistic configurations of six proteins obtained from explicit solvent simulations. The GNN model provides solvation free energy estimations much more accurately than state-of-the-art implicit solvent models, reproducing configurational distributions of explicit solvent simulations. We also demonstrate the reasonable transferability of the GNN model outside the training data. Our study offers valuable insights for building accurate coarse-grained models bottom-up.
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Affiliation(s)
- Justin Airas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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11
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Chakraborty D, Mondal B, Thirumalai D. Brewing COFFEE: A sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.07.544064. [PMID: 37333386 PMCID: PMC10274755 DOI: 10.1101/2023.06.07.544064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
DNA-protein interactions are pervasive in a number of biophysical processes ranging from transcription, gene expression, to chromosome folding. To describe the structural and dynamic properties underlying these processes accurately, it is important to create transferable computational models. Toward this end, we introduce Coarse grained force field for energy estimation, COFFEE, a robust framework for simulating DNA-protein complexes. To brew COFFEE, we integrated the energy function in the Self-Organized Polymer model with Side Chains for proteins and the Three Interaction Site model for DNA in a modular fashion, without re-calibrating any of the parameters in the original force-fields. A unique feature of COFFEE is that it describes sequence-specific DNA-protein interactions using a statistical potential (SP) derived from a dataset of high-resolution crystal structures. The only parameter in COFFEE is the strength (λ D N A P R O ) of the DNA-protein contact potential. For an optimal choice of λ D N A P R O , the crystallographic B-factors for DNA-protein complexes, with varying sizes and topologies, are quantitatively reproduced. Without any further readjustments to the force-field parameters, COFFEE predicts the scattering profiles that are in quantitative agreement with SAXS experiments as well as chemical shifts that are consistent with NMR. We also show that COFFEE accurately describes the salt-induced unraveling of nucleosomes. Strikingly, our nucleosome simulations explain the destabilization effect of ARG to LYS mutations, which does not alter the balance of electrostatic interactions, but affects chemical interactions in subtle ways. The range of applications attests to the transferability of COFFEE, and we anticipate that it would be a promising framework for simulating DNA-protein complexes at the molecular length-scale.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - Balaka Mondal
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Stop A5300, Austin TX 78712, USA
- Department of Physics, The University of Texas at Austin, 2515 Speedway,Austin TX 78712, USA
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12
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Mu ZC, Tan YL, Liu J, Zhang BG, Shi YZ. Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding. Molecules 2023; 28:4833. [PMID: 37375388 DOI: 10.3390/molecules28124833] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
DNA carries the genetic information required for the synthesis of RNA and proteins and plays an important role in many processes of biological development. Understanding the three-dimensional (3D) structures and dynamics of DNA is crucial for understanding their biological functions and guiding the development of novel materials. In this review, we discuss the recent advancements in computer methods for studying DNA 3D structures. This includes molecular dynamics simulations to analyze DNA dynamics, flexibility, and ion binding. We also explore various coarse-grained models used for DNA structure prediction or folding, along with fragment assembly methods for constructing DNA 3D structures. Furthermore, we also discuss the advantages and disadvantages of these methods and highlight their differences.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan 430073, China
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13
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Anderson DM, Jayanthi LP, Gosavi S, Meiering EM. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. Front Mol Biosci 2023; 10:1021733. [PMID: 36845544 PMCID: PMC9945329 DOI: 10.3389/fmolb.2023.1021733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.
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Affiliation(s)
| | - Lakshmi P. Jayanthi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Elizabeth M. Meiering
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada,*Correspondence: Elizabeth M. Meiering,
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14
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Effects of 2D filler on rheology of additive manufacturing polymers: Simulation and experiment on polyetherketoneketone -mica composites. POLYMER 2023. [DOI: 10.1016/j.polymer.2023.125722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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15
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Wang Y, Wang A, Mohanty U, Whitford PC. Precise Steric Features Control Aminoacyl-tRNA Accommodation on the Ribosome. J Phys Chem B 2022; 126:8447-8459. [PMID: 36251478 DOI: 10.1021/acs.jpcb.2c05513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein synthesis involves a complex series of large-scale conformational changes in the ribosome. While long-lived intermediate states of these processes can be characterized by experiments, computational methods can be used to identify the interactions that contribute to the rate-limiting free-energy barriers. To this end, we use a simplified energetic model to perform molecular dynamics (MD) simulations of aminoacyl-tRNA (aa-tRNA) accommodation on the ribosome. While numerous studies have probed the energetics of the early stages of accommodation, we focus on the final stage of accommodation, where the 3'-CCA tail of aa-tRNA enters the peptidyl transferase center (PTC). These simulations show how a distinct intermediate is induced by steric confinement of the tail, immediately before it completes accommodation. Multiple pathways for 3'-CCA tail accommodation can be quantitatively distinguished, where the tail enters the PTC by moving past a pocket enclosed by Helix 89, 90, and 92, or through an alternate route formed by Helix 93 and the P-site tRNA. C2573, located within Helix 90, is shown to provide the largest contribution to this late-accommodation steric barrier, such that sub-Å perturbations to this residue can alter the time scale of tail accommodation by nearly an order of magnitude. In terms of biological function, these calculations suggest how this late-stage sterically induced barrier may contribute to tRNA proofreading by the ribosome.
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Affiliation(s)
- Yang Wang
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts02467, United States
| | - Ailun Wang
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts02115, United States
| | - Udayan Mohanty
- Department of Chemistry, Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts02467, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts02115, United States.,Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts02115, United States
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16
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Mu ZC, Tan YL, Zhang BG, Liu J, Shi YZ. Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions. PLoS Comput Biol 2022; 18:e1010501. [PMID: 36260618 PMCID: PMC9621594 DOI: 10.1371/journal.pcbi.1010501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/31/2022] [Accepted: 09/27/2022] [Indexed: 11/07/2022] Open
Abstract
The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs. To determine 3D structures and quantify stability of single- (ss) and double-stranded (ds) DNAs is essential to unveil the mechanisms of their functions and to further guide the production and development of novel materials. Although many DNA models have been proposed to reproduce the basic structural, mechanical, or thermodynamic properties of dsDNAs based on the secondary structure information or preset constraints, there are very few models can be used to investigate the ssDNA folding or dsDNA assembly from the sequence. Furthermore, due to the polyanionic nature of DNAs, metal ions (e.g., Na+ and Mg2+) in solutions can play an essential role in DNA folding and dynamics. Nevertheless, ab initio predictions for DNA folding in ion solutions are still an unresolved problem. In this work, we developed a novel coarse-grained model to predict 3D structures and thermodynamic stabilities for both ssDNAs and dsDNAs in monovalent/divalent ion solutions from their sequences. As compared with the extensive experimental data and available existing models, we showed that the present model can successfully fold simple DNAs into their native-like structures, and can also accurately reproduce the effects of sequence and monovalent/divalent ions on structure stability for ssDNAs including pseudoknot and dsDNAs with/without bulge/internal loops.
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Affiliation(s)
- Zi-Chun Mu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China
| | - Ya-Lan Tan
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ben-Gong Zhang
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Jie Liu
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China
- * E-mail:
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17
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Abstract
Coarse-grained models have proven helpful for simulating complex systems over long time scales to provide molecular insights into various processes. Methodologies for systematic parametrization of the underlying energy function or force field that describes the interactions among different components of the system are of great interest for ensuring simulation accuracy. We present a new method, potential contrasting, to enable efficient learning of force fields that can accurately reproduce the conformational distribution produced with all-atom simulations. Potential contrasting generalizes the noise contrastive estimation method with umbrella sampling to better learn the complex energy landscape of molecular systems. When applied to the Trp-cage protein, we found that the technique produces force fields that thoroughly capture the thermodynamics of the folding process despite the use of only α-carbons in the coarse-grained model. We further showed that potential contrasting could be applied over large data sets that combine the conformational ensembles of many proteins to improve force field transferability. We anticipate potential contrasting as a powerful tool for building general-purpose coarse-grained force fields.
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Affiliation(s)
- Xinqiang Ding
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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18
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Hendrix E, Motta S, Gahl RF, He Y. Insight into the Initial Stages of the Folding Process in Onconase Revealed by UNRES. J Phys Chem B 2022; 126:7934-7942. [PMID: 36179061 DOI: 10.1021/acs.jpcb.2c04770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The unfolded state of proteins presents many challenges to elucidate the structural basis for biological function. This state is characterized by a large degree of structural heterogeneity which makes it difficult to generate structural models. However, recent experiments into the initial folding events of the 104-residue ribonuclease homologue onconase (ONC) were able to identify the regions in the protein that participate in the initial folding of this protein. Therefore, to gain additional structural insight into the unfolded state of proteins, this study utilized molecular dynamics simulations using the UNited-RESidue (UNRES) force field to evaluate whether there is a good agreement between the experimentally determined initial structures and the structures identified by computer simulations along a folding pathway. Indeed, these UNRES simulations accurately identified the two regions experimentally observed to form the initial native structure along the folding pathway of ONC. In addition, these regions are determined to be chain folding initiation sites (CFIS) according to methods developed previously. Subsequent self-organization maps (SOM) analysis has revealed key structural states involved in these early folding events.
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Affiliation(s)
- Emily Hendrix
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico87131, United States
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan20126, Italy
| | - Robert F Gahl
- Division of Extramural Activities, National Cancer Institute, National Institutes of Health, Bethesda, Maryland20850, United States
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico87131, United States.,Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico87131, United States
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19
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Wei T, Zhou M, Gu L, Zhou Y, Li M. How Shockwaves Open Tight Junctions of Blood–Brain Barrier: Comparison of Three Biomechanical Effects. J Phys Chem B 2022; 126:5094-5102. [DOI: 10.1021/acs.jpcb.2c02903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Wei
- CAS Key Laboratory of Mechanical Behavior and Design of Materials, Department of Modern Mechanics, University of Science and Technology of China, Hefei 230026, China
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Mi Zhou
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Lingzhi Gu
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Yang Zhou
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
| | - Ming Li
- Institute of Chemical Materials, China Academy of Engineering and Physics, Mianyang 621900, China
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20
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Du J, Yin H, Lu Y, Lu T, Chen T. Effects of Surface Tethering on the Thermodynamics and Kinetics of Frustrated Protein Folding. J Phys Chem B 2022; 126:4776-4786. [PMID: 35731862 DOI: 10.1021/acs.jpcb.2c01982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction between the protein and surface plays an important role in biology and biotechnology. To understand how surface tethering influences the folding behavior of frustrated proteins, in this work, we systematically study the thermodynamics and folding kinetics of the bacterial immunity protein Im7 and Fyn SH3 domain tethered to a surface using Langevin dynamics simulations. Upon surface tethering, the stabilization often results from the entropic effect, whereas the destabilization is usually caused by either an energetic or entropic effect. For the Fyn SH3 domain with a two-state folding manner, the influence of nonnative interactions on thermodynamic stability is not significant, while nonnative interactions can weaken the effect of surface tethering on the change in the folding rate. By contrast, for the frustrated protein Im7, depending on where the protein is tethered, the surface tethering can promote or suppress misfolding by modulating specific nonnative contacts, thereby altering the folding rate and folding mechanism. Because surface tethering can change the intrachain diffusivity of unfolding, the kinetic stability cannot be well captured by the thermodynamic stability at some tether points. This study should be helpful in general to understand how surface tethering affects the folding energy landscape of frustrated proteins.
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Affiliation(s)
- Jiang Du
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Hongmei Yin
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Yanfang Lu
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
| | - Teng Lu
- Computer Network Information Center of the Chinese Academy of Sciences, Beijing 100083, P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecule of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China.,Key Laboratory of Polymer Processing Engineering (South China University of Technology), Ministry of Education, Guangzhou 510641, P. R. China
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21
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Wang A, Levi M, Mohanty U, Whitford PC. Diffuse Ions Coordinate Dynamics in a Ribonucleoprotein Assembly. J Am Chem Soc 2022; 144:9510-9522. [PMID: 35593477 DOI: 10.1021/jacs.2c04082] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Proper ionic concentrations are required for the functional dynamics of RNA and ribonucleoprotein (RNP) assemblies. While experimental and computational techniques have provided many insights into the properties of chelated ions, less is known about the energetic contributions of diffuse ions to large-scale conformational rearrangements. To address this, we present a model that is designed to quantify the influence of diffuse monovalent and divalent ions on the dynamics of biomolecular assemblies. This model employs all-atom (non-H) resolution and explicit ions, where effective potentials account for hydration effects. We first show that the model accurately predicts the number of excess Mg2+ ions for prototypical RNA systems, at a level comparable to modern coarse-grained models. We then apply the model to a complete ribosome and show how the balance between diffuse Mg2+ and K+ ions can control the dynamics of tRNA molecules during translation. The model predicts differential effects of diffuse ions on the free-energy barrier associated with tRNA entry and the energy of tRNA binding to the ribosome. Together, this analysis reveals the direct impact of diffuse ions on the dynamics of an RNP assembly.
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Affiliation(s)
- Ailun Wang
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States.,Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Mariana Levi
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Udayan Mohanty
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Paul C Whitford
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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22
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Jost D. Polymer Modeling of 3D Epigenome Folding: Application to Drosophila. Methods Mol Biol 2022; 2301:293-305. [PMID: 34415542 DOI: 10.1007/978-1-0716-1390-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Mechanistic modeling in biology allows to investigate, based on first principles, if putative hypotheses are compatible with observations and to drive further experimental works. Along this line, polymer modeling has been instrumental in 3D genomics to better understand the impact of key mechanisms on the spatial genome organization. Here, I describe how polymer-based models can be practically used to study the role of epigenome in chromosome folding. I illustrate this methodology in the context of Drosophila epigenome folding.
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Affiliation(s)
- Daniel Jost
- University of Lyon, ENS de Lyon, Univ Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, Lyon, France.
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23
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Shino G, Takada S. Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models. Front Mol Biosci 2021; 8:772486. [PMID: 34869598 PMCID: PMC8636136 DOI: 10.3389/fmolb.2021.772486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/07/2021] [Indexed: 01/24/2023] Open
Abstract
Recently, the molecular mechanisms of transcription initiation have been intensively studied. Especially, the cryo-electron microscopy revealed atomic structure details in key states in the eukaryotic transcription initiation. Yet, the dynamic processes of the promoter DNA opening in the pre-initiation complex remain obscured. In this study, based on the three cryo-electron microscopic yeast structures for the closed, open, and initially transcribing complexes, we performed multiscale molecular dynamics (MD) simulations to model structures and dynamic processes of DNA opening. Combining coarse-grained and all-atom MD simulations, we first obtained the atomic model for the DNA bubble in the open complexes. Then, in the MD simulation from the open to the initially transcribing complexes, we found a previously unidentified intermediate state which is formed by the bottleneck in the fork loop 1 of Pol II: The loop opening triggered the escape from the intermediate, serving as a gatekeeper of the promoter DNA opening. In the initially transcribing complex, the non-template DNA strand passes a groove made of the protrusion, the lobe, and the fork of Rpb2 subunit of Pol II, in which several positively charged and highly conserved residues exhibit key interactions to the non-template DNA strand. The back-mapped all-atom models provided further insights on atomistic interactions such as hydrogen bonding and can be used for future simulations.
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Affiliation(s)
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
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24
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Dodero-Rojas E, Onuchic JN, Whitford PC. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. eLife 2021; 10:70362. [PMID: 34463614 PMCID: PMC8456623 DOI: 10.7554/elife.70362] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/06/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200–300 Å) conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the fusion peptides must be released from the core of the protein and associate with the host membrane. While infection relies on this transition between the prefusion and postfusion conformations, there has yet to be a biophysical characterization reported for this rearrangement. That is, structures are available for the endpoints, though the intermediate conformational processes have not been described. Interestingly, the Spike protein possesses many post-translational modifications, in the form of branched glycans that flank the surface of the assembly. With the current lack of data on the pre-to-post transition, the precise role of glycans during cell invasion has also remained unclear. To provide an initial mechanistic description of the pre-to-post rearrangement, an all-atom model with simplified energetics was used to perform thousands of simulations in which the protein transitions between the prefusion and postfusion conformations. These simulations indicate that the steric composition of the glycans can induce a pause during the Spike protein conformational change. We additionally show that this glycan-induced delay provides a critical opportunity for the fusion peptides to capture the host cell. In contrast, in the absence of glycans, the viral particle would likely fail to enter the host. This analysis reveals how the glycosylation state can regulate infectivity, while providing a much-needed structural framework for studying the dynamics of this pervasive pathogen.
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Affiliation(s)
- Esteban Dodero-Rojas
- Center for Theoretical Biological Physics, Rice University, Houston, United States
| | - Jose N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, United States.,Department of Physics and Astronomy, Rice University, Houston, United States.,Department of Chemistry, Rice University, Houston, United States.,Department of Biosciences, Rice University, Houston, United States
| | - Paul Charles Whitford
- Center for Theoretical Biological Physics, Northeastern University, Boston, United States.,Department of Physics, Northeastern University, Boston, United States
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25
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Lalwani Prakash D, Gosavi S. Understanding the Folding Mediated Assembly of the Bacteriophage MS2 Coat Protein Dimers. J Phys Chem B 2021; 125:8722-8732. [PMID: 34339197 DOI: 10.1021/acs.jpcb.1c03928] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The capsids of RNA viruses such as MS2 are great models for studying protein self-assembly because they are made almost entirely of multiple copies of a single coat protein (CP). Although CP is the minimal repeating unit of the capsid, previous studies have shown that CP exists as a homodimer (CP2) even in an acid-disassembled system, indicating that CP2 is an obligate dimer. Here, we investigate the molecular basis of this obligate dimerization using coarse-grained structure-based models and molecular dynamics simulations. We find that, unlike monomeric proteins of similar size, CP populates a single partially folded ensemble whose "foldedness" is sensitive to denaturing conditions. In contrast, CP2 folds similarly to single-domain proteins populating only the folded and the unfolded ensembles, separated by a prominent folding free energy barrier. Several intramonomer contacts form early, but the CP2 folding barrier is crossed only when the intermonomer contacts are made. A dissection of the structure of CP2 through mutant folding simulations shows that the folding barrier arises both from the topology of CP and the interface contacts of CP2. Together, our results show that CP2 is an obligate dimer because of kinetic stability, that is, dimerization induces a folding barrier and that makes it difficult for proteins in the dimer minimum to partially unfold and access the monomeric state without completely unfolding. We discuss the advantages of this obligate dimerization in the context of dimer design and virus stability.
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Affiliation(s)
- Digvijay Lalwani Prakash
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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26
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Dongre AV, Das S, Bellur A, Kumar S, Chandrashekarmath A, Karmakar T, Balaram P, Balasubramanian S, Balaram H. Structural basis for the hyperthermostability of an archaeal enzyme induced by succinimide formation. Biophys J 2021; 120:3732-3746. [PMID: 34302792 DOI: 10.1016/j.bpj.2021.07.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022] Open
Abstract
Stability of proteins from hyperthermophiles (organisms existing under boiling water conditions) enabled by a reduction of conformational flexibility is realized through various mechanisms. A succinimide (SNN) arising from the post-translational cyclization of the side chains of aspartyl/asparaginyl residues with the backbone amide -NH of the succeeding residue would restrain the torsion angle Ψ and can serve as a new route for hyperthermostability. However, such a succinimide is typically prone to hydrolysis, transforming to either an aspartyl or β-isoaspartyl residue. Here, we present the crystal structure of Methanocaldococcus jannaschii glutamine amidotransferase and, using enhanced sampling molecular dynamics simulations, address the mechanism of its increased thermostability, up to 100°C, imparted by an unexpectedly stable succinimidyl residue at position 109. The stability of SNN109 to hydrolysis is seen to arise from its electrostatic shielding by the side-chain carboxylate group of its succeeding residue Asp110, as well as through n → π∗ interactions between SNN109 and its preceding residue Glu108, both of which prevent water access to SNN. The stable succinimidyl residue induces the formation of an α-turn structure involving 13-atom hydrogen bonding, which locks the local conformation, reducing protein flexibility. The destabilization of the protein upon replacement of SNN with a Φ-restricted prolyl residue highlights the specificity of the succinimidyl residue in imparting hyperthermostability to the enzyme. The conservation of the succinimide-forming tripeptide sequence (E(N/D)(E/D)) in several archaeal GATases strongly suggests an adaptation of this otherwise detrimental post-translational modification as a harbinger of thermostability.
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Affiliation(s)
- Aparna Vilas Dongre
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Sudip Das
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Asutosh Bellur
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Anusha Chandrashekarmath
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India
| | - Tarak Karmakar
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India; Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Ticino, Switzerland; Facoltà di Informatica, Istituto di Scienze Computationali, Università della Svizzera Italiana, Lugano, Ticino, Switzerland
| | - Padmanabhan Balaram
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India.
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore, India.
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27
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Goldtzvik Y, Thirumalai D. Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin. J Chem Theory Comput 2021; 17:5358-5368. [PMID: 34251798 DOI: 10.1021/acs.jctc.1c00317] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conventional kinesin, a motor protein that transports cargo within cells, walks by taking multiple steps toward the plus end of the microtubule (MT). While significant progress has been made in understanding the details of the walking mechanism of kinesin, there are many unresolved issues. From a computational perspective, a central challenge is the large size of the system, which limits the scope of time scales accessible in standard computer simulations. Here, we create a general multiscale coarse-grained model for motors that enables us to simulate the stepping process of motors on polar tracks (actin and MT) with a focus on kinesin. Our approach greatly shortens the computation times without a significant loss in detail, thus allowing us to better describe the molecular basis of the stepping kinetics. The small number of parameters, which are determined by fitting to experimental data, allows us to develop an accurate method that may be adopted to simulate stepping in other molecular motors. The model enables us to simulate a large number of steps, which was not possible previously. We show in agreement with experiments that due to the docking of the neck linker (NL) of kinesin, sometimes deemed as the power stroke, the space explored diffusively by the tethered head is severely restricted, allowing the step to be completed in tens of microseconds. We predict that increasing the interaction strength between the NL and the motor head, achievable by mutations in the NL, decreases the stepping time but reaches a saturation value. Furthermore, the full three-dimensional dynamics of the cargo are fully resolved in our model, contributing to the predictive power and allowing us to study the important aspects of cargo-motor interactions.
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Affiliation(s)
- Yonathan Goldtzvik
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
| | - D Thirumalai
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78705, United States
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28
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Freitas FC, Fuchs G, de Oliveira RJ, Whitford PC. The dynamics of subunit rotation in a eukaryotic ribosome. BIOPHYSICA 2021; 1:204-221. [PMID: 37484008 PMCID: PMC10361705 DOI: 10.3390/biophysica1020016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Protein synthesis by the ribosome is coordinated by an intricate series of large-scale conformational rearrangements. Structural studies can provide information about long-lived states, however biological kinetics are controlled by the intervening free-energy barriers. While there has been progress describing the energy landscapes of bacterial ribosomes, very little is known about the energetics of large-scale rearrangements in eukaryotic systems. To address this topic, we constructed an all-atom model with simplified energetics and performed simulations of subunit rotation in the yeast ribosome. In these simulations, the small subunit (SSU; ~1MDa) undergoes spontaneous and reversible rotations (~8°). By enabling the simulation of this rearrangement under equilibrium conditions, these calculations provide initial insights into the molecular factors that control dynamics in eukaryotic ribosomes. Through this, we are able to identify specific inter-subunit interactions that have a pronounced influence on the rate-limiting free-energy barrier. We also show that, as a result of changes in molecular flexibility, the thermodynamic balance between the rotated and unrotated states is temperature-dependent. This effect may be interpreted in terms of differential molecular flexibility within the rotated and unrotated states. Together, these calculations provide a foundation, upon which the field may begin to dissect the energetics of these complex molecular machines.
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Affiliation(s)
- Frederico Campos Freitas
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Gabriele Fuchs
- Department of Biological Sciences, The RNA Institute, University at Albany 1400 Washington Ave, Albany, NY,12222
| | - Ronaldo Junio de Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba, MG, Brazil
| | - Paul Charles Whitford
- Department of Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
- Center for Theoretical Biological Physics, Northeastern University, 360 Huntington Ave, Boston, MA 02115
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29
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Mugnai ML, Thirumalai D. Step-Wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor. J Phys Chem B 2021; 125:1107-1117. [PMID: 33481593 DOI: 10.1021/acs.jpcb.0c10004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular motors, such as myosin, kinesin, and dynein, convert the energy released by the hydrolysis of ATP into mechanical work, thus allowing them to undergo directional motion on cytoskeletal tracks. A pivotal step in the chemomechanical transduction in myosin motors occurs after they bind to the actin filament, which triggers the release of phosphate (Pi, product of ATP hydrolysis) and the rotation of the lever arm. Here, we investigate the mechanism of phosphate release in myosin VI using extensive molecular dynamics simulations involving multiple trajectories of several μs. Because the escape of phosphate is expected to occur on time-scales on the order of milliseconds or more in myosin VI, we observed Pi release only if the trajectories were initiated with a rotated phosphate inside the nucleotide binding pocket. We discovered that although Pi populates the traditional "back door" route, phosphate exits through various other gateways, thus establishing the heterogeneity in the escape routes. Remarkably, we observed that the release of phosphate is preceded by a stepwise hydration of the ADP-bound magnesium ion. The release of the anion occurred only after four water molecules hydrated the cation (Mg2+). By performing comparative structural analyses, we show that hydration of magnesium is the key step in the phosphate release in a number of ATPases and GTPases. Nature may have evolved hydration of Mg2+ as a general molecular switch for Pi release, which is a universal step in the catalytic cycle of many machines that share little sequence or structural similarity.
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Affiliation(s)
- Mauro Lorenzo Mugnai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - D Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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30
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Terse VL, Gosavi S. The Molecular Mechanism of Domain Swapping of the C-Terminal Domain of the SARS-Coronavirus Main Protease. Biophys J 2020; 120:504-516. [PMID: 33359834 PMCID: PMC7837137 DOI: 10.1016/j.bpj.2020.11.2277] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/09/2020] [Accepted: 11/24/2020] [Indexed: 11/25/2022] Open
Abstract
In three-dimensional domain swapping, two protein monomers exchange a part of their structures to form an intertwined homodimer, whose subunits resemble the monomer. Several viral proteins domain swap to increase their structural complexity or functional avidity. The main protease (Mpro) of the severe acute respiratory syndrome (SARS) coronavirus proteolyzes viral polyproteins and has been a target for anti-SARS drug design. Domain swapping in the α-helical C-terminal domain of Mpro (MproC) locks Mpro into a hyperactive octameric form that is hypothesized to promote the early stages of viral replication. However, in the absence of a complete molecular understanding of the mechanism of domain swapping, investigations into the biological relevance of this octameric Mpro have stalled. Isolated MproC can exist as a monomer or a domain-swapped dimer. Here, we investigate the mechanism of domain swapping of MproC using coarse-grained structure-based models and molecular dynamics simulations. Our simulations recapitulate several experimental features of MproC folding. Further, we find that a contact between a tryptophan in the MproC domain-swapping hinge and an arginine elsewhere forms early during folding, modulates the folding route, and promotes domain swapping to the native structure. An examination of the sequence and the structure of the tryptophan containing hinge loop shows that it has a propensity to form multiple secondary structures and contacts, indicating that it could be stabilized into either the monomer- or dimer-promoting conformations by mutations or ligand binding. Finally, because all residues in the tryptophan loop are identical in SARS-CoV and SARS-CoV-2, mutations that modulate domain swapping may provide insights into the role of octameric Mpro in the early-stage viral replication of both viruses.
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Affiliation(s)
- Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India.
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31
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Nicholson DA, Sengupta A, Nesbitt DJ. Chirality-Dependent Amino Acid Modulation of RNA Folding. J Phys Chem B 2020; 124:11561-11572. [PMID: 33296203 DOI: 10.1021/acs.jpcb.0c07420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The preponderance of a specific d- or l-chirality in fats, sugars, amino acids, nucleic acids, and so on is ubiquitous in nature, yet the biological origin of such chiral dominance (i.e., with one enantiomer overwhelmingly present) remains an open question. One plausible proposal for the predominance of l-chirality in amino acids could be through evolutionary templating of chiral RNA-folding via chaperone activity. To help evaluate this possibility, single molecule fluorescence experiments have been performed that measure the chiral dependence of chaperone folding dynamics for the simple tetraloop-tetraloop receptor (TL-TLR) tertiary binding motif in the presence of a series of chiral amino acids. Specifically, d- vs l-arginine is found to accelerate the unfolding of this RNA motif in a chirally selective fashion, with temperature-dependent studies of the kinetics performed to extract free energy, enthalpy, and entropy landscapes for the underlying thermodynamics. Furthermore, all-atom molecular dynamics (MD) simulations are pursued to provide additional physical insight into this chiral sensitivity, which reveal enantiomer-specific sampling of nucleic acid surfaces by d- vs l-arginine and support a putative mechanism for chirally specific denaturation of RNA tertiary structure by arginine but not other amino acids.
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Affiliation(s)
- David A Nicholson
- JILA, National Institute of Standards and Technology and University of Colorado Boulder, Boulder, Colorado 80309 United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Abhigyan Sengupta
- Department of Physics, Technical University of Munich, Garching, Munich, Germany 85748
| | - David J Nesbitt
- JILA, National Institute of Standards and Technology and University of Colorado Boulder, Boulder, Colorado 80309 United States.,Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States.,Department of Physics, University of Colorado Boulder, Boulder, Colorado 80309, United States
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32
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A steric gate controls P/E hybrid-state formation of tRNA on the ribosome. Nat Commun 2020; 11:5706. [PMID: 33177497 PMCID: PMC7658246 DOI: 10.1038/s41467-020-19450-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022] Open
Abstract
The ribosome is a biomolecular machine that undergoes multiple large-scale structural rearrangements during protein elongation. Here, we focus on a conformational rearrangement during translocation, known as P/E hybrid-state formation. Using a model that explicitly represents all non-hydrogen atoms, we simulated more than 120 spontaneous transitions, where the tRNA molecule is displaced between the P and E sites of the large subunit. In addition to predicting a free-energy landscape that is consistent with previous experimental observations, the simulations reveal how a six-residue gate-like region can limit P/E formation, where sub-angstrom structural perturbations lead to an order-of-magnitude change in kinetics. Thus, this precisely defined set of residues represents a novel target that may be used to control functional dynamics in bacterial ribosomes. This theoretical analysis establishes a direct relationship between ribosome structure and large-scale dynamics, and it suggests how next-generation experiments may precisely dissect the energetics of hybrid formation on the ribosome. The ribosome undergoes multiple large-scale structural rearrangements during protein elongation. Here the authors present an all-atom model of the ribosome to study the energetics of P/E hybrid-state formation, an early conformational rearrangement occurring during translocation.
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33
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Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics. Viruses 2020; 12:v12111273. [PMID: 33171826 PMCID: PMC7695174 DOI: 10.3390/v12111273] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022] Open
Abstract
Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a large assembly. We use cryo-EM reconstructions to simulate the DNA packaging-associated 3 nm expansion of the protein shell of an initially assembled phage T7 capsid (called procapsid or capsid I). This is accompanied by a disorder-order transition and expansion-associated externalization displacement of the 420 N-terminal tails of the shell proteins. For the simulations, we use an all-atom structure-based model (1.07 million atoms), which is specifically designed to probe the influence of molecular sterics on dynamics. We find that the rate at which the N-terminal tails undergo translocation depends heavily on their position within hexons and pentons. Specifically, trans-shell displacements of the hexon E subunits are the most frequent and hexon A subunits are the least frequent. The simulations also implicate numerous tail translocation intermediates during tail translocation that involve topological traps, as well as sterically induced barriers. The presented study establishes a foundation for understanding the precise relationship between molecular structure and phage maturation.
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34
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Valente D, Werlang T. Frustration and inhomogeneous environments in relaxation of open chains with Ising-type interactions. Phys Rev E 2020; 102:022114. [PMID: 32942439 DOI: 10.1103/physreve.102.022114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/21/2020] [Indexed: 11/07/2022]
Abstract
Frustration can contribute to very slow relaxation times in large open chains, as in spin glasses and in biopolymers. However, frustration may not be sufficient to produce broken ergodicity in finite systems. Here we employ a system-plus-reservoir approach to investigate how strongly inhomogeneous environments and frustration compete in the relaxation of finite open chains. We find a sufficient condition for our inhomogeneous environments to break ergodicity. We use the microscopic model to derive a Markovian quantum master equation for a generic chain with ultrastrong intrachain couplings. We show that this microscopic model avoids a spurious broken ergodicity we find in the phenomenological model. We work out an explicit example of broken ergodicity due to the inhomogeneous environment of an unfrustrated spin chain as far as simulating a recent experiment on protein denaturation (where environment inhomogeneity is especially relevant). We finally show that an inhomogeneous environment can mitigate the effects of frustration-induced degeneracies.
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Affiliation(s)
- D Valente
- Instituto de Física, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, MT, Brazil
| | - T Werlang
- Instituto de Física, Universidade Federal de Mato Grosso, CEP 78060-900, Cuiabá, MT, Brazil
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35
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Marucci L, Barberis M, Karr J, Ray O, Race PR, de Souza Andrade M, Grierson C, Hoffmann SA, Landon S, Rech E, Rees-Garbutt J, Seabrook R, Shaw W, Woods C. Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology. Front Bioeng Biotechnol 2020; 8:942. [PMID: 32850764 PMCID: PMC7426639 DOI: 10.3389/fbioe.2020.00942] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/21/2020] [Indexed: 01/03/2023] Open
Abstract
Computer-aided design (CAD) for synthetic biology promises to accelerate the rational and robust engineering of biological systems. It requires both detailed and quantitative mathematical and experimental models of the processes to (re)design biology, and software and tools for genetic engineering and DNA assembly. Ultimately, the increased precision in the design phase will have a dramatic impact on the production of designer cells and organisms with bespoke functions and increased modularity. CAD strategies require quantitative models of cells that can capture multiscale processes and link genotypes to phenotypes. Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology. We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems. We also discuss several challenges for the realization of our vision. The possibility to describe and build whole-cells in silico offers an opportunity to develop increasingly automatized, precise and accessible CAD tools and strategies.
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Affiliation(s)
- Lucia Marucci
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Matteo Barberis
- Systems Biology, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom.,Centre for Mathematical and Computational Biology, CMCB, University of Surrey, Guildford, United Kingdom.,Synthetic Systems Biology and Nuclear Organization, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Jonathan Karr
- Icahn Institute for Data Science and Genomic Technology, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Oliver Ray
- Department of Computer Science, University of Bristol, Bristol, United Kingdom
| | - Paul R Race
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Miguel de Souza Andrade
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil.,Department of Cell Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Claire Grierson
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Stefan Andreas Hoffmann
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Sophie Landon
- Department of Engineering Mathematics, University of Bristol, Bristol, United Kingdom.,Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom
| | - Elibio Rech
- Brazilian Agricultural Research Corporation/National Institute of Science and Technology - Synthetic Biology, Brasília, Brazil
| | - Joshua Rees-Garbutt
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Richard Seabrook
- Elizabeth Blackwell Institute for Health Research (EBI), University of Bristol, Bristol, United Kingdom
| | - William Shaw
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Christopher Woods
- Bristol Centre for Synthetic Biology (BrisSynBio), University of Bristol, Bristol, United Kingdom.,School of Chemistry, University of Bristol, Bristol, United Kingdom
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36
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McCluskey AR, Hung KSW, Marzec B, Sindt JO, Sommerdijk NAJM, Camp PJ, Nudelman F. Disordered Filaments Mediate the Fibrillogenesis of Type I Collagen in Solution. Biomacromolecules 2020; 21:3631-3643. [DOI: 10.1021/acs.biomac.0c00667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew R. McCluskey
- EaStCHEM, School of Chemistry, The King’s Buildings, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Kennes S. W. Hung
- EaStCHEM, School of Chemistry, The King’s Buildings, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Bartosz Marzec
- EaStCHEM, School of Chemistry, The King’s Buildings, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Julien O. Sindt
- EPCC, University of Edinburgh, Bayes Centre, 47 Potterrow, Edinburgh EH8 9BT, U.K
| | - Nico A. J. M. Sommerdijk
- Department of Biochemistry, Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein, 6525 GA Nijmegen, The Netherlands
| | - Philip J. Camp
- EaStCHEM, School of Chemistry, The King’s Buildings, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Fabio Nudelman
- EaStCHEM, School of Chemistry, The King’s Buildings, University of Edinburgh, David Brewster Road, Edinburgh EH9 3FJ, U.K
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37
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Coarse-Grained Models of RNA Nanotubes for Large Time Scale Studies in Biomedical Applications. Biomedicines 2020; 8:biomedicines8070195. [PMID: 32640509 PMCID: PMC7400038 DOI: 10.3390/biomedicines8070195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/16/2020] [Accepted: 07/04/2020] [Indexed: 01/13/2023] Open
Abstract
In order to describe the physical properties of large time scale biological systems, coarse-grained models play an increasingly important role. In this paper we develop Coarse-Grained (CG) models for RNA nanotubes and then, by using Molecular Dynamics (MD) simulation, we study their physical properties. Our exemplifications include RNA nanotubes of 40 nm long, equivalent to 10 RNA nanorings connected in series. The developed methodology is based on a coarse-grained representation of RNA nanotubes, where each coarse bead represents a group of atoms. By decreasing computation cost, this allows us to make computations feasible for realistic structures of interest. In particular, for the developed coarse-grained models with three bead approximations, we calculate the histograms for the bond angles and the dihedral angles. From the dihedral angle histograms, we analyze the characteristics of the links used to build the nanotubes. Furthermore, we also calculate the bead distances along the chains of RNA strands in the nanoclusters. The variations in these features with the size of the nanotube are discussed in detail. Finally, we present the results on the calculation of the root mean square deviations for a developed RNA nanotube to demonstrate the equilibration of the systems for drug delivery and other biomedical applications such as medical imaging and tissue engineering.
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38
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Ruggeri FS, Mannini B, Schmid R, Vendruscolo M, Knowles TPJ. Single molecule secondary structure determination of proteins through infrared absorption nanospectroscopy. Nat Commun 2020; 11:2945. [PMID: 32522983 PMCID: PMC7287102 DOI: 10.1038/s41467-020-16728-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 05/11/2020] [Indexed: 12/21/2022] Open
Abstract
The chemical and structural properties of biomolecules determine their interactions, and thus their functions, in a wide variety of biochemical processes. Innovative imaging methods have been developed to characterise biomolecular structures down to the angstrom level. However, acquiring vibrational absorption spectra at the single molecule level, a benchmark for bulk sample characterization, has remained elusive. Here, we introduce off-resonance, low power and short pulse infrared nanospectroscopy (ORS-nanoIR) to allow the acquisition of infrared absorption spectra and chemical maps at the single molecule level, at high throughput on a second timescale and with a high signal-to-noise ratio (~10-20). This high sensitivity enables the accurate determination of the secondary structure of single protein molecules with over a million-fold lower mass than conventional bulk vibrational spectroscopy. These results pave the way to probe directly the chemical and structural properties of individual biomolecules, as well as their interactions, in a broad range of chemical and biological systems.
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Affiliation(s)
| | - Benedetta Mannini
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Roman Schmid
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | | | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, UK.
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39
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Ganguly M, Chakraborty A. Interpreting the looping rates of a polymer molecule in solution: Exact solution using a simple analytical method. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Landuzzi F, Viader-Godoy X, Cleri F, Pastor I, Ritort F. Detection of single DNA mismatches by force spectroscopy in short DNA hairpins. J Chem Phys 2020; 152:074204. [PMID: 32087630 DOI: 10.1063/1.5139284] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Identification of defective DNA structures is a difficult task, since small differences in base-pair bonding are hidden in the local structural variability of a generally random base-pair sequence. Defects, such as base mismatches, missing bases, crosslinks, and so on, occur in DNA with high frequency and must be efficiently identified and repaired to avoid dire consequences such as genetic mutations. Here, we focus on the detection of base mismatches, which is local deviations from the ideal Watson-Crick pairing rule, which may typically originate from DNA replication process, foreign chemical attack, or ionizing radiation. Experimental detection of a mismatch defect demands the ability to measure slight deviations in the free energy and molecular structure. We introduce different mismatches in short DNA hairpins (10 or 20 base pairs plus a 4-base loop) sandwiched between dsDNA handles to be used in single-molecule force spectroscopy with optical tweezers. We perform both hopping and force-pulling experiments to measure the excess free energies and deduce the characteristic kinetic signatures of the mismatch from the force-distance curves. All-atom molecular dynamics simulations lend support to the detailed interpretation of the experimental data. Such measurements, at the lowest sensitivity limits of this experimental technique, demonstrate the capability of identifying the presence of mismatches in a random complementary dsDNA sequence and provide lower bounds for the ability to distinguish different structural defects.
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Affiliation(s)
- F Landuzzi
- Department of Physics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Japan
| | - X Viader-Godoy
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - F Cleri
- I.E.M.N. (UMR Cnrs 8520), 59652 Villeneuve d'Ascq, France
| | - I Pastor
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
| | - F Ritort
- Small Biosystems Lab., Univ. de Barcelona, Diagonal 647, 08028 Barcelona, Spain
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41
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Gershenson A, Gosavi S, Faccioli P, Wintrode PL. Successes and challenges in simulating the folding of large proteins. J Biol Chem 2020; 295:15-33. [PMID: 31712314 PMCID: PMC6952611 DOI: 10.1074/jbc.rev119.006794] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Computational simulations of protein folding can be used to interpret experimental folding results, to design new folding experiments, and to test the effects of mutations and small molecules on folding. However, whereas major experimental and computational progress has been made in understanding how small proteins fold, research on larger, multidomain proteins, which comprise the majority of proteins, is less advanced. Specifically, large proteins often fold via long-lived partially folded intermediates, whose structures, potentially toxic oligomerization, and interactions with cellular chaperones remain poorly understood. Molecular dynamics based folding simulations that rely on knowledge of the native structure can provide critical, detailed information on folding free energy landscapes, intermediates, and pathways. Further, increases in computational power and methodological advances have made folding simulations of large proteins practical and valuable. Here, using serpins that inhibit proteases as an example, we review native-centric methods for simulating the folding of large proteins. These synergistic approaches range from Gō and related structure-based models that can predict the effects of the native structure on folding to all-atom-based methods that include side-chain chemistry and can predict how disease-associated mutations may impact folding. The application of these computational approaches to serpins and other large proteins highlights the successes and limitations of current computational methods and underscores how computational results can be used to inform experiments. These powerful simulation approaches in combination with experiments can provide unique insights into how large proteins fold and misfold, expanding our ability to predict and manipulate protein folding.
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Affiliation(s)
- Anne Gershenson
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003; Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003.
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065, India.
| | - Pietro Faccioli
- Dipartimento di Fisica, Universitá degli Studi di Trento, 38122 Povo (Trento), Italy; Trento Institute for Fundamental Physics and Applications, 38123 Povo (Trento), Italy.
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201.
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42
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Wang F, Diesendruck CE. Effect of disulphide loop length on mechanochemical structural stability of macromolecules. Chem Commun (Camb) 2020; 56:2143-2146. [DOI: 10.1039/c9cc07439b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Polymer chains folded with a single disulphide loop are shown to present distinct rates of mechanochemical fragmentation.
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Affiliation(s)
- Feng Wang
- Schulich Faculty of Chemistry and Russell-Berrie Nanotechnology Institute
- Technion – Israel Institute of Technology
- Haifa
- Israel
- School of Chemical Engineering
| | - Charles E. Diesendruck
- Schulich Faculty of Chemistry and Russell-Berrie Nanotechnology Institute
- Technion – Israel Institute of Technology
- Haifa
- Israel
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43
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Schuler B, Borgia A, Borgia MB, Heidarsson PO, Holmstrom ED, Nettels D, Sottini A. Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Curr Opin Struct Biol 2019; 60:66-76. [PMID: 31874413 DOI: 10.1016/j.sbi.2019.12.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Recent evidence shows that oppositely charged intrinsically disordered proteins (IDPs) can form high-affinity complexes that involve neither the formation of secondary or tertiary structure nor site-specific interactions between individual residues. Similar electrostatically dominated interactions have also been identified for positively charged IDPs binding to nucleic acids. These highly disordered polyelectrolyte complexes constitute an extreme case within the spectrum of biomolecular interactions involving disorder. Such interactions are likely to be widespread, since sequence analysis predicts proteins with highly charged disordered regions to be surprisingly numerous. Here, we summarize the insights that have emerged from the highly disordered polyelectrolyte complexes identified so far, and we highlight recent developments and future challenges in (i) establishing models for the underlying highly dynamic structural ensembles, (ii) understanding the novel binding mechanisms associated with them, and (iii) identifying the functional consequences.
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Affiliation(s)
- Benjamin Schuler
- Department of Biochemistry, University of Zurich, Switzerland; Department of Physics, University of Zurich, Switzerland.
| | - Alessandro Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Madeleine B Borgia
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Pétur O Heidarsson
- Department of Biochemistry, Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavík, Iceland
| | - Erik D Holmstrom
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside, Lawrence, KS 66045, USA; Department of Chemistry, University of Kansas, 1200 Sunnyside, Lawrence, KS 66045, USA
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, Switzerland
| | - Andrea Sottini
- Department of Biochemistry, University of Zurich, Switzerland
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44
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Shinobu A, Kobayashi C, Matsunaga Y, Sugita Y. Building a macro-mixing dual-basin Gō model using the Multistate Bennett Acceptance Ratio. Biophys Physicobiol 2019; 16:310-321. [PMID: 31984186 PMCID: PMC6975896 DOI: 10.2142/biophysico.16.0_310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/02/2019] [Indexed: 12/01/2022] Open
Abstract
The dual-basin Gō-model is a structural-based coarsegrained model for simulating a conformational transition between two known structures of a protein. Two parameters are required to produce a dual-basin potential mixed using two single-basin potentials, although the determination of mixing parameters is usually not straightforward. Here, we have developed an efficient scheme to determine the mixing parameters using the Multistate Bennett Acceptance Ratio (MBAR) method after short simulations with a set of parameters. In the scheme, MBAR allows us to predict observables at various unsimulated conditions, which are useful to improve the mixing parameters in the next round of iterative simulations. The number of iterations that are necessary for obtaining the converged mixing parameters are significantly reduced in the scheme. We applied the scheme to two proteins, the glutamine binding protein and the ribose binding protein, for showing the effectiveness in the parameter determination. After obtaining the converged parameters, both proteins show frequent conformational transitions between open and closed states, providing the theoretical basis to investigate structure-dynamics-function relationships of the proteins.
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Affiliation(s)
- Ai Shinobu
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Chigusa Kobayashi
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
| | - Yasuhiro Matsunaga
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
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45
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Chan J, Takemura K, Lin HR, Chang KC, Chang YY, Joti Y, Kitao A, Yang LW. An Efficient Timer and Sizer of Biomacromolecular Motions. Structure 2019; 28:259-269.e8. [PMID: 31780433 DOI: 10.1016/j.str.2019.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 08/22/2019] [Accepted: 10/30/2019] [Indexed: 11/28/2022]
Abstract
Life ticks as fast as how proteins move. Computationally expensive molecular dynamics simulation has been the only theoretical tool to gauge the time and sizes of these motions, though barely to their slowest ends. Here, we convert a computationally cheap elastic network model (ENM) into a molecular timer and sizer to gauge the slowest functional motions of structured biomolecules. Quasi-harmonic analysis, fluctuation profile matching, and the Wiener-Khintchine theorem are used to define the "time periods," t, for anharmonic principal components (PCs), which are validated by nuclear magnetic resonance (NMR) order parameters. The PCs with their respective "time periods" are mapped to the eigenvalues (λENM) of the corresponding ENM modes. Thus, the power laws t(ns) = 56.1λENM-1.6 and σ2(Å2) = 32.7λENM-3.0 can be established allowing the characterization of the timescales of NMR-resolved conformers, crystallographic anisotropic displacement parameters, and important ribosomal motions, as well as motional sizes of the latter.
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Affiliation(s)
- Justin Chan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Kazuhiro Takemura
- School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan
| | - Hong-Rui Lin
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Kai-Chun Chang
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
| | - Yuan-Yu Chang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
| | - Yasumasa Joti
- XFEL Utilization Division, Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, M6-13, 2-12-1 Ookayama, Meguro, Tokyo 152-8550, Japan.
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua Univ., No. 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan; Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan; Physics Division, National Center for Theoretical Sciences, Hsinchu, Taiwan.
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46
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Jin L, Tan YL, Wu Y, Wang X, Shi YZ, Tan ZJ. Structure folding of RNA kissing complexes in salt solutions: predicting 3D structure, stability, and folding pathway. RNA (NEW YORK, N.Y.) 2019; 25:1532-1548. [PMID: 31391217 PMCID: PMC6795135 DOI: 10.1261/rna.071662.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 05/08/2023]
Abstract
RNA kissing complexes are essential for genomic RNA dimerization and regulation of gene expression, and their structures and stability are critical to their biological functions. In this work, we used our previously developed coarse-grained model with an implicit structure-based electrostatic potential to predict three-dimensional (3D) structures and stability of RNA kissing complexes in salt solutions. For extensive RNA kissing complexes, our model shows great reliability in predicting 3D structures from their sequences, and our additional predictions indicate that the model can capture the dependence of 3D structures of RNA kissing complexes on monovalent/divalent ion concentrations. Moreover, the comparisons with extensive experimental data show that the model can make reliable predictions on the stability for various RNA kissing complexes over wide ranges of monovalent/divalent ion concentrations. Notably, for RNA kissing complexes, our further analyses show the important contribution of coaxial stacking to the 3D structures and stronger stability than the corresponding kissing-interface duplexes at high salts. Furthermore, our comprehensive analyses for RNA kissing complexes reveal that the thermally folding pathway for a complex sequence is mainly determined by the relative stability of two possible folded states of kissing complex and extended duplex, which can be significantly modulated by its sequence.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yao Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xunxun Wang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan 430073, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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47
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Gopi S, Aranganathan A, Naganathan AN. Thermodynamics and folding landscapes of large proteins from a statistical mechanical model. Curr Res Struct Biol 2019; 1:6-12. [PMID: 34235463 PMCID: PMC8244504 DOI: 10.1016/j.crstbi.2019.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 01/01/2023] Open
Abstract
Statistical mechanical models that afford an intermediate resolution between macroscopic chemical models and all-atom simulations have been successful in capturing folding behaviors of many small single-domain proteins. However, the applicability of one such successful approach, the Wako-Saitô-Muñoz-Eaton (WSME) model, is limited by the size of the protein as the number of conformations grows exponentially with protein length. In this work, we surmount this size limitation by introducing a novel approximation that treats stretches of 3 or 4 residues as blocks, thus reducing the phase space by nearly three orders of magnitude. The performance of the 'bWSME' model is validated by comparing the predictions for a globular enzyme (RNase H) and a repeat protein (IκBα), against experimental observables and the model without block approximation. Finally, as a proof of concept, we predict the free-energy surface of the 370-residue, multi-domain maltose binding protein and identify an intermediate in good agreement with single-molecule force-spectroscopy measurements. The bWSME model can thus be employed as a quantitative predictive tool to explore the conformational landscapes of large proteins, extract the structural features of putative intermediates, identify parallel folding paths, and thus aid in the interpretation of both ensemble and single-molecule experiments.
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Affiliation(s)
- Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Akashnathan Aranganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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48
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Yang H, Bandarkar P, Horne R, Leite VBP, Chahine J, Whitford PC. Diffusion of tRNA inside the ribosome is position-dependent. J Chem Phys 2019; 151:085102. [PMID: 31470725 DOI: 10.1063/1.5113814] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In recent years, there has been a growing interest to quantify the energy landscape that governs ribosome dynamics. However, in order to quantitatively integrate theoretical predictions and experimental measurements, it is essential that one has a detailed understanding of the associated diffusive properties. Here, all-atom explicit-solvent simulations (50 μs of aggregate sampling) predict that the diffusion coefficient of a tRNA molecule will depend on its position within the ribosome. Specifically, during aa-tRNA accommodation (i.e., the process by which tRNA enters the ribosome), the apparent diffusion coefficient decreases by approximately an order of magnitude. By comparing these to values obtained with an energetically "smooth" model, we show that the observed nonuniform behavior likely arises from electrostatic and solvation interactions between the tRNA and ribosome. These calculations also reveal the hierarchical character of ribosomal energetics, where steric interactions induce a large-scale free-energy barrier, and short-scale roughness determines the rate of diffusive movement across the landscape.
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Affiliation(s)
- Huan Yang
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave., Boston, Massachusetts 02115, USA
| | - Prasad Bandarkar
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave., Boston, Massachusetts 02115, USA
| | - Ransom Horne
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave., Boston, Massachusetts 02115, USA
| | - Vitor B P Leite
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto, Brazil
| | - Jorge Chahine
- São Paulo State University (UNESP), IBILCE, São José do Rio Preto, Brazil
| | - Paul C Whitford
- Department of Physics, Northeastern University, Dana Research Center 111, 360 Huntington Ave., Boston, Massachusetts 02115, USA
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49
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Eddy NR, Onuchic JN. Rotation-Activated and Cooperative Zipping Characterize Class I Viral Fusion Protein Dynamics. Biophys J 2019; 114:1878-1888. [PMID: 29694865 DOI: 10.1016/j.bpj.2018.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/15/2018] [Accepted: 03/06/2018] [Indexed: 11/19/2022] Open
Abstract
Class I viral fusion proteins are α-helical proteins that facilitate membrane fusion between viral and host membranes through large conformational transitions. Although prefusion and postfusion crystal structures have been solved for many of these proteins, details about how they transition between these states have remained elusive. This work presents the first, to our knowledge, computational survey of transitions between pre- and postfusion configurations for several class I viral fusion proteins using structure-based models to analyze their dynamics. As suggested by their structural similarities, all proteins share common mechanistic features during their transitions that can be characterized by a diffusive rotational search followed by cooperative N- and C-terminal zipping. Instead of predicting a stable spring-loaded intermediate, our model suggests that helical bundle formation is mediated by N- and C-terminal interactions late in the transition. Shared transition features suggest a global mechanism in which fusion is activated by slow protein-core rotation.
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Affiliation(s)
- Nathanial R Eddy
- Department of Physics and Astronomy; Center for Theoretical Biological Physics, Rice University, Houston, Texas
| | - José N Onuchic
- Department of Physics and Astronomy; Center for Theoretical Biological Physics, Rice University, Houston, Texas.
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50
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Thirumalai D, Hyeon C, Zhuravlev PI, Lorimer GH. Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines. Chem Rev 2019; 119:6788-6821. [DOI: 10.1021/acs.chemrev.8b00760] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
| | - Changbong Hyeon
- Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Pavel I. Zhuravlev
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - George H. Lorimer
- Biophysics Program, Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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