1
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Wang H, Benter S, Dononelli W, Neudecker T. JEDI: A versatile code for strain analysis of molecular and periodic systems under deformation. J Chem Phys 2024; 160:152501. [PMID: 38639312 DOI: 10.1063/5.0199247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024] Open
Abstract
Stretching or compression can induce significant energetic, geometric, and spectroscopic changes in materials. To fully exploit these effects in the design of mechano- or piezo-chromic materials, self-healing polymers, and other mechanoresponsive devices, a detailed knowledge about the distribution of mechanical strain in the material is essential. Within the past decade, Judgement of Energy DIstribution (JEDI) analysis has emerged as a useful tool for this purpose. Based on the harmonic approximation, the strain energy in each bond length, bond angle, and dihedral angle of the deformed system is calculated using quantum chemical methods. This allows the identification of the force-bearing scaffold of the system, leading to an understanding of mechanochemical processes at the most fundamental level. Here, we present a publicly available code that generalizes the JEDI analysis, which has previously only been available for isolated molecules. Now, the code has been extended to two- and three-dimensional periodic systems, supramolecular clusters, and substructures of chemical systems under various types of deformation. Due to the implementation of JEDI into the Atomic Simulation Environment, the JEDI analysis can be interfaced with a plethora of program packages that allow the calculation of electronic energies for molecular systems and systems with periodic boundary conditions. The automated generation of a color-coded three-dimensional structure via the Visual Molecular Dynamics program allows insightful visual analyses of the force-bearing scaffold of the strained system.
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Affiliation(s)
- Henry Wang
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße 6, D-28359 Bremen, Germany
| | - Sanna Benter
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße 6, D-28359 Bremen, Germany
| | - Wilke Dononelli
- Hybrid Materials Interfaces Group, Am Fallturm 1, D-28359 Bremen, Germany
- Bremen Center for Computational Materials Science, Am Fallturm 1, D-28359 Bremen, Germany
- MAPEX Center for Materials and Processes, Bibliothekstraße 1, D-28359 Bremen, Germany
| | - Tim Neudecker
- University of Bremen, Institute for Physical and Theoretical Chemistry, Leobener Straße 6, D-28359 Bremen, Germany
- Bremen Center for Computational Materials Science, Am Fallturm 1, D-28359 Bremen, Germany
- MAPEX Center for Materials and Processes, Bibliothekstraße 1, D-28359 Bremen, Germany
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2
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Wu Y, Cao S, Qiu Y, Huang X. Tutorial on how to build non-Markovian dynamic models from molecular dynamics simulations for studying protein conformational changes. J Chem Phys 2024; 160:121501. [PMID: 38516972 DOI: 10.1063/5.0189429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
Protein conformational changes play crucial roles in their biological functions. In recent years, the Markov State Model (MSM) constructed from extensive Molecular Dynamics (MD) simulations has emerged as a powerful tool for modeling complex protein conformational changes. In MSMs, dynamics are modeled as a sequence of Markovian transitions among metastable conformational states at discrete time intervals (called lag time). A major challenge for MSMs is that the lag time must be long enough to allow transitions among states to become memoryless (or Markovian). However, this lag time is constrained by the length of individual MD simulations available to track these transitions. To address this challenge, we have recently developed Generalized Master Equation (GME)-based approaches, encoding non-Markovian dynamics using a time-dependent memory kernel. In this Tutorial, we introduce the theory behind two recently developed GME-based non-Markovian dynamic models: the quasi-Markov State Model (qMSM) and the Integrative Generalized Master Equation (IGME). We subsequently outline the procedures for constructing these models and provide a step-by-step tutorial on applying qMSM and IGME to study two peptide systems: alanine dipeptide and villin headpiece. This Tutorial is available at https://github.com/xuhuihuang/GME_tutorials. The protocols detailed in this Tutorial aim to be accessible for non-experts interested in studying the biomolecular dynamics using these non-Markovian dynamic models.
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Affiliation(s)
- Yue Wu
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Siqin Cao
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Yunrui Qiu
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Xuhui Huang
- Department of Chemistry, Theoretical Chemistry Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
- Data Science Institute, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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3
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Gradisch R, Schlögl K, Lazzarin E, Niello M, Maier J, Mayer FP, Alves da Silva L, Skopec SMC, Blakely RD, Sitte HH, Mihovilovic MD, Stockner T. Ligand coupling mechanism of the human serotonin transporter differentiates substrates from inhibitors. Nat Commun 2024; 15:417. [PMID: 38195746 PMCID: PMC10776687 DOI: 10.1038/s41467-023-44637-6] [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: 07/17/2023] [Accepted: 12/22/2023] [Indexed: 01/11/2024] Open
Abstract
The presynaptic serotonin transporter (SERT) clears extracellular serotonin following vesicular release to ensure temporal and spatial regulation of serotonergic signalling and neurotransmitter homeostasis. Prescription drugs used to treat neurobehavioral disorders, including depression, anxiety, and obsessive-compulsive disorder, trap SERT by blocking the transport cycle. In contrast, illicit drugs of abuse like amphetamines reverse SERT directionality, causing serotonin efflux. Both processes result in increased extracellular serotonin levels. By combining molecular dynamics simulations with biochemical experiments and using a homologous series of serotonin analogues, we uncovered the coupling mechanism between the substrate and the transporter, which triggers the uptake of serotonin. Free energy analysis showed that only scaffold-bound substrates could initiate SERT occlusion through attractive long-range electrostatic interactions acting on the bundle domain. The associated spatial requirements define substrate and inhibitor properties, enabling additional possibilities for rational drug design approaches.
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Affiliation(s)
- Ralph Gradisch
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Katharina Schlögl
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060, Vienna, Austria
| | - Erika Lazzarin
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Marco Niello
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
- Genetics of Cognition Laboratory, Neuroscience area, Istituto Italiano di Tecnologia, via Morego, 30, 16163, Genova, Italy
| | - Julian Maier
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Felix P Mayer
- Florida Atlantic University, Department of Biomedical Science, Jupiter, FL, 33458, USA
- Stiles-Nicholson Brain Institute, Jupiter, FL, 33458, USA
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Leticia Alves da Silva
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Sophie M C Skopec
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Randy D Blakely
- Florida Atlantic University, Department of Biomedical Science, Jupiter, FL, 33458, USA
- Stiles-Nicholson Brain Institute, Jupiter, FL, 33458, USA
| | - Harald H Sitte
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria
- Al-Ahliyya Amman University, Hourani Center for Applied Scientific Research, Amman, Jordan
- Medical University of Vienna, Center for Addiction Research and Science, Waehringer Straße 13A, 1090, Vienna, Austria
| | - Marko D Mihovilovic
- TU Wien, Institute of Applied Synthetic Chemistry, Getreidemarkt 9, 1060, Vienna, Austria
| | - Thomas Stockner
- Medical University of Vienna, Institute of Physiology and Pharmacology, Waehringer Straße 13A, 1090, Vienna, Austria.
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4
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Woods KN. Modeling of protein hydration dynamics is supported by THz spectroscopy of highly diluted solutions. Front Chem 2023; 11:1131935. [PMID: 37361018 PMCID: PMC10290188 DOI: 10.3389/fchem.2023.1131935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in highly dilute (HD) solutions of initial proteins. THz spectroscopy measurements have been conducted as a means to analyze and characterize the collective dynamics of the HD samples. MD simulations have also been performed that have successfully reproduced the observed signatures from experimental measurement. Using this joint experimental-computational approach we determine that the HD process associated with the preparation of the highly diluted samples used in this investigation induces a dynamical transition that results in collective changes in the hydrogen-bond network of the solvent. The dynamical transition in the solvent is triggered by changes in the mobility and hydrogen-bonding interactions of the surface molecules in the HD samples and is characterized by dynamical heterogeneity. We have uncovered that the reorganization of the sample surface residue dynamics at the solvent-protein interface leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.
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5
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Ali AAAI, Gulzar A, Wolf S, Stock G. Nonequilibrium Modeling of the Elementary Step in PDZ3 Allosteric Communication. J Phys Chem Lett 2022; 13:9862-9868. [PMID: 36251493 DOI: 10.1021/acs.jpclett.2c02821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
While allostery is of paramount importance for protein signaling and regulation, the underlying dynamical process of allosteric communication is not well understood. The PDZ3 domain represents a prime example of an allosteric single-domain protein, as it features a well-established long-range coupling between the C-terminal α3-helix and ligand binding. In an intriguing experiment, Hamm and co-workers employed photoswitching of the α3-helix to initiate a conformational change of PDZ3 that propagates from the C-terminus to the bound ligand within 200 ns. Performing extensive nonequilibrium molecular dynamics simulations, the modeling of the experiment reproduces the measured time scales and reveals a detailed picture of the allosteric communication in PDZ3. In particular, a correlation analysis identifies a network of contacts connecting the α3-helix and the core of the protein, which move in a concerted manner. Representing a one-step process and involving direct α3-ligand contacts, this cooperative transition is considered as the elementary step in the propagation of conformational change.
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Affiliation(s)
- Ahmed A A I Ali
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
| | - Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
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6
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Diez G, Nagel D, Stock G. Correlation-Based Feature Selection to Identify Functional Dynamics in Proteins. J Chem Theory Comput 2022; 18:5079-5088. [PMID: 35793551 DOI: 10.1021/acs.jctc.2c00337] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To interpret molecular dynamics simulations of biomolecular systems, systematic dimensionality reduction methods are commonly employed. Among others, this includes principal component analysis (PCA) and time-lagged independent component analysis (TICA), which aim to maximize the variance and the time scale of the first components, respectively. A crucial first step of such an analysis is the identification of suitable and relevant input coordinates (the so-called features), such as backbone dihedral angles and interresidue distances. As typically only a small subset of those coordinates is involved in a specific biomolecular process, it is important to discard the remaining uncorrelated motions or weakly correlated noise coordinates. This is because they may exhibit large amplitudes or long time scales and therefore will be erroneously considered important by PCA and TICA, respectively. To discriminate collective motions underlying functional dynamics from uncorrelated motions, the correlation matrix of the input coordinates is block-diagonalized by a clustering method. This strategy avoids possible bias due to presumed functional observables and conformational states or variation principles that maximize variance or time scales. Considering several linear and nonlinear correlation measures and various clustering algorithms, it is shown that the combination of linear correlation and the Leiden community detection algorithm yields excellent results for all considered model systems. These include the functional motion of T4 lysozyme to demonstrate the successful identification of collective motion, as well as the folding of the villin headpiece to highlight the physical interpretation of the correlated motions in terms of a functional mechanism.
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Affiliation(s)
- Georg Diez
- Biomolecular Dynamics, Institute of Physics, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
| | - Daniel Nagel
- Biomolecular Dynamics, Institute of Physics, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert-Ludwigs-Universität, 79104 Freiburg, Germany
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7
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Igaev M, Grubmüller H. Bending-torsional elasticity and energetics of the plus-end microtubule tip. Proc Natl Acad Sci U S A 2022; 119:e2115516119. [PMID: 35302883 PMCID: PMC8944587 DOI: 10.1073/pnas.2115516119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/10/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceThe mechanochemical basis of microtubule growth, which is essential for the normal function and division of eukaryotic cells, has remained elusive and controversial, despite extensive work. In particular, recent findings have created the paradox that the microtubule plus-end tips look very similar during both growing and shrinking phases, thereby challenging the traditional textbook picture. Our large-scale atomistic simulations resolve this paradox and explain microtubule growth and shrinkage dynamics as a process governed by energy barriers between protofilament conformations, the heights of which are in turn fine-tuned by different nucleotide states, thus implementing an information-driven Brownian ratchet.
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Affiliation(s)
- Maxim Igaev
- Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
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8
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Occlusion of the human serotonin transporter is mediated by serotonin-induced conformational changes in the bundle domain. J Biol Chem 2022; 298:101613. [PMID: 35065961 PMCID: PMC8867121 DOI: 10.1016/j.jbc.2022.101613] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 12/04/2022] Open
Abstract
The human serotonin transporter (hSERT) terminates neurotransmission by removing serotonin (5HT) from the synaptic cleft, an essential process for proper functioning of serotonergic neurons. Structures of the hSERT have revealed its molecular architecture in four conformations, including the outward-open and occluded states, and show the transporter’s engagement with co-transported ions and the binding mode of inhibitors. In this study, we investigated the molecular mechanism by which the hSERT occludes and sequesters the substrate 5HT. This first step of substrate uptake into cells is a structural change consisting of the transition from the outward-open to the occluded state. Inhibitors such as the antidepressants citalopram, fluoxetine, and sertraline inhibit this step of the transport cycle. Using molecular dynamics simulations, we reached a fully occluded state, in which the transporter-bound 5HT becomes fully shielded from both sides of the membrane by two closed hydrophobic gates. Analysis of 5HT-triggered occlusion showed that bound 5HT serves as an essential trigger for transporter occlusion. Moreover, simulations revealed a complex sequence of steps and showed that movements of bundle domain helices are only partially correlated. 5HT-triggered occlusion is initially dominated by movements of transmembrane helix 1b, while in the final step, only transmembrane helix 6a moves and relaxes an intermediate change in its secondary structure.
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9
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Woods KN. New insights into the microscopic interactions associated with the physical mechanism of action of highly diluted biologics. Sci Rep 2021; 11:13774. [PMID: 34215838 PMCID: PMC8253741 DOI: 10.1038/s41598-021-93326-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/21/2021] [Indexed: 11/08/2022] Open
Abstract
In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in exceptionally dilute solutions of initial proteins. Using both THz spectroscopy and molecular dynamics simulations we have uncovered that the high dilution method of sample preparation results in the reorganization of the sample surface residue dynamics at the solvent-protein interface that leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.
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Affiliation(s)
- Kristina N Woods
- Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians-Universität, 80538, Munich, Germany.
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10
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D'Amico RN, Bosken YK, O'Rourke KF, Murray AM, Admasu W, Chang CEA, Boehr DD. Substitution of a Surface-Exposed Residue Involved in an Allosteric Network Enhances Tryptophan Synthase Function in Cells. Front Mol Biosci 2021; 8:679915. [PMID: 34124159 PMCID: PMC8187860 DOI: 10.3389/fmolb.2021.679915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Networks of noncovalent amino acid interactions propagate allosteric signals throughout proteins. Tryptophan synthase (TS) is an allosterically controlled bienzyme in which the indole product of the alpha subunit (αTS) is transferred through a 25 Å hydrophobic tunnel to the active site of the beta subunit (βTS). Previous nuclear magnetic resonance and molecular dynamics simulations identified allosteric networks in αTS important for its function. We show here that substitution of a distant, surface-exposed network residue in αTS enhances tryptophan production, not by activating αTS function, but through dynamically controlling the opening of the indole channel and stimulating βTS activity. While stimulation is modest, the substitution also enhances cell growth in a tryptophan-auxotrophic strain of Escherichia coli compared to complementation with wild-type αTS, emphasizing the biological importance of the network. Surface-exposed networks provide new opportunities in allosteric drug design and protein engineering, and hint at potential information conduits through which the functions of a metabolon or even larger proteome might be coordinated and regulated.
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Affiliation(s)
- Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Yuliana K Bosken
- Department of Chemistry, The University of California Riverside, Riverside, CA, United States
| | - Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Alec M Murray
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Woudasie Admasu
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
| | - Chia-En A Chang
- Department of Chemistry, The University of California Riverside, Riverside, CA, United States
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA, United States
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11
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Role of bacterial RNA polymerase gate opening dynamics in DNA loading and antibiotics inhibition elucidated by quasi-Markov State Model. Proc Natl Acad Sci U S A 2021; 118:2024324118. [PMID: 33883282 DOI: 10.1073/pnas.2024324118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To initiate transcription, the holoenzyme (RNA polymerase [RNAP] in complex with σ factor) loads the promoter DNA via the flexible loading gate created by the clamp and β-lobe, yet their roles in DNA loading have not been characterized. We used a quasi-Markov State Model (qMSM) built from extensive molecular dynamics simulations to elucidate the dynamics of Thermus aquaticus holoenzyme's gate opening. We showed that during gate opening, β-lobe oscillates four orders of magnitude faster than the clamp, whose opening depends on the Switch 2's structure. Myxopyronin, an antibiotic that binds to Switch 2, was shown to undergo a conformational selection mechanism to inhibit clamp opening. Importantly, we reveal a critical but undiscovered role of β-lobe, whose opening is sufficient for DNA loading even when the clamp is partially closed. These findings open the opportunity for the development of antibiotics targeting β-lobe of RNAP. Finally, we have shown that our qMSMs, which encode non-Markovian dynamics based on the generalized master equation formalism, hold great potential to be widely applied to study biomolecular dynamics.
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12
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Daday C, de Groot BL. Lipid-protein forces predict conformational changes in a mechanosensitive channel. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:181-186. [PMID: 33355710 PMCID: PMC8071793 DOI: 10.1007/s00249-020-01488-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/29/2022]
Abstract
The mechanosensitive TREK-2 potassium channel, a member of the K2P family, has essential physiological roles and is, therefore, a pharmaceutical target. A combination of experimental and computational studies have established that of the two known conformations, "up" and "down", membrane tension directly favors the "up" state, which displays a higher conductance. However, these studies did not reveal the exact mechanism by which the membrane affects the channel conformation. In this work, we show that changes in protein-lipid interaction patterns suffice in predicting this conformational change, and pinpoint potentially important residues involved in this phenomenon.
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Affiliation(s)
- Csaba Daday
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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13
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Karpov PA, Rayevsky AV, Sheremet YA, Yemets AI, Blume YB. Structural Biological Characteristics of CK1-Like Protein Kinase Isotypes Associated with Regulation of Plant Microtubules. CYTOL GENET+ 2020. [DOI: 10.3103/s0095452720040052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Bosken YK, Cholko T, Lou YC, Wu KP, Chang CEA. Insights Into Dynamics of Inhibitor and Ubiquitin-Like Protein Binding in SARS-CoV-2 Papain-Like Protease. Front Mol Biosci 2020; 7:174. [PMID: 32850963 PMCID: PMC7417481 DOI: 10.3389/fmolb.2020.00174] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/06/2020] [Indexed: 11/28/2022] Open
Abstract
Covid-19 is caused by a novel form of coronavirus for which there are currently no vaccines or anti-viral drugs. This virus, termed SARS-CoV-2 (CoV2), contains Papain-like protease (PLpro) involved in viral replication and immune response evasion. Drugs targeting this protease therefore have great potential for inhibiting the virus, and have proven successful in older coronaviruses. Here, we introduce two effective inhibitors of SARS-CoV-1 (CoV1) and MERS-CoV to assess their potential for inhibiting CoV2 PLpro. We ran 1 μs molecular dynamics (MD) simulations of CoV2, CoV1, and MERS-CoV ligand-free PLpro to characterize the dynamics of CoV2 PLpro, and made comparisons between the three to elucidate important similarities and differences relevant to drug design and ubiquitin-like protein binding for deubiquitinating and deISGylating activity of CoV2. Next, we simulated the inhibitors bound to CoV1 and CoV2 PLpro in various poses and at different known binding sites to analyze their binding modes. We found that the naphthalene-based ligand shows strong potential as an inhibitor of CoV2 PLpro by binding at the putative naphthalene inhibitor binding site in both computational predictions and experimental assays. Our modeling work suggested strategies to improve naphthalene-based compounds, and our results from molecular docking showed that the newly designed compounds exhibited improved binding affinity. The other ligand, chemotherapy drug 6-mercaptopurine (6MP), showed little to no stable intermolecular interaction with PLpro and quickly dissociated or remained highly mobile. We demonstrate multiple ways to improve the binding affinity of the naphthalene-based inhibitor scaffold by engaging new residues in the unused space of the binding site. Analysis of CoV2 PLpro also brings insights into recognition of ubiquitin-like proteins that may alter innate immune response.
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Affiliation(s)
- Yuliana K Bosken
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Timothy Cholko
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
| | - Yuan-Chao Lou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Kuen-Phon Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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15
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D'Amico RN, Murray AM, Boehr DD. Driving Protein Conformational Cycles in Physiology and Disease: "Frustrated" Amino Acid Interaction Networks Define Dynamic Energy Landscapes: Amino Acid Interaction Networks Change Progressively Along Alpha Tryptophan Synthase's Catalytic Cycle. Bioessays 2020; 42:e2000092. [PMID: 32720327 DOI: 10.1002/bies.202000092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/09/2020] [Indexed: 12/22/2022]
Abstract
A general framework by which dynamic interactions within a protein will promote the necessary series of structural changes, or "conformational cycle," required for function is proposed. It is suggested that the free-energy landscape of a protein is biased toward this conformational cycle. Fluctuations into higher energy, although thermally accessible, conformations drive the conformational cycle forward. The amino acid interaction network is defined as those intraprotein interactions that contribute most to the free-energy landscape. Some network connections are consistent in every structural state, while others periodically change their interaction strength according to the conformational cycle. It is reviewed here that structural transitions change these periodic network connections, which then predisposes the protein toward the next set of network changes, and hence the next structural change. These concepts are illustrated by recent work on tryptophan synthase. Disruption of these dynamic connections may lead to aberrant protein function and disease states.
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Affiliation(s)
- Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, 107 Chemistry Building, University Park, PA, 16802, USA
| | - Alec M Murray
- Department of Chemistry, The Pennsylvania State University, 107 Chemistry Building, University Park, PA, 16802, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, 107 Chemistry Building, University Park, PA, 16802, USA
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16
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Sadeghi M, Balke J, Schneider C, Nagano S, Stellmacher J, Lochnit G, Lang C, Weise C, Hughes J, Alexiev U. Transient Deprotonation of the Chromophore Affects Protein Dynamics Proximal and Distal to the Linear Tetrapyrrole Chromophore in Phytochrome Cph1. Biochemistry 2020; 59:1051-1062. [PMID: 32069394 DOI: 10.1021/acs.biochem.9b00967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phytochromes are biological red/far-red light sensors found in many organisms. Prototypical phytochromes, including Cph1 from the cyanobacterium Synechocystis 6803, act as photochemical switches that interconvert between stable red (Pr)- and metastable far-red (Pfr)-absorbing states induced by photoisomerization of the bilin chromophore. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY) and the C-terminal transmitter (output) module, usually a histidine kinase, as in the case of Cph1. The chromophore deprotonates transiently during the Pr → Pfr photoconversion in association with extensive global structural changes required for signal transmission. Here, we performed equilibrium studies in the Pr state, involving pH titration of the linear tetrapyrrole chromophore in different Cph1 constructs, and measurement of pH-dependent structural changes at various positions in the protein using picosecond time-resolved fluorescence anisotropy. The fluorescent reporter group was attached at positions 371 (PHY domain), 305 (GAF domain), and 120 (PAS domain), as well as at sites in the PAS-GAF bidomain. We show direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains. Our results suggest that chromophore deprotonation is closely associated with a higher protein mobility (conformational space) both in proximal and in distal protein sites, implying a causal relationship that might be important for the global large protein arrangements and thus intramolecular signal transduction.
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Affiliation(s)
- Maryam Sadeghi
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Jens Balke
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Constantin Schneider
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Soshichiro Nagano
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Johannes Stellmacher
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
| | - Günter Lochnit
- Justus-Liebig-Universität, Institut für Medizinische Biochemie, D-35390 Giessen, Germany
| | - Christina Lang
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Chris Weise
- Freie Universität Berlin, Institut für Chemie und Biochemie, D-14195 Berlin, Germany
| | - Jon Hughes
- Justus-Liebig-Universität, Institut für Pflanzenphysiologie, D-35390 Giessen, Germany
| | - Ulrike Alexiev
- Freie Universität Berlin, Institut für Experimentalphysik, D-14195 Berlin, Germany
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17
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Wang J, Samanta R, Custer G, Look C, Matysiak S, Beckett D. Tuning Allostery through Integration of Disorder to Order with a Residue Network. Biochemistry 2020; 59:790-801. [PMID: 31899864 DOI: 10.1021/acs.biochem.9b01006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In allostery, a signal from one site in a protein is transmitted to a second site to alter its function. Due to its ubiquity in biology and the potential for its exploitation in drug and protein design, the molecular basis of allosteric communication continues to be the subject of intense research. Although allosterically coupled sites are frequently characterized by disorder, how communication between disordered segments occurs remains obscure. Allosteric activation of Escherichia coli BirA dimerization occurs via coupled distant disorder-to-order transitions. In this work, combined structural and computational studies reveal an extensive residue network in BirA. Substitution of several network residues yields large perturbations to allostery. Force distribution analysis reveals that disruptions to the disorder-to-order transitions through amino acid substitution are manifested in shifts in the energy experienced by network residues as well as alterations in packing of an α-helix that plays a critical role in allostery. The combined results reveal a highly distributed allosteric mechanism that is robust to sequence change.
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Affiliation(s)
- Jingheng Wang
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
| | - Riya Samanta
- Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States
| | - Gregory Custer
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Christopher Look
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Silvina Matysiak
- Fischell Department of Bioengineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Dorothy Beckett
- Department of Chemistry & Biochemistry , University of Maryland , College Park , Maryland 20742 , United States
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18
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O'Rourke KF, Sahu D, Bosken YK, D'Amico RN, Chang CEA, Boehr DD. Coordinated Network Changes across the Catalytic Cycle of Alpha Tryptophan Synthase. Structure 2019; 27:1405-1415.e5. [PMID: 31257109 DOI: 10.1016/j.str.2019.05.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 03/22/2019] [Accepted: 05/30/2019] [Indexed: 12/23/2022]
Abstract
Networks of noncovalent interactions are important for protein structural dynamics. We used nuclear magnetic resonance chemical shift covariance analyses on an inactive variant of the alpha subunit of tryptophan synthase to map amino acid interaction networks across its catalytic cycle. Although some network connections were common to every enzyme state, many of the network connections strengthened or weakened over the catalytic cycle; these changes were highly coordinated. These results suggest a higher level of network organization. Our analyses identified periodic, second-order networks that show highly coordinated interaction changes across the catalytic cycle. These periodic networks may help synchronize the sequence of structural transitions necessary for enzyme function. Molecular dynamics simulations identified interaction changes across the catalytic cycle, including those involving the catalytic residue Glu49, which may help drive other interaction changes throughout the enzyme structure. Similar periodic networks may direct structural transitions and allosteric interactions in other proteins.
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Affiliation(s)
- Kathleen F O'Rourke
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Debashish Sahu
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuliana K Bosken
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Rebecca N D'Amico
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Chia-En A Chang
- Department of Chemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - David D Boehr
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA.
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19
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Jahed Z, Haydari Z, Rathish A, Mofrad MRK. Kindlin Is Mechanosensitive: Force-Induced Conformational Switch Mediates Cross-Talk among Integrins. Biophys J 2019; 116:1011-1024. [PMID: 30819565 DOI: 10.1016/j.bpj.2019.01.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 01/22/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mechanical stresses directly regulate the function of several proteins of the integrin-mediated focal adhesion complex as they experience intra- and extracellular forces. Kindlin is a largely overlooked member of the focal adhesion complex whose roles in cellular mechanotransduction are only recently being identified. Recent crystallographic experiments have revealed that kindlins can form dimers that bind simultaneously to two integrins, providing a mechanistic explanation of how kindlins may promote integrin activation and clustering. In this study, using the newly identified molecular structure, we modeled the response of the kindlin2 dimer in complex with integrin β1 to mechanical cytoskeletal forces on integrins. Using molecular dynamics simulations, we show that forces on integrins are directly transmitted to the kindlin2 dimerization site, resulting in a shift in an R577-S550/E553 interaction network at this site. Under force, R577 on one protomer switches from interacting with S550 to forming new hydrogen bonds with E553 on the neighboring protomer, resulting in the strengthening of the kindlin2 dimer in complex with integrin β1. This force-induced strengthening is similar to the catch-bond mechanisms that have previously been observed in other adhesion molecules. Based on our results, we propose that the kindlin2 dimer is mechanosensitive and can strengthen integrin-mediated focal adhesions under force by shifting the interactions at its dimerization sites.
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Affiliation(s)
- Zeinab Jahed
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California
| | - Zainab Haydari
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California
| | - Akshay Rathish
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, California; Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California.
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20
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Leitner DM, Yamato T. MAPPING ENERGY TRANSPORT NETWORKS IN PROTEINS. REVIEWS IN COMPUTATIONAL CHEMISTRY 2018. [DOI: 10.1002/9781119518068.ch2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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21
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Passam F, Chiu J, Ju L, Pijning A, Jahan Z, Mor-Cohen R, Yeheskel A, Kolšek K, Thärichen L, Aponte-Santamaría C, Gräter F, Hogg PJ. Mechano-redox control of integrin de-adhesion. eLife 2018; 7:e34843. [PMID: 29932420 PMCID: PMC6054529 DOI: 10.7554/elife.34843] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/21/2018] [Indexed: 12/17/2022] Open
Abstract
How proteins harness mechanical force to control function is a significant biological question. Here we describe a human cell surface receptor that couples ligand binding and force to trigger a chemical event which controls the adhesive properties of the receptor. Our studies of the secreted platelet oxidoreductase, ERp5, have revealed that it mediates release of fibrinogen from activated platelet αIIbβ3 integrin. Protein chemical studies show that ligand binding to extended αIIbβ3 integrin renders the βI-domain Cys177-Cys184 disulfide bond cleavable by ERp5. Fluid shear and force spectroscopy assays indicate that disulfide cleavage is enhanced by mechanical force. Cell adhesion assays and molecular dynamics simulations demonstrate that cleavage of the disulfide induces long-range allosteric effects within the βI-domain, mainly affecting the metal-binding sites, that results in release of fibrinogen. This coupling of ligand binding, force and redox events to control cell adhesion may be employed to regulate other protein-protein interactions.
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Affiliation(s)
| | - Joyce Chiu
- The Centenary InstituteNewtownAustralia
- National Health and Medical Research Council Clinical Trials CentreUniversity of SydneySydneyAustralia
| | - Lining Ju
- Heart Research Institute and Charles Perkins CentreUniversity of SydneySydneyAustralia
| | | | | | - Ronit Mor-Cohen
- The Amalia Biron Research Institute of Thrombosis and Hemostasis, Sheba Medical Center, Tel Hashomer and Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Adva Yeheskel
- The Bioinformatics Unit, George S. Wise Faculty of Life ScienceTel Aviv UniversityTel AvivIsrael
| | - Katra Kolšek
- Heidelberg Institute of Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Lena Thärichen
- Heidelberg Institute of Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Camilo Aponte-Santamaría
- Heidelberg Institute of Theoretical StudiesHeidelbergGermany
- Max Planck Tandem Group in Computational BiophysicsUniversity of Los AndesBogotáColombia
| | - Frauke Gräter
- Heidelberg Institute of Theoretical StudiesHeidelbergGermany
- Interdisciplinary Center for Scientific ComputingHeidelberg UniversityHeidelbergGermany
| | - Philip J Hogg
- The Centenary InstituteNewtownAustralia
- National Health and Medical Research Council Clinical Trials CentreUniversity of SydneySydneyAustralia
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22
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Asciutto EK, Pochapsky TC. Some Surprising Implications of NMR-directed Simulations of Substrate Recognition and Binding by Cytochrome P450 cam (CYP101A1). J Mol Biol 2018; 430:1295-1310. [PMID: 29596916 DOI: 10.1016/j.jmb.2018.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 02/05/2023]
Abstract
Cytochrome P450cam (CYP101A1) catalyzes the stereospecific 5-exo hydroxylation of d-camphor by molecular oxygen. Previously, residual dipolar couplings measured for backbone amide 1H-15N correlations in both substrate-free and bound forms of CYP101A1 were used as restraints in soft annealing molecular dynamic simulations in order to identify average conformations of the enzyme with and without substrate bound. Multiple substrate-dependent conformational changes remote from the enzyme active site were identified, and site-directed mutagenesis and activity assays confirmed the importance of these changes in substrate recognition. The current work makes use of perturbation response scanning (PRS) and umbrella sampling molecular dynamic of the residual dipolar coupling-derived CYP101A1 structures to probe the roles of remote structural features in enforcing the regio- and stereospecific nature of the hydroxylation reaction catalyzed by CYP101A1. An improper dihedral angle Ψ was defined and used to maintain substrate orientation in the CYP101A1 active site, and it was observed that different values of Ψ result in different PRS response maps. Umbrella sampling methods show that the free energy of the system is sensitive to Ψ, and bound substrate forms an important mechanical link in the transmission of mechanical coupling through the enzyme structure. Finally, a qualitative approach to interpreting PRS maps in terms of the roles of secondary structural features is proposed.
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Affiliation(s)
- Eliana K Asciutto
- School of Science and Technology, UNSAM and CONICET, Campus Migueletes, 25 de Mayo y Francia, Buenos Aires, Argentina
| | - Thomas C Pochapsky
- Department of Chemistry and Rosenstiel Basic Biomedical Sciences Research Institute, MS 015, Brandeis University, 415 South St., Waltham, MA 02454-9110, USA.
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23
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Chudinova EM, Karpov PA, Fokin AI, Yemets AI, Lytvyn DI, Nadezhdina ES, Blume YB. MAST-like protein kinase IREH1 from Arabidopsis thaliana co-localizes with the centrosome when expressed in animal cells. PLANTA 2017; 246:959-969. [PMID: 28717875 DOI: 10.1007/s00425-017-2742-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
The similarity of IREH1 (Incomplete Root Hair Elongation 1) and animal MAST kinases was confirmed; IREH1cDNA was cloned while expressing in cultured animal cells co-localized with the centrosome. In mammals and fruit flies, microtubule-associated serine/threonine-protein kinases (MAST) are strongly involved in the regulation of the microtubule system. Higher plants also possess protein kinases homologous to MASTs, but their function and interaction with the cytoskeleton remain unclear. Here, we confirmed the sequence and structural similarity of MAST-related putative protein kinase IREH1 (At3g17850) and known animal MAST kinases. We report the first cloning of full-length cDNA of the IREH1 from Arabidopsis thaliana. Recombinant GFP-IREH1 protein was expressed in different cultured animal cells. It revealed co-localization with the centrosome without influencing cell morphology and microtubule arrangement. Structural N-terminal region of the IREH1 molecule co-localized with centrosome as well.
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Affiliation(s)
- Elena M Chudinova
- Institute of Protein Research of Russian Academy of Sciences, Moscow, Russia.
| | - Pavel A Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Artem I Fokin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Alla I Yemets
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Dmytro I Lytvyn
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Elena S Nadezhdina
- Institute of Protein Research of Russian Academy of Sciences, Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Yaroslav B Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kiev, Ukraine
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24
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Fisette O, Wingbermühle S, Schäfer LV. Partial Dissociation of Truncated Peptides Influences the Structural Dynamics of the MHCI Binding Groove. Front Immunol 2017; 8:408. [PMID: 28458665 PMCID: PMC5394104 DOI: 10.3389/fimmu.2017.00408] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/22/2017] [Indexed: 12/29/2022] Open
Abstract
Antigen processing on MHCI involves the exchange of low-affinity peptides by high-affinity, immunodominant ones. This peptide editing process is mediated by tapasin and ERAAP at the peptide C- and N-terminus, respectively. Since tapasin does not contact the peptide directly, a sensing mechanism involving conformational changes likely allows tapasin to distinguish antigen-loaded MHCI molecules from those occupied by weakly bound, non-specific peptides. To understand this mechanism at the atomic level, we performed molecular dynamics simulations of MHCI allele B*44:02 loaded with peptides truncated or modified at the C- or N-terminus. We show that the deletion of peptide anchor residues leads to reversible, partial dissociation of the peptide from MHCI on the microsecond timescale. Fluctuations in the MHCI α2-1 helix segment, bordering the binding groove and cradled by tapasin in the PLC, are influenced by the peptide C-terminus occupying the nearby F-pocket. Simulations of tapasin complexed with MHCI bound to a low-affinity peptide show that tapasin widens the MHCI binding groove near the peptide C-terminus and weakens the attractive forces between MHCI and the peptide. Our simulations thus provide a detailed, spatially resolved picture of MHCI plasticity, revealing how peptide loading status can affect key structural regions contacting tapasin.
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Affiliation(s)
- Olivier Fisette
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Sebastian Wingbermühle
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
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25
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Ahalawat N, Murarka RK. Molecular Mechanism of Nucleotide-Dependent Allosteric Regulation in AMP-Activated Protein Kinase. J Phys Chem B 2017; 121:2919-2930. [PMID: 28345916 DOI: 10.1021/acs.jpcb.6b11223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy homeostasis, is an important drug target for type 2 diabetes, obesity, and cancer. Binding of adenosine nucleotides to the regulatory γ-subunit tightly regulates the activity of this enzyme. Though recent crystal structures of AMPK have provided important insights into the allosteric activation of AMPK, molecular details of the regulatory mechanism of AMPK activation is still elusive. Here, we have performed extensive all-atom molecular dynamics (MD) simulations and shown that the kinase domain (KD) and γ-subunit come closer resulting in a more compact heterotrimeric AMPK complex in AMP-bound state compared to the ATP-bound state. The binding of ATP at site 3 of regulatory γ-subunit allosterically inhibits AMPK by destabilizing different regulatory regions of α-subunit: the autoinhibitory domain, the linker region, and the activation loop of the kinase core. The catalytically important residues experience a change in mechanical stress, and major rearrangements in community structure derived from residue-residue interaction energy-based network are observed in KD and α-linker region upon binding of different nucleotides. Our results also highlight the role of conserved charged residues forming an ionic network near the site 3 of γ-subunit in allosteric communications.
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Affiliation(s)
- Navjeet Ahalawat
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066, MP, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri, Bhopal 462 066, MP, India
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26
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Cruz-Chú ER, Xiao S, Patil SP, Gkagkas K, Gräter F. Organic Filling Mitigates Flaw-Sensitivity of Nanoscale Aragonite. ACS Biomater Sci Eng 2017; 3:260-268. [PMID: 33465925 DOI: 10.1021/acsbiomaterials.6b00504] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Engineering at nanoscale holds the promise of tuning materials with extraordinary properties. However, macroscopic approaches commonly used to predict mechanical properties do not fully apply at nanoscale level. A controversial feature is the presence of nanoflaws in aragonite nacre, as it is expected that flaws would weaken the material, whereas nacre still shows high toughness and rupture strength. Here, we performed molecular dynamics and finite element simulations emulating flaws found in aragonite nacre. Our simulations reveal two regimes for fracture: nacre remains flaw-insensitive only for flaws smaller than 1.2 nm depth, or flaws of a few atoms, whereas larger flaws follow a Griffith-like trend resembling macroscopic fracture. We tested an alternative mechanism for flaw-insensitivity in nacre, and investigated the mechanical effect of organic filling to mitigate fracture. We found that a single nacre protein, perlucin, decreases the stress concentration at the fracture point, producing enhancements of up to 15% in rupture strength. Our study reveals a more comprehensive understanding of mechanical stability at the nanoscale and offers new routes toward hybrid nanomaterials.
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Affiliation(s)
- Eduardo R Cruz-Chú
- Computational Science and Engineering Laboratory, ETH Zürich, Clausiusstrasse 33, Zürich 8092, Switzerland.,Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany
| | - Shijun Xiao
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany.,CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai 200031, China
| | - Sandeep P Patil
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany.,Institute of General Mechanics, RWTH Aachen University, Aachen 52062, Germany
| | - Konstantinos Gkagkas
- Advanced Technology Division, Toyota Motor Europe NV/SA, Technical Center, Zaventem 1930, Belgium
| | - Frauke Gräter
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, Heidelberg 69118, Germany.,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg INF 368, Germany
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27
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Czub J, Wieczór M, Prokopowicz B, Grubmüller H. Mechanochemical Energy Transduction during the Main Rotary Step in the Synthesis Cycle of F 1-ATPase. J Am Chem Soc 2017; 139:4025-4034. [PMID: 28253614 DOI: 10.1021/jacs.6b11708] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
F1-ATPase is a highly efficient molecular motor that can synthesize ATP driven by a mechanical torque. Its ability to function reversibly in either direction requires tight mechanochemical coupling between the catalytic domain and the rotating central shaft, as well as temporal control of substrate binding and product release. Despite great efforts and significant progress, the molecular details of this synchronized and fine-tuned energy conversion mechanism are not fully understood. Here, we use extensive molecular dynamics simulations to reconcile recent single-molecule experiments with structural data and provide a consistent thermodynamic, kinetic and mechanistic description of the main rotary substep in the synthetic cycle of mammalian ATP synthase. The calculated free energy profiles capture a discrete pattern in the rotation of the central γ-shaft, with a metastable intermediate located-consistently with recent experimental findings-at 70° relative to the X-ray position. We identify this rotary step as the ATP-dependent substep, and find that the associated free energy input supports the mechanism involving concurrent nucleotide binding and release. During the main substep, our simulations show no significant opening of the ATP-bound β subunit; instead, we observe that mechanical energy is transmitted to its nucleotide binding site, thus lowering the affinity for ATP. Simultaneously, the empty subunit assumes a conformation that enables the enzyme to harness the free energy of ADP binding to drive ATP release. Finally, we show that ligand exchange is regulated by a checkpoint mechanism, an apparent prerequisite for high efficiency in protein nanomotors.
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Affiliation(s)
- Jacek Czub
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Miłosz Wieczór
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Bartosz Prokopowicz
- Department of Physical Chemistry, Gdansk University of Technology , ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry , Am Fassberg 11, 37077 Göttingen, Germany
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28
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Zhou B, Hogg PJ, Gräter F. One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor. Biophys J 2017; 112:78-86. [PMID: 28076818 PMCID: PMC5232894 DOI: 10.1016/j.bpj.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/19/2016] [Accepted: 12/01/2016] [Indexed: 11/12/2022] Open
Abstract
Tissue factor (TF) is a transmembrane glycoprotein that plays distinct roles in the initiation of extrinsic coagulation cascade and thrombosis. TF contains two disulfide bonds, one each in the N-terminal and C-terminal extracellular domains. The C-domain disulfide, Cys186-Cys209, has a -RHStaple configuration in crystal structures, suggesting that this disulfide carries high pre-stress. The redox state of this disulfide has been proposed to regulate TF encryption/decryption. Ablating the N-domain Cys49-Cys57 disulfide bond was found to increase the redox potential of the Cys186-Cys209 bond, implying an allosteric communication between the domains. Using molecular dynamics simulations, we observed that the Cys186-Cys209 disulfide bond retained the -RHStaple configuration, whereas the Cys49-Cys57 disulfide bond fluctuated widely. The Cys186-Cys209 bond featured the typical -RHStaple disulfide properties, such as a longer S-S bond length, larger C-S-S angles, and higher bonded prestress, in comparison to the Cys49-Cys57 bond. Force distribution analysis was used to sense the subtle structural changes upon ablating the disulfide bonds, and allowed us to identify a one-way allosteric communication mechanism from the N-terminal to the C-terminal domain. We propose a force propagation pathway using a shortest-pathway algorithm, which we suggest is a useful method for searching allosteric signal transduction pathways in proteins. As a possible explanation for the pathway being one-way, we identified a pronounced lower degree of conformational fluctuation, or effectively higher stiffness, in the N-terminal domain. Thus, the changes of the rigid domain (N-terminal domain) can induce mechanical force propagation to the soft domain (C-terminal domain), but not vice versa.
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Affiliation(s)
- Beifei Zhou
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology (PICB), Shanghai, China; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Philip J Hogg
- The Centenary Institute and National Health and Medical Research Council Clinical Trials Centre, University of Sydney, Sydney, Australia
| | - Frauke Gräter
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; University of Heidelberg, Interdisciplinary Center for Scientific Computing, Heidelberg, Germany.
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29
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Stauch T, Dreuw A. Advances in Quantum Mechanochemistry: Electronic Structure Methods and Force Analysis. Chem Rev 2016; 116:14137-14180. [PMID: 27767298 DOI: 10.1021/acs.chemrev.6b00458] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In quantum mechanochemistry, quantum chemical methods are used to describe molecules under the influence of an external force. The calculation of geometries, energies, transition states, reaction rates, and spectroscopic properties of molecules on the force-modified potential energy surfaces is the key to gain an in-depth understanding of mechanochemical processes at the molecular level. In this review, we present recent advances in the field of quantum mechanochemistry and introduce the quantum chemical methods used to calculate the properties of molecules under an external force. We place special emphasis on quantum chemical force analysis tools, which can be used to identify the mechanochemically relevant degrees of freedom in a deformed molecule, and spotlight selected applications of quantum mechanochemical methods to point out their synergistic relationship with experiments.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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30
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Prieß M, Schäfer LV. Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F. Biophys J 2016; 110:2407-2418. [PMID: 27276259 PMCID: PMC4906252 DOI: 10.1016/j.bpj.2016.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/30/2016] [Accepted: 04/20/2016] [Indexed: 01/14/2023] Open
Abstract
Substrate translocation by ATP-binding cassette (ABC) transporters involves coupling of ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) to conformational changes in the transmembrane domains. We used molecular dynamics simulations to investigate the atomic-level mechanism of conformational coupling in the ABC transporter BtuCD-F, which imports vitamin B12 across the inner membrane of Escherichia coli. Our simulations show how an engineered disulfide bond across the NBD dimer interface reduces conformational fluctuations and hence configurational entropy. As a result, the disulfide bond is under substantial mechanical stress. Releasing this entropic spring, as is the case in the wild-type transporter, combined with analyzing the pairwise forces between individual residues, unravels the coupling mechanism. The identified pathways along which force is propagated from the NBDs via the coupling helix to the transmembrane domains are composed of highly conserved residues, underlining their functional relevance. This study not only reveals the details of conformational coupling in BtuCD-F, it also provides a promising approach to other long-range conformational couplings, e.g., in ABC exporters or other ATP-driven molecular machines.
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Affiliation(s)
- Marten Prieß
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany.
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31
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Karpov P, Demchuk O, Britsun V, Lytvyn D, Pydiura N, Rayevsky A, Samofalova D, Spivak S, Volochnyuk D, Yemets A, Blume Y. New Imidazole Inhibitors of Mycobacterial FtsZ: the Way from High-Throughput Molecular Screening in Grid up to in vitro Verification. SCIENCE AND INNOVATION 2016. [DOI: 10.15407/scine12.03.043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
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32
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Affiliation(s)
- Zhenyan Jiang
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, 91058Germany
| | - Hansi Zhang
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, 91058Germany
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, University of Erlangen-Nürnberg, Erlangen, 91058Germany
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33
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Fisette O, Wingbermühle S, Tampé R, Schäfer LV. Molecular mechanism of peptide editing in the tapasin-MHC I complex. Sci Rep 2016; 6:19085. [PMID: 26754481 PMCID: PMC4709564 DOI: 10.1038/srep19085] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 11/30/2015] [Indexed: 11/30/2022] Open
Abstract
Immune recognition of infected or malignantly transformed cells relies on antigenic peptides exposed at the cell surface by major histocompatibility complex class I (MHC I) molecules. Selection and loading of peptides onto MHC I is orchestrated by the peptide-loading complex (PLC), a multiprotein assembly whose structure has not yet been resolved. Tapasin, a central component of the PLC, stabilises MHC I and catalyses the exchange of low-affinity against high-affinity, immunodominant peptides. Up to now, the molecular basis of this peptide editing mechanism remained elusive. Here, using all-atom molecular dynamics (MD) simulations, we unravel the atomic details of how tapasin and antigen peptides act on the MHC I binding groove. Force distribution analysis reveals an intriguing molecular tug-of-war mechanism: only high-affinity peptides can exert sufficiently large forces to close the binding groove, thus overcoming the opposite forces exerted by tapasin to open it. Tapasin therefore accelerates the release of low-affinity peptides until a high-affinity antigen binds, promoting subsequent PLC break-down. Fluctuation and entropy analyses show how tapasin chaperones MHC I by stabilising it in a peptide-receptive conformation. Our results explain previous experiments and mark a key step towards a better understanding of adaptive immunity.
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Affiliation(s)
- Olivier Fisette
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, 44780, Germany
| | | | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt, 60438, Germany
| | - Lars V. Schäfer
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, 44780, Germany
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34
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Schoeler C, Bernardi RC, Malinowska KH, Durner E, Ott W, Bayer EA, Schulten K, Nash MA, Gaub HE. Mapping Mechanical Force Propagation through Biomolecular Complexes. NANO LETTERS 2015; 15:7370-6. [PMID: 26259544 PMCID: PMC4721519 DOI: 10.1021/acs.nanolett.5b02727] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Here we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. The results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.
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35
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Stauch T, Dreuw A. On the use of different coordinate systems in mechanochemical force analyses. J Chem Phys 2015; 143:074118. [PMID: 26298126 DOI: 10.1063/1.4928973] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Force analyses are crucial for a comprehensive understanding of mechanochemical processes. The choice of coordinate system in these kinds of analyses is a nontrivial task that determines the quality and validity of the obtained results. Here, we study the suitability of different sets of coordinates for mechanical force analyses, i.e., normal modes, delocalized internal, redundant internal, and Z-matrix coordinates. After discussing the theoretical foundations of force analyses using different coordinate systems, we investigate a number of test molecules. We show that normal modes and Z-matrix coordinates deliver useful results only if certain requirements are fulfilled and that only redundant internal coordinates yield meaningful results in all cases.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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36
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Louet M, Seifert C, Hensen U, Gräter F. Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces. PLoS Comput Biol 2015; 11:e1004358. [PMID: 26244893 PMCID: PMC4526232 DOI: 10.1371/journal.pcbi.1004358] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 05/28/2015] [Indexed: 11/23/2022] Open
Abstract
The Catabolite Activator Protein (CAP) is a showcase example for entropic allostery. For full activation and DNA binding, the homodimeric protein requires the binding of two cyclic AMP (cAMP) molecules in an anti-cooperative manner, the source of which appears to be largely of entropic nature according to previous experimental studies. We here study at atomic detail the allosteric regulation of CAP with Molecular dynamics (MD) simulations. We recover the experimentally observed entropic penalty for the second cAMP binding event with our recently developed force covariance entropy estimator and reveal allosteric communication pathways with Force Distribution Analyses (FDA). Our observations show that CAP binding results in characteristic changes in the interaction pathways connecting the two cAMP allosteric binding sites with each other, as well as with the DNA binding domains. We identified crucial relays in the mostly symmetric allosteric activation network, and suggest point mutants to test this mechanism. Our study suggests inter-residue forces, as opposed to coordinates, as a highly sensitive measure for structural adaptations that, even though minute, can very effectively propagate allosteric signals. The Catabolite Activator Protein (CAP) is a well-studied example for how cellular catabolite levels are integrated into the gene regulation. Its affinity for a specific stretch of DNA can be switched on by the binding of two nucleotide molecules termed cAMP to its two protomers. Even though the nucleotides occupy structurally identical binding pockets, the second cAMP binding occurs at an affinity orders of magnitude lower than the first cAMP binding. The question arises how, in the absence of structural changes, the first binding can affect the second. An answer from experiments has been that the communication is largely of entropic nature, i.e. the second cAMP binding would lead to a pronounced reduction in atomic fluctuations of the protein without affecting the atomic mean positions. We here revisited this question by performing Molecular Dynamics simulations. By measuring correlations of forces, a newly derived method outperforming the more common coordinate-based approach, we could recover the previously determined entropic penalty. In addition, however, we observed unobtrusive structural changes of side-chain interactions leading to the occlusion of the second binding pocket that add a critical ‘enthalpic’ component hitherto overlooked. Our study provides a mechanistic view onto the intriguing anti-cooperativity of CAP.
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Affiliation(s)
- Maxime Louet
- Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany
| | - Christian Seifert
- Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany
| | - Ulf Hensen
- Eidgenössische Technische Hochschule Zürich, Department of Biosystem Science and Engineering, Basel, Switzerland
| | - Frauke Gräter
- Heidelberg Institutes for Theoretical Studies gGmbH, Heidelberg, Germany; CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
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37
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Avdoshenko SM, Makarov DE. Finding mechanochemical pathways and barriers without transition state search. J Chem Phys 2015; 142:174106. [PMID: 25956089 DOI: 10.1063/1.4919541] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In covalent mechanochemistry, precise application of mechanical stress to molecules of interest ("mechanophores") is used to induce to promote desired reaction pathways. Computational prediction of such phenomena and rational mechanophore design involves the computationally costly task of finding relevant transition-state saddles on force-deformed molecular potential energy surfaces (PESs). Finding a transition state often requires an initial guess about the pathway by which the reaction will proceed. Unfortunately, chemical intuition often fails when predicting likely consequences of mechanical stress applied to molecular systems. Here, we describe a fully deterministic method for finding mechanochemically relevant transition states and reaction pathways. The method is based on the observation that application of a sufficiently high mechanical force will eventually destabilize any molecular structure. Mathematically, such destabilization proceeds via a "catastrophe" occurring at a critical force where the energy minimum corresponding to the stable molecular structure coalesces with a transition state. Catastrophe theory predicts the force-deformed PES to have universal behavior in the vicinity of the critical force, allowing us to deduce the molecular structure of the transition state just below the critical force analytically. We then use the previously developed method of tracking transition-state evolution with the force to map out the entire reaction path and to predict the complete force dependence of the reaction barrier. Beyond its applications in mechanochemistry, this approach may be useful as a general method of finding transition states using fictitious forces to target specific reaction mechanisms.
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Affiliation(s)
- Stanislav M Avdoshenko
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | - Dmitrii E Makarov
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
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38
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Papaleo E. Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity. Front Mol Biosci 2015; 2:28. [PMID: 26075210 PMCID: PMC4445042 DOI: 10.3389/fmolb.2015.00028] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/08/2015] [Indexed: 12/11/2022] Open
Abstract
In the last years, we have been observing remarkable improvements in the field of protein dynamics. Indeed, we can now study protein dynamics in atomistic details over several timescales with a rich portfolio of experimental and computational techniques. On one side, this provides us with the possibility to validate simulation methods and physical models against a broad range of experimental observables. On the other side, it also allows a complementary and comprehensive view on protein structure and dynamics. What is needed now is a better understanding of the link between the dynamic properties that we observe and the functional properties of these important cellular machines. To make progresses in this direction, we need to improve the physical models used to describe proteins and solvent in molecular dynamics, as well as to strengthen the integration of experiments and simulations to overcome their own limitations. Moreover, now that we have the means to study protein dynamics in great details, we need new tools to understand the information embedded in the protein ensembles and in their dynamic signature. With this aim in mind, we should enrich the current tools for analysis of biomolecular simulations with attention to the effects that can be propagated over long distances and are often associated to important biological functions. In this context, approaches inspired by network analysis can make an important contribution to the analysis of molecular dynamics simulations.
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Affiliation(s)
- Elena Papaleo
- Structural Biology and Nuclear Magnetic Resonance Laboratory, Department of Biology, University of Copenhagen Copenhagen, Denmark
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39
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Stauch T, Dreuw A. A quantitative quantum-chemical analysis tool for the distribution of mechanical force in molecules. J Chem Phys 2015; 140:134107. [PMID: 24712780 DOI: 10.1063/1.4870334] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The promising field of mechanochemistry suffers from a general lack of understanding of the distribution and propagation of force in a stretched molecule, which limits its applicability up to the present day. In this article, we introduce the JEDI (Judgement of Energy DIstribution) analysis, which is the first quantum chemical method that provides a quantitative understanding of the distribution of mechanical stress energy among all degrees of freedom in a molecule. The method is carried out on the basis of static or dynamic calculations under the influence of an external force and makes use of a Hessian matrix in redundant internal coordinates (bond lengths, bond angles, and dihedral angles), so that all relevant degrees of freedom of a molecule are included and mechanochemical processes can be interpreted in a chemically intuitive way. The JEDI method is characterized by its modest computational effort, with the calculation of the Hessian being the rate-determining step, and delivers, except for the harmonic approximation, exact ab initio results. We apply the JEDI analysis to several example molecules in both static quantum chemical calculations and Born-Oppenheimer Molecular Dynamics simulations in which molecules are subject to an external force, thus studying not only the distribution and the propagation of strain in mechanically deformed systems, but also gaining valuable insights into the mechanochemically induced isomerization of trans-3,4-dimethylcyclobutene to trans,trans-2,4-hexadiene. The JEDI analysis can potentially be used in the discussion of sonochemical reactions, molecular motors, mechanophores, and photoswitches as well as in the development of molecular force probes.
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Affiliation(s)
- Tim Stauch
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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40
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Calculation and visualization of atomistic mechanical stresses in nanomaterials and biomolecules. PLoS One 2014; 9:e113119. [PMID: 25503996 PMCID: PMC4263534 DOI: 10.1371/journal.pone.0113119] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 10/23/2014] [Indexed: 11/19/2022] Open
Abstract
Many biomolecules have machine-like functions, and accordingly are discussed in terms of mechanical properties like force and motion. However, the concept of stress, a mechanical property that is of fundamental importance in the study of macroscopic mechanics, is not commonly applied in the biomolecular context. We anticipate that microscopical stress analyses of biomolecules and nanomaterials will provide useful mechanistic insights and help guide molecular design. To enable such applications, we have developed Calculator of Atomistic Mechanical Stress (CAMS), an open-source software package for computing atomic resolution stresses from molecular dynamics (MD) simulations. The software also enables decomposition of stress into contributions from bonded, nonbonded and Generalized Born potential terms. CAMS reads GROMACS topology and trajectory files, which are easily generated from AMBER files as well; and time-varying stresses may be animated and visualized in the VMD viewer. Here, we review relevant theory and present illustrative applications.
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41
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Abstract
Currently, Dual Specificity YAK1-Related Kinases (MNB/DYRK) were found in slime molds, protista, fungi, and animals, but the existence of plant homologues is still unclear. In the present study, we have identified 14 potential plant homologues with the previously unknown functions, based on the strong sequence similarity. The results of bioinformatics analysis revealed their correspondence to DYRK1A, DYRK1B, DYRK3, and DYRK4. For two plant homologues of animal DYRK1A from Physcomitrella patens and Arabidopsis thaliana spatial structures of catalytic domains were predicted, as well as their complexes with ADP and selective inhibitor d15. Comparative analysis of 3D-structures of the human DYRK1A and plant homologues, their complexes with the specific inhibitors, and results of molecular dynamics confirm their structural and functional similarity with high probability. Preliminary data indicate the presence of potential MNB/DYRK specific phosphorylation sites in such proteins associated with plant cytoskeleton as plant microtubule-associated proteins WVD2 and WDL1, and FH5 and SCAR2 involved in the organization and polarity of the actin cytoskeleton and some kinesin-like microtubule motor proteins.
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42
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Bhattacharya S, Lee S, Grisshammer R, Tate CG, Vaidehi N. Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors. J Chem Theory Comput 2014; 10:5149-5160. [PMID: 25400524 PMCID: PMC4230369 DOI: 10.1021/ct500616v] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 01/22/2023]
Abstract
![]()
G protein-coupled
receptors (GPCRs) are highly dynamic and often
denature when extracted in detergents. Deriving thermostable mutants
has been a successful strategy to stabilize GPCRs in detergents, but
this process is experimentally tedious. We have developed a computational
method to predict the position of the thermostabilizing mutations
for a given GPCR sequence. We have validated the method against experimentally
measured thermostability data for single mutants of the β1-adrenergic receptor (β1AR), adenosine A2A receptor (A2AR) and neurotensin receptor 1 (NTSR1).
To make these predictions we started from homology models of these
receptors of varying accuracies and generated an ensemble of conformations
by sampling the rigid body degrees of freedom of transmembrane helices.
Then, an all-atom force field function was used to calculate the enthalpy
gain, known as the “stability score” upon mutation of
every residue, in these receptor structures, to alanine. For all three
receptors, β1AR, A2AR, and NTSR1, we observed
that mutations of hydrophobic residues in the transmembrane domain
to alanine that have high stability scores correlate with high experimental
thermostability. The prediction using the stability score improves
when using an ensemble of receptor conformations compared to a single
structure, showing that receptor flexibility is important. We also
find that our previously developed LITiCon method for generating conformation
ensembles is similar in performance to predictions using ensembles
obtained from microseconds of molecular dynamics simulations (which
is computationally hundred times slower than LITiCon). We improved
the thermostability prediction by including other properties such
as residue-based stress and the extent of allosteric communication
by each residue in the stability score. Our method is the first step
toward a computational method for rapid prediction of thermostable
mutants of GPCRs.
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Affiliation(s)
- Supriyo Bhattacharya
- Division of Immunology, Beckman Research Institute of the City of Hope , 1500 East Duarte Rd, Duarte, California 91010, United States
| | - Sangbae Lee
- Division of Immunology, Beckman Research Institute of the City of Hope , 1500 East Duarte Rd, Duarte, California 91010, United States
| | - Reinhard Grisshammer
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health , Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Nagarajan Vaidehi
- Division of Immunology, Beckman Research Institute of the City of Hope , 1500 East Duarte Rd, Duarte, California 91010, United States
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43
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Avdoshenko SM, Konda SSM, Makarov DE. On the calculation of internal forces in mechanically stressed polyatomic molecules. J Chem Phys 2014; 141:134115. [DOI: 10.1063/1.4896944] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Stanislav M. Avdoshenko
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
| | | | - Dmitrii E. Makarov
- Institute for Computational Engineering and Sciences, University of Texas at Austin, Austin, Texas 78712, USA
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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44
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Zhou B, Baldus IB, Li W, Edwards SA, Gräter F. Identification of allosteric disulfides from prestress analysis. Biophys J 2014; 107:672-681. [PMID: 25099806 PMCID: PMC4129481 DOI: 10.1016/j.bpj.2014.06.025] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 11/23/2022] Open
Abstract
Disulfide bonds serve to form physical cross-links between residues in protein structures, thereby stabilizing the protein fold. Apart from this purely structural role, they can also be chemically active, participating in redox reactions, and they may even potentially act as allosteric switches controlling protein functions. Specific types of disulfide bonds have been identified in static protein structures from their distinctive pattern of dihedral bond angles, and the allosteric function of such bonds is purported to be related to the torsional strain they store. Using all-atom molecular-dynamics simulations for ∼700 disulfide bonded proteins, we analyzed the intramolecular mechanical forces in 20 classes of disulfide bonds. We found that two particular classes, the -RHStaple and the -/+RHHook disulfides, are indeed more stressed than other disulfide bonds, but the stress is carried primarily by stretching of the S-S bond and bending of the neighboring bond angles, rather than by dihedral torsion. This stress corresponds to a tension force of magnitude ∼200 pN, which is balanced by repulsive van der Waals interactions between the cysteine Cα atoms. We confirm stretching of the S-S bond to be a general feature of the -RHStaples and the -/+RHHooks by analyzing ∼20,000 static protein structures. Given that forced stretching of S-S bonds is known to accelerate their cleavage, we propose that prestress of allosteric disulfide bonds has the potential to alter the reactivity of a disulfide, thereby allowing us to readily switch between functional states.
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Affiliation(s)
- Beifei Zhou
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Ilona B Baldus
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Wenjin Li
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois
| | - Scott A Edwards
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; College of Physics Science and Technology, Shenzhen University, Shenzhen, Guangdong, China
| | - Frauke Gräter
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai, China; Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
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45
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Woods KN. Using THz time-scale infrared spectroscopy to examine the role of collective, thermal fluctuations in the formation of myoglobin allosteric communication pathways and ligand specificity. SOFT MATTER 2014; 10:4387-4402. [PMID: 24801988 DOI: 10.1039/c3sm53229a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this investigation we use THz time-scale spectroscopy to conduct an initial set of studies on myoglobin with the aim of providing further insight into the global, collective thermal fluctuations in the protein that have been hypothesized to play a prominent role in the dynamic formation of transient ligand channels as well as in shaping the molecular level basis for ligand discrimination. Using the two ligands O2 and CO, we have determined that the perturbation from the heme-ligand complex has a strong influence on the characteristics of the myoglobin collective dynamics that are excited upon binding. Further, the differences detected in the collective protein motions in Mb-O2 compared with those in Mb-CO appear to be intimately tied with the pathways of long-range allosteric communication in the protein, which ultimately determine the trajectories selected by the respective ligands on the path to and from the heme-binding cavity.
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Affiliation(s)
- K N Woods
- Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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46
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Lee S, Bhattacharya S, Grisshammer R, Tate C, Vaidehi N. Dynamic behavior of the active and inactive states of the adenosine A(2A) receptor. J Phys Chem B 2014; 118:3355-65. [PMID: 24579769 PMCID: PMC3983344 DOI: 10.1021/jp411618h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
![]()
The adenosine A2A receptor
(A2AR) belongs
to the superfamily of membrane proteins called the G-protein-coupled
receptors (GPCRs) that form one of the largest superfamilies of drug
targets. Deriving thermostable mutants has been one of the strategies
used for crystallization of A2AR in both the agonist and
antagonist bound conformational states. The crystal structures do
not reveal differences in the activation mechanism of the mutant receptors
compared to the wild type receptor, that have been observed experimentally.
These differences stem from the dynamic behavior of the mutant receptors.
Furthermore, it is not understood how the mutations confer thermostability.
Since these details are difficult to obtain from experiments, we have
used atomic level simulations to elucidate the dynamic behavior of
the agonist and antagonist bound mutants as well the wild type A2AR. We found that significant enthalpic contribution leads
to stabilization of both the inactive state (StaR2) and active-like
state (GL31) thermostable mutants of A2AR. Stabilization
resulting from mutations of bulky residues to alanine is due to the
formation of interhelical hydrogen bonds and van der Waals packing
that improves the transmembrane domain packing. The thermostable mutant
GL31 shows less movement of the transmembrane helix TM6 with respect
to TM3 than the wild type receptor. While restricted dynamics of GL31
is advantageous in its purification and crystallization, it could
also be the reason why these mutants are not efficient in activating
the G proteins. We observed that the calculated stress on each residue
is higher in the wild type receptor compared to the thermostable mutants,
and this stress is required for activation to occur. Thus, reduced
dynamic behavior of the thermostable mutants leading to lowered activation
of these receptors originates from reduced stress on each residue.
Finally, accurate calculation of the change in free energy for single
mutations shows good correlation with the change in the measured thermostability.
These results provide insights into the effect of mutations that can
be incorporated in deriving thermostable mutants for other GPCRs.
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Affiliation(s)
- Sangbae Lee
- Division of Immunology, Beckman Research Institute of the City of Hope , 1500 East Duarte Road, Duarte, California 91010, United States
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Palmai Z, Seifert C, Gräter F, Balog E. An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis. PLoS Comput Biol 2014; 10:e1003444. [PMID: 24465199 PMCID: PMC3900376 DOI: 10.1371/journal.pcbi.1003444] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 12/03/2013] [Indexed: 11/18/2022] Open
Abstract
3-Phosphogycerate kinase (PGK) is a two domain enzyme, which transfers a phosphate group between its two substrates, 1,3-bisphosphoglycerate bound to the N-domain and ADP bound to the C-domain. Indispensable for the phosphoryl transfer reaction is a large conformational change from an inactive open to an active closed conformation via a hinge motion that should bring substrates into close proximity. The allosteric pathway resulting in the active closed conformation has only been partially uncovered. Using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA), we describe an allosteric pathway, which connects the substrate binding sites to the interdomain hinge region. Glu192 of alpha-helix 7 and Gly394 of loop L14 act as hinge points, at which these two secondary structure elements straighten, thereby moving the substrate-binding domains towards each other. The long-range allosteric pathway regulating hPGK catalytic activity, which is partially validated and can be further tested by mutagenesis, highlights the virtue of monitoring internal forces to reveal signal propagation, even if only minor conformational distortions, such as helix bending, initiate the large functional rearrangement of the macromolecule. 3-Phosphoglycerate kinase (PGK) is an essential enzyme for living organisms. It catalyzes the phospho-transfer reaction between two catabolites during carbohydrate metabolism. In addition to this physiological role, human PGK has been shown to phosphorylate L-nucleoside analogues, potential drugs against viral infection and cancer. PGK is a two domain enzyme, with the two substrates bound to the two separate domains. In order to perform its function the enzyme has to undergo a large conformational change involving a hinge bending to bring the substrates into close proximity. The allosteric pathway from the open non-reactive state of PGK to the closed reactive state as triggered by substrate binding has only been partially uncovered by experimental studies. Here we describe a complete allosteric pathway, which connects the substrate binding sites to the interdomain hinge region using Molecular Dynamics simulations combined with Force Distribution Analysis (FDA). While previously identified key residues involved in PGK domain closure are part of this pathway, we here fill the numerous gaps in the pathway by identifying newly uncovered residues and interesting candidates for future mutational studies.
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Affiliation(s)
- Zoltan Palmai
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Christian Seifert
- Molecular Biomechanics, Heidelberger Institut für Theoretische Studien gGmbH, Heidelberg, Germany
| | - Frauke Gräter
- Molecular Biomechanics, Heidelberger Institut für Theoretische Studien gGmbH, Heidelberg, Germany
- MPG-CAS Partner Institute and Key Laboratory for Computational Biology, Shanghai, China
- * E-mail: (FG); (EB)
| | - Erika Balog
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
- * E-mail: (FG); (EB)
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Han N, Mu Y. Locking the 150-cavity open: in silico design and verification of influenza neuraminidase inhibitors. PLoS One 2013; 8:e73344. [PMID: 24015302 PMCID: PMC3755005 DOI: 10.1371/journal.pone.0073344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 07/29/2013] [Indexed: 11/22/2022] Open
Abstract
Neuraminidase (NA) of influenza is a key target for virus infection control and the recently discovered open 150-cavity in group-1 NA provides new opportunity for novel inhibitors design. In this study, we used a combination of theoretical methods including fragment docking, molecular linking and molecular dynamics simulations to design ligands that specifically target at the 150-cavity. Through in silico screening of a fragment compound library on the open 150-cavity of NA, a few best scored fragment compounds were selected to link with Zanamivir, one NA-targeting drug. The resultant new ligands may bind both the active site and the 150-cavity of NA simultaneously. Extensive molecular dynamics simulations in explicit solvent were applied to validate the binding between NA and the designed ligands. Moreover, two control systems, a positive control using Zanamivir and a negative control using a low-affinity ligand 3-(p-tolyl) allyl-Neu5Ac2en (ETT, abbreviation reported in the PDB) found in a recent experimental work, were employed to calibrate the simulation method. During the simulations, ETT was observed to detach from NA, on the contrary, both Zanamivir and our designed ligand bind NA firmly. Our study provides a prospective way to design novel inhibitors for controlling the spread of influenza virus.
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Affiliation(s)
- Nanyu Han
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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Li W, Edwards SA, Lu L, Kubar T, Patil SP, Grubmüller H, Groenhof G, Gräter F. Force Distribution Analysis of Mechanochemically Reactive Dimethylcyclobutene. Chemphyschem 2013; 14:2687-97. [DOI: 10.1002/cphc.201300252] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 06/06/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Wenjin Li
- CAS‐MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (P.R. China)
- Department of Theoretical and Computational Biophysics, Max‐Planck‐Institute for Biophysical Chemistry, Goettingen (Germany)
| | - Scott A. Edwards
- College of Physics and Technology, Shenzhen University, 3688 Nanhai Ave, Shenzhen 518060, Guangdong (P.R. China)
| | - Lanyuan Lu
- Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University (Singapore)
| | - Tomas Kubar
- Institute for Physical Chemistry, Karlsruhe Institute of Technology (Germany)
| | - Sandeep P. Patil
- Heidelberg Institute for Theoretical Studies, Heidelberg (Germany)
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max‐Planck‐Institute for Biophysical Chemistry, Goettingen (Germany)
| | - Gerrit Groenhof
- Department of Theoretical and Computational Biophysics, Max‐Planck‐Institute for Biophysical Chemistry, Goettingen (Germany)
- Department of Chemistry, Nanoscience Center, University of Jyväskylä, FI‐40014 Jyväskylä (Finland)
| | - Frauke Gräter
- CAS‐MPG Partner Institute and Key Laboratory for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (P.R. China)
- Heidelberg Institute for Theoretical Studies, Heidelberg (Germany)
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50
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Protein mechanics: how force regulates molecular function. Biochim Biophys Acta Gen Subj 2013; 1830:4762-8. [PMID: 23791949 DOI: 10.1016/j.bbagen.2013.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 05/26/2013] [Accepted: 06/04/2013] [Indexed: 12/13/2022]
Abstract
BACKGROUND Regulation of proteins is ubiquitous and vital for any organism. Protein activity can be altered chemically, by covalent modifications or non-covalent binding of co-factors. Mechanical forces are emerging as an additional way of regulating proteins, by inducing a conformational change or by partial unfolding. SCOPE We review some advances in experimental and theoretical techniques to study protein allostery driven by mechanical forces, as opposed to the more conventional ligand driven allostery. In this respect, we discuss recent single molecule pulling experiments as they have substantially augmented our view on the protein allostery by mechanical signals in recent years. Finally, we present a computational analysis technique, Force Distribution Analysis, that we developed to reveal allosteric pathways in proteins. MAJOR CONCLUSIONS Any kind of external perturbation, being it ligand binding or mechanical stretching, can be viewed as an external force acting on the macromolecule, rendering force-based experimental or computational techniques, a very general approach to the mechanics involved in protein allostery. GENERAL SIGNIFICANCE This unifying view might aid to decipher how complex allosteric protein machineries are regulated on the single molecular level.
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