1
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Nakata N, Okamoto R, Sumi T, Koga K, Morita T, Imamura H. Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein. Protein Sci 2023; 32:e4763. [PMID: 37622187 PMCID: PMC10519159 DOI: 10.1002/pro.4763] [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: 05/15/2023] [Revised: 08/07/2023] [Accepted: 08/21/2023] [Indexed: 08/26/2023]
Abstract
Alcohols and urea are widely used as effective protein denaturants. Among monohydric alcohols, 2,2,2-trifluoroethanol (TFE) has large cosolvent effects as a helix stabilizer in proteins. In contrast, urea efficiently denatures ordered native structures, including helices, into coils. These opposing cosolvent effects of TFE and urea are well known, even though both preferentially bind to proteins; however, the underlying molecular mechanism remains controversial. Cosolvent-dependent relative stability between native and denatured states is rigorously related to the difference in preferential binding parameters (PBPs) between these states. In this study, GCN4-p1 with two-stranded coiled coil helices was employed as a model protein, and molecular dynamics simulations for the helix dimer and isolated coil were conducted in aqueous solutions with 2 M TFE and urea. As 2 M cosolvent aqueous solutions did not exhibit clustering of cosolvent molecules, we were able to directly investigate the molecular origin of the excess PBP without considering the enhancement effect of PBPs arising from the concentration fluctuations. The calculated excess PBPs of TFE for the helices and those of urea for the coils were consistent with experimentally observed stabilization of helix by TFE and that of coil by urea. The former was caused by electrostatic interactions between TFE and side chains of the helices, while the latter was attributed to both electrostatic and dispersion interactions between urea and the main chains. Unexpectedly, reverse-micelle-like orientations of TFE molecules strengthened the electrostatic interactions between TFE and the side chains, resulting in strengthening of TFE solvation.
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Affiliation(s)
- Noa Nakata
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
| | - Ryuichi Okamoto
- Graduate School of Information Science, University of HyogoKobeHyogoJapan
| | - Tomonari Sumi
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Kenichiro Koga
- Department of Chemistry, Faculty of ScienceOkayama UniversityOkayamaJapan
- Research Institute for Interdisciplinary Science, Okayama UniversityOkayamaJapan
| | - Takeshi Morita
- Department of ChemistryGraduate School of Science, Chiba UniversityChibaJapan
| | - Hiroshi Imamura
- Department of Bio‐ScienceNagahama Institute of Bio‐Science and TechnologyNagahamaShigaJapan
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2
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Sun H, Yao C, You K, Chen C, Liu S, Xu Z. Nanopore single-molecule biosensor in protein denaturation analysis. Anal Chim Acta 2023; 1243:340830. [PMID: 36697181 DOI: 10.1016/j.aca.2023.340830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/02/2023] [Accepted: 01/11/2023] [Indexed: 01/13/2023]
Abstract
Unclear issues in protein studies include but not limited to the stability and denaturation mechanism in the presence of denaturants. Herein, we report a dynamic monitoring approach based on nanopore single-molecule biosensor, which can detect the protein's folding and unfolding transitions by recording a nanopore ionic current. When gradually increasing the concentration of denaturant guanidine hydrochloride (GdmCl), sensitive responses were observed with lysozyme unfolding. The emergence of the featured biphasic-pulse demonstrated the existence of a stable intermediate. It was the first time to experimentally confirm the dynamic equilibrium between the intermediate and the native states at single molecule level, therefore consolidating the standpoint of lysozyme denaturation process following the three-state model. Additionally, we got more insights into the conformation about the intermediate as globular-like structure, larger gyration radius, and enhanced positive charge density. We considered that the manner of denaturant toward lysozyme adopts the "direct" model based on stronger electrostatic and van der Waals forces. Nanopore biosensor exhibited excellent sensitivity with a low detection concentration of 280 pM and reproducibility in analysing the folding intermediate of lysozyme.
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Affiliation(s)
- Hong Sun
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China.
| | - Chuan Yao
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Kaibo You
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Can Chen
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Shuoshuo Liu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
| | - Zhihong Xu
- Key Laboratory of Micro-Nano Materials for Energy Storage and Conversion of Henan Province, Institute of Surface Micro and Nano Materials, College of Chemical and Materials Engineering, Xuchang University, Henan, 461000, PR China
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3
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Ajayi S, Asakereh I, Rezasoltani H, Davidson D, Khajehpour M. Does Urea Preferentially Interact with Amide Moieties or Nonpolar Sidechains? A Question Answered Through a Judicious Selection of Model Systems. Chemphyschem 2022; 24:e202200731. [PMID: 36478636 DOI: 10.1002/cphc.202200731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/02/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
The transfer model suggests that urea unfolds proteins mainly by increasing the solubility of the amide backbone, probably through urea-induced increase in hydrogen bonding. Other studies suggest that urea addition increases the magnitude of solvent-solute van der Waals interactions, which increases the solubility of nonpolar sidechains. More recent analyses hypothesize that urea has a similar effect in increasing the solubility of backbone and sidechain groups. In this work, we compare the effects of urea addition on the solvation of amides and alkyl groups. At first, we study the effects of urea addition upon solvent hydrogen bonding acidity and basicity through the perturbation in the fluorescence spectrum of probes 1-AN and 1-DMAN. Our results demonstrate that the solvent's hydrogen bonding properties are minimally affected by urea addition. Subsequently, we show that urea addition does not perturb the intra-molecular hydrogen bonding in salicylic acid significantly. Finally, we investigate how urea preferentially interacts with amide and alkyl groups moieties in water by comparing the effects of urea addition upon the solubility of acetaminophen and 4-tertbutylphenol. We show that urea affects amide and t-butyl solubility (lowers the transfer free energy of both amide (backbone) and alkyl (sidechain) groups) in a similar fashion. In other words, preferential interaction of urea with both moieties contributes to protein denaturation.
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Affiliation(s)
- Simisola Ajayi
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Iman Asakereh
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Hanieh Rezasoltani
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - David Davidson
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Mazdak Khajehpour
- Department of Chemistry, the, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
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4
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Hammami F, Issaoui N, Nasr S. Investigation of hydrogen bonded structure of urea-water mixtures through Infra-red spectroscopy and non-covalent interaction (NCI) theoretical approach. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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5
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Dilip.H.N., Chakraborty D. Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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6
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Jaganade T, Chattopadhyay A, Pazhayam NM, Priyakumar UD. Energetic, Structural and Dynamic Properties of Nucleobase-Urea Interactions that Aid in Urea Assisted RNA Unfolding. Sci Rep 2019; 9:8805. [PMID: 31217494 PMCID: PMC6584539 DOI: 10.1038/s41598-019-45010-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 05/28/2019] [Indexed: 01/21/2023] Open
Abstract
Understanding the structure-function relationships of RNA has become increasingly important given the realization of its functional role in various cellular processes. Chemical denaturation of RNA by urea has been shown to be beneficial in investigating RNA stability and folding. Elucidation of the mechanism of unfolding of RNA by urea is important for understanding the folding pathways. In addition to studying denaturation of RNA in aqueous urea, it is important to understand the nature and strength of interactions of the building blocks of RNA. In this study, a systematic examination of the structural features and energetic factors involving interactions between nucleobases and urea is presented. Results from molecular dynamics (MD) simulations on each of the five DNA/RNA bases in water and eight different concentrations of aqueous urea, and free energy calculations using the thermodynamic integration method are presented. The interaction energies between all the nucleobases with the solvent environment and the transfer free energies become more favorable with respect to increase in the concentration of urea. Preferential interactions of urea versus water molecules with all model systems determined using Kirkwood-Buff integrals and two-domain models indicate preference of urea by nucleobases in comparison to water. The modes of interaction between urea and the nucleobases were analyzed in detail. In addition to the previously identified hydrogen bonding and stacking interactions between urea and nucleobases that stabilize the unfolded states of RNA in aqueous solution, NH-π interactions are proposed to be important. Dynamic properties of each of these three modes of interactions have been presented. The study provides fundamental insights into the nature of interaction of urea molecules with nucleobases and how it disrupts nucleic acids.
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Affiliation(s)
- Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Aditya Chattopadhyay
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Nila M Pazhayam
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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7
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Quantum mechanical investigation of the nature of nucleobase-urea stacking interaction, a crucial driving force in RNA unfolding in aqueous urea. J CHEM SCI 2018. [DOI: 10.1007/s12039-018-1563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Jahan I, Nayeem SM. Effect of Urea, Arginine, and Ethanol Concentration on Aggregation of 179CVNITV 184 Fragment of Sheep Prion Protein. ACS OMEGA 2018; 3:11727-11741. [PMID: 30320270 PMCID: PMC6173503 DOI: 10.1021/acsomega.8b00875] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 09/06/2018] [Indexed: 06/08/2023]
Abstract
Understanding protein aggregation is of utmost importance as it is responsible for causing several neurodegenerative diseases and one of the serious impediments in large-scale biopharmaceutical production. The prion protein is responsible for pathological states in fatal transmissible spongiform conditions, such as Creutzfeldt-Jakob disease and bovine spongiform encephalopathy. The peptide fragment 178-191 of Syrian hamster prion protein is known to be amyloidogenic. Here, we identified the fragment 179CVNITV184 as an aggregation-prone fragment in sheep prion protein. This fragment is conserved sequence among sheep and Syrian hamster prion protein and also falls in the previously identified amyloidogenic sequence. The mechanistic details of the aggregation behavior are analyzed in three different concentrations of urea, arginine, and ethanol. Urea and arginine are found to be aggregation suppressors, but ethanol enhances the protein aggregation through β-sheet formation. We have also analyzed the influence of these osmolyte on water dynamics in the presence of the octamer of this aggregation-prone fragment and correlated this water dynamics with the aggregation behavior of the octamer.
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9
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Ahalawat N, Mondal J. Assessment and optimization of collective variables for protein conformational landscape: GB1 β-hairpin as a case study. J Chem Phys 2018; 149:094101. [PMID: 30195312 DOI: 10.1063/1.5041073] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Collective variables (CVs), when chosen judiciously, can play an important role in recognizing rate-limiting processes and rare events in any biomolecular systems. However, high dimensionality and inherent complexities associated with such biochemical systems render the identification of an optimal CV a challenging task, which in turn precludes the elucidation of an underlying conformational landscape in sufficient details. In this context, a relevant model system is presented by a 16-residue β-hairpin of GB1 protein. Despite being the target of numerous theoretical and computational studies for understanding the protein folding, the set of CVs optimally characterizing the conformational landscape of the β-hairpin of GB1 protein has remained elusive, resulting in a lack of consensus on its folding mechanism. Here we address this by proposing a pair of optimal CVs which can resolve the underlying free energy landscape of the GB1 hairpin quite efficiently. Expressed as a linear combination of a number of traditional CVs, the optimal CV for this system is derived by employing the recently introduced time-structured independent component analysis approach on a large number of independent unbiased simulations. By projecting the replica-exchange simulated trajectories along these pair of optimized CVs, the resulting free energy landscape of this system is able to resolve four distinct well-separated metastable states encompassing the extensive ensembles of folded, unfolded, and molten globule states. Importantly, the optimized CVs were found to be capable of automatically recovering a novel partial helical state of this protein, without needing to explicitly invoke helicity as a constituent CV. Furthermore, a quantitative sensitivity analysis of each constituent in the optimized CV provided key insights on the relative contributions of the constituent CVs in the overall free energy landscapes. Finally, the kinetic pathways connecting these metastable states, constructed using a Markov state model, provide an optimum description of the underlying folding mechanism of the peptide. Taken together, this work offers a quantitatively robust approach toward comprehensive mapping of the underlying folding landscape of a quintessential model system along its optimized CV.
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Affiliation(s)
- Navjeet Ahalawat
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research, Center for Interdisciplinary Sciences, Hyderabad 500107, India
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10
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Di Leva FS, Tomassi S, Di Maro S, Reichart F, Notni J, Dangi A, Marelli UK, Brancaccio D, Merlino F, Wester HJ, Novellino E, Kessler H, Marinelli L. Von einer Helix zu einem kleinen Ring: Metadynamik-inspirierte, selektive Liganden für αvβ6-Integrin. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Francesco Saverio Di Leva
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italien
| | - Stefano Tomassi
- DiSTABiF; Università degli Studi della Campania Luigi Vanvitelli; Via Vivaldi 43 81100 Caserta Italien
| | - Salvatore Di Maro
- DiSTABiF; Università degli Studi della Campania Luigi Vanvitelli; Via Vivaldi 43 81100 Caserta Italien
| | - Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Johannes Notni
- Lehrstuhl für Pharmazeutische Radiochemie; Technische Universität München; Walther-Meißner Straße 3 85748 Garching Deutschland
| | - Abha Dangi
- Central NMR Facility and Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road 411008 Pune Indien
| | - Udaya Kiran Marelli
- Institute for Advanced Study and Center of Integrated Protein Science; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
- Central NMR Facility and Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road 411008 Pune Indien
| | - Diego Brancaccio
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italien
| | - Francesco Merlino
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italien
| | - Hans-Jürgen Wester
- Lehrstuhl für Pharmazeutische Radiochemie; Technische Universität München; Walther-Meißner Straße 3 85748 Garching Deutschland
| | - Ettore Novellino
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italien
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Deutschland
| | - Luciana Marinelli
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italien
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11
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Di Leva FS, Tomassi S, Di Maro S, Reichart F, Notni J, Dangi A, Marelli UK, Brancaccio D, Merlino F, Wester HJ, Novellino E, Kessler H, Marinelli L. From a Helix to a Small Cycle: Metadynamics-Inspired αvβ6 Integrin Selective Ligands. Angew Chem Int Ed Engl 2018; 57:14645-14649. [DOI: 10.1002/anie.201803250] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Francesco Saverio Di Leva
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italy
| | - Stefano Tomassi
- DiSTABiF; Università degli Studi della Campania Luigi Vanvitelli; Via Vivaldi 43 81100 Caserta Italy
| | - Salvatore Di Maro
- DiSTABiF; Università degli Studi della Campania Luigi Vanvitelli; Via Vivaldi 43 81100 Caserta Italy
| | - Florian Reichart
- Institute for Advanced Study and Center of Integrated Protein Science; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
| | - Johannes Notni
- Lehrstuhl für Pharmazeutische Radiochemie; Technische Universität München; Walther-Meißner Straße 3 85748 Garching Germany
| | - Abha Dangi
- Central NMR Facility and Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road 411008 Pune India
| | - Udaya Kiran Marelli
- Institute for Advanced Study and Center of Integrated Protein Science; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
- Central NMR Facility and Division of Organic Chemistry; CSIR-National Chemical Laboratory; Dr. Homi Bhabha Road 411008 Pune India
| | - Diego Brancaccio
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italy
| | - Francesco Merlino
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italy
| | - Hans-Jürgen Wester
- Lehrstuhl für Pharmazeutische Radiochemie; Technische Universität München; Walther-Meißner Straße 3 85748 Garching Germany
| | - Ettore Novellino
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italy
| | - Horst Kessler
- Institute for Advanced Study and Center of Integrated Protein Science; Department Chemie; Technische Universität München; Lichtenbergstraße 4 85748 Garching Germany
| | - Luciana Marinelli
- Dipartimento di Farmacia; Università degli Studi di Napoli Federico II; Via D. Montesano 49 80131 Naples Italy
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12
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Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD. Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State. J Am Chem Soc 2017; 139:14931-14946. [DOI: 10.1021/jacs.7b05463] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Siddharth Goyal
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Aditya Chattopadhyay
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Koushik Kasavajhala
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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13
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Gao M, Held C, Patra S, Arns L, Sadowski G, Winter R. Crowders and Cosolvents-Major Contributors to the Cellular Milieu and Efficient Means to Counteract Environmental Stresses. Chemphyschem 2017; 18:2951-2972. [DOI: 10.1002/cphc.201700762] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/15/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Mimi Gao
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Christoph Held
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Satyajit Patra
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Loana Arns
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
| | - Gabriele Sadowski
- TU Dortmund University; Department of Biochemical and Chemical Engineering; Emil-Figge-Str. 70 44227 Dortmund Germany
| | - Roland Winter
- TU Dortmund University; Faculty of Chemistry and Chemical Biology; Physical Chemistry I-Biophysical Chemistry; Otto Hahn Str. 4a 44227 Dortmund Germany
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14
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Gimondi I, Salvalaglio M. CO2 packing polymorphism under pressure: Mechanism and thermodynamics of the I-III polymorphic transition. J Chem Phys 2017; 147:114502. [DOI: 10.1063/1.4993701] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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15
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Saeedi M, Lyubartsev AP, Jalili S. Anesthetics mechanism on a DMPC lipid membrane model: Insights from molecular dynamics simulations. Biophys Chem 2017; 226:1-13. [DOI: 10.1016/j.bpc.2017.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/23/2017] [Accepted: 03/25/2017] [Indexed: 12/20/2022]
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16
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Pathak AK, Bandyopadhyay T. Water isotope effect on the thermostability of a polio viral RNA hairpin: A metadynamics study. J Chem Phys 2017; 146:165104. [DOI: 10.1063/1.4982049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Arup K. Pathak
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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17
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18
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Meloni R, Tiana G. Thermodynamic and structural effect of urea and guanidine chloride on the helical and on a hairpin fragment of GB1 from molecular simulations. Proteins 2017; 85:753-763. [PMID: 28120530 DOI: 10.1002/prot.25255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 02/04/2023]
Abstract
With the help of molecular-dynamics simulations, we studied the effect of urea and guanidine chloride on the thermodynamic and structural properties of the helical fragment of protein GB1, comparing them with those of its second beta hairpin. We showed that the helical fragment in different solvents populates an ensemble of states that is more complex than that of the hairpin, and thus the associated experimental observables (circular-dichroism spectra, secondary chemical shifts, m values), that we back-calculated from the simulations and compared with the actual data, are more difficult to interpret. We observed that in the case of both peptides, urea binds tightly to their backbone, while guanidine exerts its denaturing effect in a more subtle way, strongly affecting the electrostatic properties of the solution. This difference can have consequences in the way denaturation experiments are interpreted. Proteins 2017; 85:753-763. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- R Meloni
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, Milano, 20133, Italy
| | - G Tiana
- Center for Complexity and Biosystems and Department of Physics, Università degli Studi di Milano and INFN, via Celoria 16, Milano, 20133, Italy
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19
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Chen J, Gong X, Zeng C, Wang Y, Zhang G. Mechanical Insight into Resistance of Betaine to Urea-Induced Protein Denaturation. J Phys Chem B 2016; 120:12327-12333. [DOI: 10.1021/acs.jpcb.6b10172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jiantao Chen
- Faculty of Materials Science and
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- College of Light Industry
and Food Sciences, South China University of Technology, Guangzhou 510640, P. R. China
| | - Xiangjun Gong
- Faculty of Materials Science and
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- College of Light Industry
and Food Sciences, South China University of Technology, Guangzhou 510640, P. R. China
| | - Chaoxi Zeng
- Faculty of Materials Science and
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- College of Light Industry
and Food Sciences, South China University of Technology, Guangzhou 510640, P. R. China
| | - Yonghua Wang
- Faculty of Materials Science and
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- College of Light Industry
and Food Sciences, South China University of Technology, Guangzhou 510640, P. R. China
| | - Guangzhao Zhang
- Faculty of Materials Science and
Engineering, South China University of Technology, Guangzhou 510640, P. R. China
- College of Light Industry
and Food Sciences, South China University of Technology, Guangzhou 510640, P. R. China
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20
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Du H, Liu Z, Jennings R, Qian X. The effects of salt ions on the dynamics and thermodynamics of lysozyme unfolding. SEP SCI TECHNOL 2016. [DOI: 10.1080/01496395.2016.1229336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Hongbo Du
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Zizhao Liu
- Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Renee Jennings
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
| | - Xianghong Qian
- Department of Biomedical Engineering, University of Arkansas, Fayetteville, Arkansas, USA
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21
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Aznauryan M, Delgado L, Soranno A, Nettels D, Huang JR, Labhardt AM, Grzesiek S, Schuler B. Comprehensive structural and dynamical view of an unfolded protein from the combination of single-molecule FRET, NMR, and SAXS. Proc Natl Acad Sci U S A 2016; 113:E5389-98. [PMID: 27566405 PMCID: PMC5027429 DOI: 10.1073/pnas.1607193113] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The properties of unfolded proteins are essential both for the mechanisms of protein folding and for the function of the large group of intrinsically disordered proteins. However, the detailed structural and dynamical characterization of these highly dynamic and conformationally heterogeneous ensembles has remained challenging. Here we combine and compare three of the leading techniques for the investigation of unfolded proteins, NMR spectroscopy (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET), with the goal of quantitatively testing their consistency and complementarity and for obtaining a comprehensive view of the unfolded-state ensemble. Using unfolded ubiquitin as a test case, we find that its average dimensions derived from FRET and from structural ensembles calculated using the program X-PLOR-NIH based on NMR and SAXS restraints agree remarkably well; even the shapes of the underlying intramolecular distance distributions are in good agreement, attesting to the reliability of the approaches. The NMR-based results provide a highly sensitive way of quantifying residual structure in the unfolded state. FRET-based nanosecond fluorescence correlation spectroscopy allows long-range distances and chain dynamics to be probed in a time range inaccessible by NMR. The combined techniques thus provide a way of optimally using the complementarity of the available methods for a quantitative structural and dynamical description of unfolded proteins both at the global and the local level.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | | | - Andrea Soranno
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Jie-Rong Huang
- Institute of Biochemistry and Molecular Biology, National Yang Ming University, Taipei City 112, Taiwan
| | | | | | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland; Department of Physics, University of Zurich, 8057 Zurich, Switzerland
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22
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Sun H, Chen P, Li D, Li Y, Hou T. Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1. J Chem Theory Comput 2016; 12:851-60. [DOI: 10.1021/acs.jctc.5b00973] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | | | | | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
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23
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Owczarz M, Casalini T, Motta AC, Morbidelli M, Arosio P. Contribution of Electrostatics in the Fibril Stability of a Model Ionic-Complementary Peptide. Biomacromolecules 2015; 16:3792-801. [PMID: 26594824 DOI: 10.1021/acs.biomac.5b01092] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In this work we quantified the role of electrostatic interactions in the self-assembly of a model amphiphilic peptide (RADA 16-I) into fibrillar structures by a combination of size exclusion chromatography and molecular simulations. For the peptide under investigation, it is found that a net charge of +0.75 represents the ideal condition to promote the formation of regular amyloid fibrils. Lower net charges favor the formation of amorphous precipitates, while larger net charges destabilize the fibrillar aggregates and promote a reversible dissociation of monomers from the ends of the fibrils. By quantifying the dependence of the equilibrium constant of this reversible reaction on the pH value and the peptide net charge, we show that electrostatic interactions contribute largely to the free energy of fibril formation. The addition of both salt and a charged destabilizer (guanidinium hydrochloride) at moderate concentration (0.3-1 M) shifts the monomer-fibril equilibrium toward the fibrillar state. Whereas the first effect can be explained by charge screening of electrostatic repulsion only, the promotion of fibril formation in the presence of guanidinium hydrochloride is also attributed to modifications of the peptide conformation. The results of this work indicate that the global peptide net charge is a key property that correlates well with the fibril stability, although the peptide conformation and the surface charge distribution also contribute to the aggregation propensity.
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Affiliation(s)
- Marta Owczarz
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Tommaso Casalini
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Anna C Motta
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Massimo Morbidelli
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Paolo Arosio
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
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24
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Peter EK, Pivkin IV, Shea JE. A kMC-MD method with generalized move-sets for the simulation of folding of α-helical and β-stranded peptides. J Chem Phys 2015; 142:144903. [DOI: 10.1063/1.4915919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Emanuel K. Peter
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Igor V. Pivkin
- Faculty of Informatics, Institute of Computational Science, University of Lugano, Lugano, Switzerland
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, and Department of Physics, University of California, Santa Barbara, California 93106, USA
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25
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Kasavajhala K, Bikkina S, Patil I, MacKerell AD, Priyakumar UD. Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution. J Phys Chem B 2015; 119:3755-61. [PMID: 25668757 DOI: 10.1021/jp512414f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Urea has long been used to investigate protein folding and, more recently, RNA folding. Studies have proposed that urea denatures RNA by participating in stacking interactions and hydrogen bonds with nucleic acid bases. In this study, the ability of urea to form unconventional stacking interactions with RNA bases is investigated using ab initio calculations (RI-MP2 and CCSD(T) methods with the aug-cc-pVDZ basis set). A total of 29 stable nucleobase-urea stacked complexes are identified in which the intermolecular interaction energies (up to -14 kcal/mol) are dominated by dispersion effects. Natural bond orbital (NBO) and atoms in molecules (AIM) calculations further confirm strong interactions between urea and nucleobases. Calculations on model systems with multiple urea and water molecules interacting with a guanine base lead to a hypothesis that urea molecules along with water are able to form cage-like structures capable of trapping nucleic acid bases in extrahelical states by forming both hydrogen-bonded and dispersion interactions, thereby contributing to the unfolding of RNA in the presence of urea in aqueous solution.
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Affiliation(s)
- Koushik Kasavajhala
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad, 500032, India
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26
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Ardevol A, Tribello GA, Ceriotti M, Parrinello M. Probing the Unfolded Configurations of a β-Hairpin Using Sketch-Map. J Chem Theory Comput 2015; 11:1086-93. [DOI: 10.1021/ct500950z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Albert Ardevol
- Computational
Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
| | - Gareth A. Tribello
- Atomistic
Simulation Centre, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Michele Ceriotti
- Laboratory
of Computational Science and Modelling, EPFL, CH-1015 Lausanne, Switzerland
| | - Michele Parrinello
- Computational
Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI-Campus, Via Giuseppe Buffi 13, C-6900 Lugano, Switzerland
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27
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Abstract
The publication of high-resolution structures for all of the opioid receptor subfamilies has unveiled exciting opportunities for mechanistic insight into the molecular mechanisms underlying the biology of nociception, reward, and higher cognitive functions, as well as promises for progress in several clinical areas such as pain management, physiological dependence, addiction, and mood disorders. To turn this promise into novel and improved therapeutic entities, however, this information needs to be supplemented with research strategies that explore the dynamic behavior of the proteins and their interactions with other receptors and ligands in their physiological environment.Here we describe state-of-the-art molecular dynamics computational protocols, based on all-atom and coarse-grained modeling techniques, designed to estimate crucial thermodynamic and kinetic parameters describing the binding of small-molecule ligands and the formation of supramolecular complexes.
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28
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Barducci A, Pfaendtner J, Bonomi M. Tackling sampling challenges in biomolecular simulations. Methods Mol Biol 2015; 1215:151-71. [PMID: 25330963 DOI: 10.1007/978-1-4939-1465-4_8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular dynamics (MD) simulations are a powerful tool to give an atomistic insight into the structure and dynamics of proteins. However, the time scales accessible in standard simulations, which often do not match those in which interesting biological processes occur, limit their predictive capabilities. Many advanced sampling techniques have been proposed over the years to overcome this limitation. This chapter focuses on metadynamics, a method based on the introduction of a time-dependent bias potential to accelerate sampling and recover equilibrium properties of a few descriptors that are able to capture the complexity of a process at a coarse-grained level. The theory of metadynamics and its combination with other popular sampling techniques such as the replica exchange method is briefly presented. Practical applications of these techniques to the study of the Trp-Cage miniprotein folding are also illustrated. The examples contain a guide for performing these calculations with PLUMED, a plugin to perform enhanced sampling simulations in combination with many popular MD codes.
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Affiliation(s)
- Alessandro Barducci
- Laboratory of Statistical Biophysics, School of Basic Sciences, Ecole Polytechnique Fédérale de Lausanne, 1015, Lausanne, Switzerland
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29
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Bandyopadhyay D, Mohan S, Ghosh SK, Choudhury N. Molecular Dynamics Simulation of Aqueous Urea Solution: Is Urea a Structure Breaker? J Phys Chem B 2014; 118:11757-68. [DOI: 10.1021/jp505147u] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dibyendu Bandyopadhyay
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Sadhana Mohan
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Swapan K. Ghosh
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Niharendu Choudhury
- Heavy water Division and ‡Theoretical Chemistry
Section, Bhabha Atomic Research Centre, Mumbai 400 085, India
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30
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On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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31
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Bian Y, Zhang J, Wang J, Wang W. On the accuracy of metadynamics and its variations in a protein folding process. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.931680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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32
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Sun H, Li Y, Tian S, Wang J, Hou T. P-loop conformation governed crizotinib resistance in G2032R-mutated ROS1 tyrosine kinase: clues from free energy landscape. PLoS Comput Biol 2014; 10:e1003729. [PMID: 25033171 PMCID: PMC4102447 DOI: 10.1371/journal.pcbi.1003729] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 06/02/2014] [Indexed: 01/04/2023] Open
Abstract
Tyrosine kinases are regarded as excellent targets for chemical drug therapy of carcinomas. However, under strong purifying selection, drug resistance usually occurs in the cancer cells within a short term. Many cases of drug resistance have been found to be associated with secondary mutations in drug target, which lead to the attenuated drug-target interactions. For example, recently, an acquired secondary mutation, G2032R, has been detected in the drug target, ROS1 tyrosine kinase, from a crizotinib-resistant patient, who responded poorly to crizotinib within a very short therapeutic term. It was supposed that the mutation was located at the solvent front and might hinder the drug binding. However, a different fact could be uncovered by the simulations reported in this study. Here, free energy surfaces were characterized by the drug-target distance and the phosphate-binding loop (P-loop) conformational change of the crizotinib-ROS1 complex through advanced molecular dynamics techniques, and it was revealed that the more rigid P-loop region in the G2032R-mutated ROS1 was primarily responsible for the crizotinib resistance, which on one hand, impaired the binding of crizotinib directly, and on the other hand, shortened the residence time induced by the flattened free energy surface. Therefore, both of the binding affinity and the drug residence time should be emphasized in rational drug design to overcome the kinase resistance. Cancers can eventually confer drug resistance to the continued medication. In most cases, mutations occurred in a drug target can attenuate the binding affinity of the drugs. Here, we studied the drug resistance mechanisms of the mutations G2032R in the ROS1 tyrosine kinase in fusion-type NSCLC. It is well known that the phosphate-binding loop (P-loop) plays a vital role in the binding of competitive inhibitors in tyrosine kinases, and numerous mutations have been found occurred around the P-loop, which may affect the binding/unbinding process of a drug. Free energy surfaces were constructed to characterize the impact of the mutation to the binding/unbinding process of a well-known NSCLC drug, crizotinib. Two advanced free energy calculation methods, namely funnel based well-tempered metadynamics and umbrella sampling based absolute binding free energy calculation achieved consistent results with the experimental data, suggesting that the rigid P-loop of the mutated target was mainly responsible for the crizotinib resistance to ROS1 tyrosine kinase.
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Affiliation(s)
- Huiyong Sun
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Sheng Tian
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
| | - Junmei Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tingjun Hou
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, Suzhou, Jiangsu, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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33
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Ray S, Bender S, Kang S, Lin R, Glicksman MA, Liu M. The Parkinson disease-linked LRRK2 protein mutation I2020T stabilizes an active state conformation leading to increased kinase activity. J Biol Chem 2014; 289:13042-53. [PMID: 24695735 DOI: 10.1074/jbc.m113.537811] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effect of leucine-rich repeat kinase 2 (LRRK2) mutation I2020T on its kinase activity has been controversial, with both increased and decreased effects being reported. We conducted steady-state and pre-steady-state kinetic studies on LRRKtide and its analog LRRKtide(S). Their phosphorylation differs by the rate-limiting steps: product release is rate-limiting for LRRKtide and phosphoryl transfer is rate-limiting for LRRKtide(S). As a result, we observed that the I2020T mutant is more active than wild type (WT) LRRK2 for LRRKtide(S) phosphorylation, whereas it is less active than WT for LRRKtide phosphorylation. Our pre-steady-state kinetic data suggest that (i) the I2020T mutant accelerates the rates of phosphoryl transfer of both reactions by 3-7-fold; (ii) this increase is masked by a rate-limiting product release step for LRRKtide phosphorylation; and (iii) the observed lower activity of the mutant for LRRKtide phosphorylation is a consequence of its instability: the concentration of the active form of the mutant is 3-fold lower than WT. The I2020T mutant has a dramatically low KATP and therefore leads to resistance to ATP competitive inhibitors. Two well known DFG-out or type II inhibitors are also weaker toward the mutant because they inhibit the mutant in an unexpected ATP competitive mechanism. The I2020 residue lies next to the DYG motif of the activation loop of the LRRK2 kinase domain. Our modeling and metadynamic simulations suggest that the I2020T mutant stabilizes the DYG-in active conformation and creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP competitive fashion.
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Affiliation(s)
- Soumya Ray
- From the Laboratory for Drug Discovery in Neurodegeneration, Harvard NeuroDiscovery Center, and
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34
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Piana S, Klepeis JL, Shaw DE. Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations. Curr Opin Struct Biol 2014; 24:98-105. [DOI: 10.1016/j.sbi.2013.12.006] [Citation(s) in RCA: 294] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/19/2013] [Accepted: 12/20/2013] [Indexed: 01/15/2023]
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35
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Meloni R, Camilloni C, Tiana G. Sampling the Denatured State of Polypeptides in Water, Urea, and Guanidine Chloride to Strict Equilibrium Conditions with the Help of Massively Parallel Computers. J Chem Theory Comput 2014; 10:846-54. [DOI: 10.1021/ct400879v] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Roberto Meloni
- Department of Physics, Università degli Studi di Milano, via Celoria 16, 20133 Milano, Italy
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Guido Tiana
- Department of Physics, Università degli Studi di Milano, and INFN, via Celoria 16, 20133 Milano, Italy
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36
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 291] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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37
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Cai Z, Li J, Yin C, Yang Z, Wu J, Zhou R. Effect of urea concentration on aggregation of amyloidogenic hexapeptides (NFGAIL). J Phys Chem B 2013; 118:48-57. [PMID: 24328094 DOI: 10.1021/jp407776e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We have performed large-scale all-atom molecular dynamics (MD) simulations to study the aggregation behavior of four NFGAIL hexapeptides in the aqueous urea solution, with a urea concentration ranging from 0 to 5 M. We find that urea in general suppresses the peptide aggregation, but suppression slows down in the intermediation concentration regime around 3 M. Two competing mechanisms of urea are determined: urea molecules accumulated near the first solvation shell (FSS) tend to unfold the hexapeptide, which favors aggregation; on the other hand, the tight hydrogen bonds formed between urea and peptide mainchains hinder the association of peptides which disfavors the formation of the β-sheet. Furthermore, the different nonlinear urea concentration dependences of the urea-peptide and peptide-peptide hydrogen bonds lead to a nonmonotonic behavior, with a weak enhancement in the peptide aggregation around 3 M.
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Affiliation(s)
- Zhuowei Cai
- Department of Physics, Zhejiang University , Hangzhou, 310027, China
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38
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Candotti M, Pérez A, Ferrer-Costa C, Rueda M, Meyer T, Gelpí JL, Orozco M. Exploring early stages of the chemical unfolding of proteins at the proteome scale. PLoS Comput Biol 2013; 9:e1003393. [PMID: 24348236 PMCID: PMC3861036 DOI: 10.1371/journal.pcbi.1003393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 10/29/2013] [Indexed: 11/18/2022] Open
Abstract
After decades of using urea as denaturant, the kinetic role of this molecule in the unfolding process is still undefined: does urea actively induce protein unfolding or passively stabilize the unfolded state? By analyzing a set of 30 proteins (representative of all native folds) through extensive molecular dynamics simulations in denaturant (using a range of force-fields), we derived robust rules for urea unfolding that are valid at the proteome level. Irrespective of the protein fold, presence or absence of disulphide bridges, and secondary structure composition, urea concentrates in the first solvation shell of quasi-native proteins, but with a density lower than that of the fully unfolded state. The presence of urea does not alter the spontaneous vibration pattern of proteins. In fact, it reduces the magnitude of such vibrations, leading to a counterintuitive slow down of the atomic-motions that opposes unfolding. Urea stickiness and slow diffusion is, however, crucial for unfolding. Long residence urea molecules placed around the hydrophobic core are crucial to stabilize partially open structures generated by thermal fluctuations. Our simulations indicate that although urea does not favor the formation of partially open microstates, it is not a mere spectator of unfolding that simply displaces to the right of the folded←→unfolded equilibrium. On the contrary, urea actively favors unfolding: it selects and stabilizes partially unfolded microstates, slowly driving the protein conformational ensemble far from the native one and also from the conformations sampled during thermal unfolding. The delicate equilibrium between the folded and functional structure of a protein and its unfolded state is highly dependent on environmental variables such as the solvent. For example the co-solvent urea is a well-known protein denaturant that displaces the equilibrium towards unstructured and non-functional conformations of proteins. However the molecular mechanism behind its ability remains an enigma and the interpretation of the experimental data is still ambiguous. By analyzing a set of representative proteins through extensive molecular dynamics simulations in urea, we provide a robust and consensus picture of the first stages of urea-driven protein unfolding and elucidate the role of urea in accelerating protein unfolding. Our results suggest that urea, thanks to its stickiness and slow diffusion, benefits from the intrinsic flexibility of proteins and stabilizes partially open-states, slowly driving the protein toward unfolding.
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Affiliation(s)
- Michela Candotti
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain
| | - Alberto Pérez
- Laufer Center, Stony Brook University, Stony Brook, New York, United States of America
| | - Carles Ferrer-Costa
- Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain
| | - Manuel Rueda
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tim Meyer
- Theoretische und Computergestützte Biophysik, Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Josep Lluís Gelpí
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain
- Joint Research Program in Computational Biology, Institute for Research in Biomedicine and Barcelona Supercomputing Center, Barcelona, Spain
- Department of Biochemistry and Molecular Biology, University of Barcelona, Barcelona, Spain
- * E-mail:
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39
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Free-energy landscape of protein oligomerization from atomistic simulations. Proc Natl Acad Sci U S A 2013; 110:E4708-13. [PMID: 24248370 DOI: 10.1073/pnas.1320077110] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage.
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40
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Mukherji D, Kremer K. Coil–Globule–Coil Transition of PNIPAm in Aqueous Methanol: Coupling All-Atom Simulations to Semi-Grand Canonical Coarse-Grained Reservoir. Macromolecules 2013. [DOI: 10.1021/ma401877c] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Debashish Mukherji
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max-Planck Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany
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41
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Carr JK, Buchanan LE, Schmidt JR, Zanni MT, Skinner JL. Structure and dynamics of urea/water mixtures investigated by vibrational spectroscopy and molecular dynamics simulation. J Phys Chem B 2013; 117:13291-300. [PMID: 23841646 DOI: 10.1021/jp4037217] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Urea/water is an archetypical "biological" mixture and is especially well-known for its relevance to protein thermodynamics as urea acts as a protein denaturant at high concentration. This behavior has given rise to an extended debate concerning urea's influence on water structure. On the basis of a variety of methods and of definitions of the water structure, urea has been variously described as a structure-breaker, a structure-maker, or as remarkably neutral toward water. Because of its sensitivity to microscopic structure and dynamics, vibrational spectroscopy can help resolve these debates. We report experimental and theoretical spectroscopic results for the OD stretch of HOD/H2O/urea mixtures (linear IR, 2DIR, and pump-probe anisotropy decay) and for the CO stretch of urea-D4/D2O mixtures (linear IR only). Theoretical results are obtained using existing approaches for water and a modification of a frequency map developed for acetamide. All absorption spectra are remarkably insensitive to urea concentration, consistent with the idea that urea only very weakly perturbs the water structure. Both this work and experiments by Rezus and Bakker, however, show that water's rotational dynamics are slowed down by urea. Analysis of the simulations casts doubt on the suggestion that urea immobilizes particular doubly hydrogen bonded water molecules.
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Affiliation(s)
- J K Carr
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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42
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Koishi T, Yasuoka K, Willow SY, Fujikawa S, Zeng XC. Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study. J Chem Theory Comput 2013; 9:2540-51. [PMID: 26583851 DOI: 10.1021/ct3010968] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have designed various nanoslit systems, whose opposing surfaces can be either hydrophobic, hydrophilic, or simply a water-vapor interface, for the molecular dynamics simulation of confined water with three different protein denaturants, i.e., urea, guanidinium chloride (GdmCl), and methanol, respectively. Particular attention is placed on the preferential adsorption of the denaturant molecules onto the opposing surfaces and associated resident time in the vicinal layer next to the surfaces, as well as their implication in the denaturing efficiency of different denaturant molecules. Our simulation results show that among the three denaturants, the occupancy of methanol in the vicinal layer is the highest while the residence time of Gdm is the longest. Although the occupancy and the residence time of urea in the vicinal layer is less than those of the other two denaturant molecules, urea entails "all-around" properties for being a highly effective denaturant. The distinct characteristics of three denaturants may suggest a different molecular mechanism for the protein denaturation. This comparative simulation by design allows us to gain additional insights, on the molecular level, into the denaturation effect and related hydrophobic effect.
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Affiliation(s)
- Takahiro Koishi
- Department of Applied Physics, University of Fukui, 3-9-1 Bunkyo,Fukui 910-8507, Japan
| | - Kenji Yasuoka
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Soohaeng Yoo Willow
- Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, South Korea
| | - Shigenori Fujikawa
- International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
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43
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Toward an atomistic description of the urea-denatured state of proteins. Proc Natl Acad Sci U S A 2013; 110:5933-8. [PMID: 23536295 DOI: 10.1073/pnas.1216589110] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present here the characterization of the structural, dynamics, and energetics of properties of the urea-denatured state of ubiquitin, a small prototypical soluble protein. By combining state-of-the-art molecular dynamics simulations with NMR and small-angle X-ray scattering data, we were able to: (i) define the unfolded state ensemble, (ii) understand the energetics stabilizing unfolded structures in urea, (iii) describe the dedifferential nature of the interactions of the fully unfolded proteins with urea and water, and (iv) characterize the early stages of protein refolding when chemically denatured proteins are transferred to native conditions. The results presented herein are unique in providing a complete picture of the chemically unfolded state of proteins and contribute to deciphering the mechanisms that stabilize the native state of proteins, as well as those that maintain them unfolded in the presence of urea.
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44
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Liu M, Bender SA, Cuny GD, Sherman W, Glicksman M, Ray SS. Type II kinase inhibitors show an unexpected inhibition mode against Parkinson's disease-linked LRRK2 mutant G2019S. Biochemistry 2013; 52:1725-36. [PMID: 23379419 PMCID: PMC3966205 DOI: 10.1021/bi3012077] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A number of well-known type II inhibitors (ATP-noncompetitive) that bind kinases in their DFG-out conformation were tested against wild-type LRRK2 and the most common Parkinson's disease-linked mutation, G2019S. We found that traditional type II inhibitors exhibit surprising variability in their inhibition mechanism between the wild type (WT) and the G2019S mutant of LRRK2. The type II kinase inhibitors were found to work in an ATP-competitive fashion against the G2019S mutant, whereas they appear to follow the expected noncompetitive mechanism against WT. Because the G2019S mutation lies in the DXG motif (DYG in LRRK2 but DFG in most other kinases) of the activation loop, we explored the structural consequence of the mutation on loop dynamics using an enhanced sampling method called metadynamics. The simulations suggest that the G2019S mutation stabilizes the DYG-in state of LRRK2 through a series of hydrogen bonds, leading to an increase in the conformational barrier between the active and inactive forms of the enzyme and a relative stabilization of the active form. The conformational bias toward the active form of LRRK2 mutants has two primary consequences. (1) The mutant enzyme becomes hyperactive, a known contributor to the Parkinsonian phenotype, as a consequence of being "locked" into the activated state, and (2) the mutation creates an unusual allosteric pocket that can bind type II inhibitors but in an ATP-competitive fashion. Our results suggest that developing type II inhibitors, which are generally considered superior to type I inhibitors because of desirable selectivity profiles, might be especially challenging for the G2019S LRRK2 mutant.
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Affiliation(s)
- Min Liu
- Harvard NeuroDiscovery Center, Harvard University, 65 Landsdowne St., #452, Cambridge, MA 02139
| | | | - Gregory D Cuny
- Harvard NeuroDiscovery Center, Harvard University, 65 Landsdowne St., #452, Cambridge, MA 02139
| | - Woody Sherman
- Schrodinger, 120 W. 45 Street, New York, NY, 10036
- Proteus Discovery Inc. 411 Massachusetts avenue, Cambridge, MA 02139-410
| | - Marcie Glicksman
- Harvard NeuroDiscovery Center, Harvard University, 65 Landsdowne St., #452, Cambridge, MA 02139
| | - Soumya S. Ray
- Harvard NeuroDiscovery Center, Harvard University, 65 Landsdowne St., #452, Cambridge, MA 02139
- Department of Neurology, Brigham and Women’s Hospital
- Center for Neurologic Diseases, Brigham and Women’s Hospital
- Proteus Discovery Inc. 411 Massachusetts avenue, Cambridge, MA 02139-410
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45
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Vagenende V, Trout BL. Quantitative characterization of local protein solvation to predict solvent effects on protein structure. Biophys J 2013; 103:1354-62. [PMID: 22995508 DOI: 10.1016/j.bpj.2012.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 07/19/2012] [Accepted: 08/03/2012] [Indexed: 12/14/2022] Open
Abstract
Characterization of solvent preferences of proteins is essential to the understanding of solvent effects on protein structure and stability. Although it is generally believed that solvent preferences at distinct loci of a protein surface may differ, quantitative characterization of local protein solvation has remained elusive. In this study, we show that local solvation preferences can be quantified over the entire protein surface from extended molecular dynamics simulations. By subjecting microsecond trajectories of two proteins (lysozyme and antibody fragment D1.3) in 4 M glycerol to rigorous statistical analyses, solvent preferences of individual protein residues are quantified by local preferential interaction coefficients. Local solvent preferences for glycerol vary widely from residue to residue and may change as a result of protein side-chain motions that are slower than the longest intrinsic solvation timescale of ∼10 ns. Differences of local solvent preferences between distinct protein side-chain conformations predict solvent effects on local protein structure in good agreement with experiment. This study extends the application scope of preferential interaction theory and enables molecular understanding of solvent effects on protein structure through comprehensive characterization of local protein solvation.
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Affiliation(s)
- Vincent Vagenende
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A STAR), Centros, Singapore.
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46
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De Sancho D, Mittal J, Best RB. Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation. J Chem Theory Comput 2013; 9:1743-53. [PMID: 26587632 DOI: 10.1021/ct301033r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The C-terminal β-hairpin of protein G is a 16-residue peptide that folds in a two-state fashion akin to many larger proteins. However, with an experimental folding time of ∼6 μs, it remains a challenging system for all-atom, explicitly solvated, molecular dynamics simulations. Here, we use a large simulation data set (0.7 ms total) of the hairpin at 300 and 350 K to interpret its folding via a master equation approach. We find a separation of over an order of magnitude between the longest and second longest relaxation times, with the slowest relaxation corresponding to folding. However, in spite of this apparent two-state dynamics, the folding rate determined based on a first-passage time analysis depends on the initial conditions chosen, with a nonexponential distribution of first passage times being obtained in some cases. Using the master equation model, we are now able to account quantitatively for the observed distribution of first passage times. The deviation from the expected exponential distribution for a two-state system arises from slow dynamics in the unfolded state, associated with formation and melting of helical structures. Our results help to reconcile recent findings of slow dynamics in unfolded proteins with observed two-state folding kinetics. At the same time, they indicate that care is required in estimating folding kinetics from many short folding simulations. Last, we are able to use the master equation model to obtain details of the folding mechanism and folding transition state, which appear consistent with the "zipper" mechanism inferred from the experiment.
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Affiliation(s)
- David De Sancho
- Cambridge University, Department of Chemistry, Lensfield Road Cambridge CB2 1EW, United Kingdom
| | - Jeetain Mittal
- Department of Chemical Engineering, 111 Research Drive, Iacocca Hall, Bethlehem, Pennsylvania 18015, United States
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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47
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Abstract
Proteins are marginally stable, and the folding/unfolding equilibrium of proteins in aqueous solution can easily be altered by the addition of small organic molecules known as cosolvents. Cosolvents that shift the equilibrium toward the unfolded ensemble are termed denaturants, whereas those that favor the folded ensemble are known as protecting osmolytes. Urea is a widely used denaturant in protein folding studies, and the molecular mechanism of its action has been vigorously debated in the literature. Here we review recent experimental as well as computational studies that show an emerging consensus in this problem. Urea has been shown to denature proteins through a direct mechanism, by interacting favorably with the peptide backbone as well as the amino acid side chains. In contrast, the molecular mechanism by which the naturally occurring protecting osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins is not clear. Recent studies have established the strong interaction of TMAO with water. Detailed molecular simulations, when used with force fields that incorporate these interactions, can provide insight into this problem. We present the development of a model for TMAO that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins.
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Affiliation(s)
- Deepak R Canchi
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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48
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Kleinjung J, Fraternali F. Urea-Water Solvation Forces on Prion Structures. J Chem Theory Comput 2012; 8:3977-3984. [PMID: 23066353 PMCID: PMC3466777 DOI: 10.1021/ct300264w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Indexed: 01/28/2023]
Abstract
Solvation forces are crucial determinants in the equilibrium between the folded and unfolded state of proteins. Particularly interesting are the solvent forces of denaturing solvent mixtures on folded and misfolded states of proteins involved in neurodegeneration. The C-terminal globular domain of the ovine prion protein (1UW3) and its analogue H2H3 in the α-rich and β-rich conformation were used as model structures to study the solvation forces in 4 M aqueous urea using molecular dynamics. The model structures display very different secondary structures and solvent exposures. Most protein atoms favor interactions with urea over interactions with water. The force difference between protein-urea and protein-water interactions correlates with hydrophobicity; i.e., urea interacts preferentially with hydrophobic atoms, in agreement with results from solvent transfer experiments. Solvent Shannon entropy maps illustrate the mobility gradient of the urea-water mixture from the first solvation shell to the bulk. Single urea molecules replace water in the first solvation shell preferably at locations of relatively high solvent entropy.
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Affiliation(s)
- Jens Kleinjung
- Division of Mathematical Biology,
MRC National Institute for Medical Research, The Ridgeway, Mill Hill,
London NW7 1AA, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and
Molecular Biophysics, King’s College London, New Hunt’s
House, London SE1 1UL, United Kingdom
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49
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Salvalaglio M, Vetter T, Giberti F, Mazzotti M, Parrinello M. Uncovering Molecular Details of Urea Crystal Growth in the Presence of Additives. J Am Chem Soc 2012; 134:17221-33. [DOI: 10.1021/ja307408x] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matteo Salvalaglio
- Institute of Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
- Department of Chemistry and
Applied Biosciences, ETH Zurich, Zurich,
Switzerland
| | - Thomas Vetter
- Institute of Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Federico Giberti
- Department of Chemistry and
Applied Biosciences, ETH Zurich, Zurich,
Switzerland
| | - Marco Mazzotti
- Institute of Process Engineering, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Michele Parrinello
- Department of Chemistry and
Applied Biosciences, ETH Zurich, Zurich,
Switzerland
- Facoltà
di Informatica,
Istituto di Scienze Computazionali, Università della Svizzera Italiana Via G. Buffi 13, 6900 Lugano
Switzerland
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50
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Johnston JM, Wang H, Provasi D, Filizola M. Assessing the relative stability of dimer interfaces in g protein-coupled receptors. PLoS Comput Biol 2012; 8:e1002649. [PMID: 22916005 PMCID: PMC3420924 DOI: 10.1371/journal.pcbi.1002649] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 06/29/2012] [Indexed: 11/18/2022] Open
Abstract
Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors (GPCRs) associate in the plasma membrane to form homo- and/or heteromers. Nevertheless, the stoichiometry, fraction and lifetime of such receptor complexes in living cells remain topics of intense debate. Motivated by experimental data suggesting differing stabilities for homomers of the cognate human β1- and β2-adrenergic receptors, we have carried out approximately 160 microseconds of biased molecular dynamics simulations to calculate the dimerization free energy of crystal structure-based models of these receptors, interacting at two interfaces that have often been implicated in GPCR association under physiological conditions. Specifically, results are presented for simulations of coarse-grained (MARTINI-based) and atomistic representations of each receptor, in homodimeric configurations with either transmembrane helices TM1/H8 or TM4/3 at the interface, in an explicit lipid bilayer. Our results support a definite contribution to the relative stability of GPCR dimers from both interface sequence and configuration. We conclude that β1- and β2-adrenergic receptor homodimers with TM1/H8 at the interface are more stable than those involving TM4/3, and that this might be reconciled with experimental studies by considering a model of oligomerization in which more stable TM1 homodimers diffuse through the membrane, transiently interacting with other protomers at interfaces involving other TM helices.
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Affiliation(s)
| | | | | | - Marta Filizola
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, New York, United States of America
- * E-mail:
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