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Qi G, Vrettas MD, Biancaniello C, Sanz-Hernandez M, Cafolla CT, Morgan JWR, Wang Y, De Simone A, Wales DJ. Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data. J Chem Theory Comput 2022; 18:7733-7750. [PMID: 36395419 DOI: 10.1021/acs.jctc.2c00657] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Some recent advances in biomolecular simulation and global optimization have used hybrid restraint potentials, where harmonic restraints that penalize conformations inconsistent with experimental data are combined with molecular mechanics force fields. These hybrid potentials can be used to improve the performance of molecular dynamics, structure prediction, energy landscape sampling, and other computational methods that rely on the accuracy of the underlying force field. Here, we develop a hybrid restraint potential based on NapShift, an artificial neural network trained to predict protein nuclear magnetic resonance (NMR) chemical shifts from sequence and structure. In addition to providing accurate predictions of experimental chemical shifts, NapShift is fully differentiable with respect to atomic coordinates, which allows us to use it for structural refinement. By employing NapShift to predict chemical shifts from the protein conformation at each simulation step, we can compute an energy penalty and the corresponding hybrid restraint forces based on the difference between the predicted values and the experimental chemical shifts. The performance of the hybrid restraint potential was benchmarked using both basin-hopping global optimization and molecular dynamics simulations. In each case, the NapShift hybrid potential improved the accuracy, leading to better structure prediction via basin-hopping and increased local stability in molecular dynamics simulations. Our results suggest that neural network hybrid potentials based on NMR observables can enhance a broad range of molecular simulation methods, and the prediction accuracy will improve as more experimental training data become available.
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Affiliation(s)
- Guowei Qi
- Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, U.K
| | - Michail D Vrettas
- Department of Pharmacy, University of Naples Federico II, 80131Naples, Italy
| | - Carmen Biancaniello
- Department of Pharmacy, University of Naples Federico II, 80131Naples, Italy
| | - Maximo Sanz-Hernandez
- Department of Life Sciences, Imperial College London, South Kensington, LondonSW7 2AZ, U.K
| | - Conor T Cafolla
- Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, U.K
| | - John W R Morgan
- Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, U.K
| | - Yifei Wang
- Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, U.K
| | - Alfonso De Simone
- Department of Pharmacy, University of Naples Federico II, 80131Naples, Italy
| | - David J Wales
- Department of Chemistry, University of Cambridge, Lensfield Road, CambridgeCB2 1EW, U.K
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2
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Ilie IM, Caflisch A. Antibody binding increases the flexibility of the prion protein. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140827. [PMID: 35931365 DOI: 10.1016/j.bbapap.2022.140827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/29/2022] [Accepted: 07/27/2022] [Indexed: 06/15/2023]
Abstract
Prion diseases are associated with the conversion of the cellular prion protein (PrP) into a pathogenic conformer (PrPSc). A proposed therapeutic approach to avoid the pathogenic transformation is to develop antibodies that bind to PrP and stabilize its structure. POM1 and POM6 are two monoclonal antibodies that bind the globular domain of PrP and have different biological responses, i.e., trigger neurotoxicity mimicking prion infections (POM1) or prevent neurotoxicity (POM6). The crystal structures of PrP in complex with the two antibodies show similar epitopes which seems inconsistent with the opposite phenotypes. Here, we investigate the influence of the POM1 and POM6 antibodies on the flexibility of the mouse PrP by molecular dynamics simulations. The simulations reveal that the POM6/PrP interface is less stable than the POM1/PrP interface, ascribable to localized polar mismatches at the interface, despite the former complex having a larger epitope than the latter. In the presence of any of the two antibodies, the flexibility of the globular domain increases everywhere except for the β1-α1 loop in the POM1/PrP complex which suggests the involvement of this loop in the pathological conversion. The secondary structure of PrP is preserved whereas the polar interactions involving residues Glu146, Arg156 and Arg208 are modified upon antibody binding.
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Affiliation(s)
- Ioana M Ilie
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland.
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3
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Chatterjee S, Salimi A, Lee JY. Unraveling the Histidine Tautomerism Effect on the Initial Stages of Prion Misfolding: New Insights from a Computational Perspective. ACS Chem Neurosci 2021; 12:3203-3213. [PMID: 34382391 DOI: 10.1021/acschemneuro.1c00376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The aggregation and structural conversion of normal prion peptide (PrPC) into the pathogenic scrapie form (PrPSc), which can act as a seed to enhance prion amyloid fiber formation, is believed to be a crucial event in prionopathies. Previous research suggests that the prion monomer may play an important role in oligomer generation during disease pathogenesis. In the present study, extensive replica-exchange molecular dynamics (REMD) simulations were conducted to explore the conformational characteristics of the huPrP (125-160) monomer under the histidine tautomerism effect. Investigating the structural characteristics and fibrilization process is challenging because two histidine tautomers [Nε2-H (ε) and Nδ1-H (δ)] can occur in the open neutral state. Molecular dynamics (MD) simulation outcomes have shown that the toxic εδ and δδ isomer (containing several and broader local minima) had the highest α-helix structures, with contents of 21.11% and 21.01%, respectively, and may have a strong influence on the organizational behavior of a monomeric prion. The amino acids aspartate 20 (D20)-asparagine 29 (N29) and isoleucine 15 (I15)-histidine 16 (H16), D20-arginine 27 (R27) as well as N29 formed α-helix with the highest probabilities in the δδ and εδ isomer, accordingly. On the basis of our findings, we propose the histidine tautomerization hypothesis as a new prion accumulation mechanism, which may exist to induce the formation of prion accumulates. Overall, our tautomerism hypothesis constitutes a promising perspective for enhancing understanding of prion disease pathobiology and may help in the design of a good inhibitor.
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Affiliation(s)
| | - Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
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4
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Palaniappan C, Narayanan RC, Sekar K. Mutation-Dependent Refolding of Prion Protein Unveils Amyloidogenic-Related Structural Ramifications: Insights from Molecular Dynamics Simulations. ACS Chem Neurosci 2021; 12:2810-2819. [PMID: 34296847 DOI: 10.1021/acschemneuro.1c00142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The main focus of prion structural biology studies is to understand the molecular basis of prion diseases caused by misfolding, and aggregation of the cellular prion protein PrPC remains elusive. Several genetic mutations are linked with human prion diseases and driven by the conformational conversion of PrPC to the toxic PrPSc. The main goal of this study is to gain a better insight into the molecular effect of disease-associated V210I mutation on this process by molecular dynamics simulations. This inherited mutation elicited copious structural changes in the β1-α1-β2 subdomain, including an unfolding of a helix α1 and the elongation of the β-sheet. These unusual structural changes likely appeared to detach the β1-α1-β2 subdomain from the α2-α3 core, an early misfolding event necessary for the conformational conversion of PrPC to PrPSc. Ultimately, the unfolded α1 and its prior β1-α1 loop further engaged with unrestrained conformational dynamics and were widely considered as amyloidogenic-inducing traits. Furthermore, the resulting folding intermediate possesses a highly unstable β1-α1-β2 subdomain, thereby enhancing the aggregation of misfolded PrPC through intermolecular interactions between frequently refolding regions. Briefly, these remarkable changes as seen in the mutant β1-α1-β2 subdomain are consistent with previous experimental results and thus provide a molecular basis of PrPC misfolding associated with the conformational conversion of PrPC to PrPSc.
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Affiliation(s)
| | - Rahul C. Narayanan
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
| | - Kanagaraj Sekar
- Department of Computational and Data Sciences, Indian Institute of Science, Bangalore 560 012, India
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5
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Sanz-Hernández M, De Simone A. Backbone NMR assignments of the C-terminal domain of the human prion protein and its disease-associated T183A variant. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:193-196. [PMID: 33590433 PMCID: PMC7974147 DOI: 10.1007/s12104-021-10005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Transmissible spongiform encephalopathies (TSEs) are fatal neurodegenerative disorders associated with the misfolding and aggregation of the human prion protein (huPrP). Despite efforts into investigating the process of huPrP aggregation, the mechanisms triggering its misfolding remain elusive. A number of TSE-associated mutations of huPrP have been identified, but their role at the onset and progression of prion diseases is unclear. Here we report the NMR assignments of the C-terminal globular domain of the wild type huPrP and the pathological mutant T183A. The differences in chemical shifts between the two variants reveal conformational alterations in some structural elements of the mutant, whereas the analyses of secondary shifts and random coil index provide indications on the putative mechanisms of misfolding of T183A huPrP.
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Affiliation(s)
- Máximo Sanz-Hernández
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London, SW7 2AZ, UK.
- Department of Pharmacy, University of Naples "Federico II", 80131, Naples, Italy.
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6
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Mechanism of misfolding of the human prion protein revealed by a pathological mutation. Proc Natl Acad Sci U S A 2021; 118:2019631118. [PMID: 33731477 PMCID: PMC7999870 DOI: 10.1073/pnas.2019631118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The misfolding and aggregation of the human prion protein (PrP) is associated with transmissible spongiform encephalopathies (TSEs). Intermediate conformations forming during the conversion of the cellular form of PrP into its pathological scrapie conformation are key drivers of the misfolding process. Here, we analyzed the properties of the C-terminal domain of the human PrP (huPrP) and its T183A variant, which is associated with familial forms of TSEs. We show that the mutation significantly enhances the aggregation propensity of huPrP, such as to uniquely induce amyloid formation under physiological conditions by the sole C-terminal domain of the protein. Using NMR spectroscopy, biophysics, and metadynamics simulations, we identified the structural characteristics of the misfolded intermediate promoting the aggregation of T183A huPrP and the nature of the interactions that prevent this species to be populated in the wild-type protein. In support of these conclusions, POM antibodies targeting the regions that promote PrP misfolding were shown to potently suppress the aggregation of this amyloidogenic mutant.
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7
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Myers R, Cembran A, Fernandez-Funez P. Insight From Animals Resistant to Prion Diseases: Deciphering the Genotype - Morphotype - Phenotype Code for the Prion Protein. Front Cell Neurosci 2020; 14:254. [PMID: 33013324 PMCID: PMC7461849 DOI: 10.3389/fncel.2020.00254] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/24/2020] [Indexed: 12/30/2022] Open
Abstract
Prion diseases are a group of neurodegenerative diseases endemic in humans and several ruminants caused by the misfolding of native prion protein (PrP) into pathological conformations. Experimental work and the mad-cow epidemic of the 1980s exposed a wide spectrum of animal susceptibility to prion diseases, including a few highly resistant animals: horses, rabbits, pigs, and dogs/canids. The variable susceptibility to disease offers a unique opportunity to uncover the mechanisms governing PrP misfolding, neurotoxicity, and transmission. Previous work indicates that PrP-intrinsic differences (sequence) are the main contributors to disease susceptibility. Several residues have been cited as critical for encoding PrP conformational stability in prion-resistant animals, including D/E159 in dog, S167 in horse, and S174 in rabbit and pig PrP (all according to human numbering). These amino acids alter PrP properties in a variety of assays, but we still do not clearly understand the structural correlates of PrP toxicity. Additional insight can be extracted from comparative structural studies, followed by molecular dynamics simulations of selected mutations, and testing in manipulable animal models. Our working hypothesis is that protective amino acids generate more compact and stable structures in a C-terminal subdomain of the PrP globular domain. We will explore this idea in this review and identify subdomains within the globular domain that may hold the key to unravel how conformational stability and disease susceptibility are encoded in PrP.
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Affiliation(s)
- Ryan Myers
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, United States
| | - Alessandro Cembran
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, United States
| | - Pedro Fernandez-Funez
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN, United States
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8
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Sridhar A, Orozco M, Collepardo-Guevara R. Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1. Nucleic Acids Res 2020; 48:5318-5331. [PMID: 32356891 PMCID: PMC7261198 DOI: 10.1093/nar/gkaa285] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/02/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins are crucial elements of chromatin heterogenous organization. While disorder in the histone tails enables a large variation of inter-nucleosome arrangements, disorder within the chromatin-binding proteins facilitates promiscuous binding to a wide range of different molecular targets, consistent with structural heterogeneity. Among the partially disordered chromatin-binding proteins, the H1 linker histone influences a myriad of chromatin characteristics including compaction, nucleosome spacing, transcription regulation, and the recruitment of other chromatin regulating proteins. Although it is now established that the long C-terminal domain (CTD) of H1 remains disordered upon nucleosome binding and that such disorder favours chromatin fluidity, the structural behaviour and thereby the role/function of the N-terminal domain (NTD) within chromatin is yet unresolved. On the basis of microsecond-long parallel-tempering metadynamics and temperature-replica exchange atomistic molecular dynamics simulations of different H1 NTD subtypes, we demonstrate that the NTD is completely unstructured in solution but undergoes an important disorder-to-order transition upon nucleosome binding: it forms a helix that enhances its DNA binding ability. Further, we show that the helical propensity of the H1 NTD is subtype-dependent and correlates with the experimentally observed binding affinity of H1 subtypes, suggesting an important functional implication of this disorder-to-order transition.
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Affiliation(s)
- Akshay Sridhar
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Modesto Orozco
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Baldiri i Reixac, 19, 08028 Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Av. Diagonal 647. 08028 Barcelona, Spain
| | - Rosana Collepardo-Guevara
- Maxwell Centre, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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9
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Qu F, ElOmari K, Wagner A, De Simone A, Beis K. Desolvation of the substrate-binding protein TauA dictates ligand specificity for the alkanesulfonate ABC importer TauABC. Biochem J 2019; 476:3649-3660. [PMID: 31802112 PMCID: PMC6906117 DOI: 10.1042/bcj20190779] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/20/2019] [Accepted: 11/22/2019] [Indexed: 12/02/2022]
Abstract
Under limiting sulfur availability, bacteria can assimilate sulfur from alkanesulfonates. Bacteria utilize ATP-binding cassette (ABC) transporters to internalise them for further processing to release sulfur. In gram-negative bacteria the TauABC and SsuABC ensure internalization, although, these two systems have common substrates, the former has been characterized as a taurine specific system. TauA and SsuA are substrate-binding proteins (SBPs) that bind and bring the alkanesulfonates to the ABC importer for transport. Here, we have determined the crystal structure of TauA and have characterized its thermodynamic binding parameters by isothermal titration calorimetry in complex with taurine and different alkanesulfonates. Our structures revealed that the coordination of the alkanesulfonates is conserved, with the exception of Asp205 that is absent from SsuA, but the thermodynamic parameters revealed a very high enthalpic penalty cost for binding of the other alkanesulfonates relative to taurine. Our molecular dynamic simulations indicated that the different levels of hydration of the binding site contributed to the selectivity for taurine over the other alkanesulfonates. Such selectivity mechanism is very likely to be employed by other SBPs of ABC transporters.
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Affiliation(s)
- Feng Qu
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
| | - Kamel ElOmari
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Armin Wagner
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, U.K
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, U.K
- Rutherford Appleton Laboratory, Research Complex at Harwell, Oxfordshire OX11 0DE, U.K
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10
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Ilie IM, Caflisch A. Simulation Studies of Amyloidogenic Polypeptides and Their Aggregates. Chem Rev 2019; 119:6956-6993. [DOI: 10.1021/acs.chemrev.8b00731] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ioana M. Ilie
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zürich, Zürich CH-8057, Switzerland
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11
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Fusco G, Sanz-Hernandez M, Ruggeri FS, Vendruscolo M, Dobson CM, De Simone A. Molecular determinants of the interaction of EGCG with ordered and disordered proteins. Biopolymers 2018; 109:e23117. [DOI: 10.1002/bip.23117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Giuliana Fusco
- Department of Life Sciences; Imperial College London; London SW7 2AZ United Kingdom
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | | | - Francesco S. Ruggeri
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry; University of Cambridge; Cambridge CB2 1EW United Kingdom
| | - Alfonso De Simone
- Department of Life Sciences; Imperial College London; London SW7 2AZ United Kingdom
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12
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Sanz-Hernández M, De Simone A. The PROSECCO server for chemical shift predictions in ordered and disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2017; 69:147-156. [PMID: 29119515 PMCID: PMC5711976 DOI: 10.1007/s10858-017-0145-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/12/2017] [Indexed: 06/07/2023]
Abstract
The chemical shifts measured in solution-state and solid-state nuclear magnetic resonance (NMR) are powerful probes of the structure and dynamics of protein molecules. The exploitation of chemical shifts requires methods to correlate these data with the protein structures and sequences. We present here an approach to calculate accurate chemical shifts in both ordered and disordered proteins using exclusively the information contained in their sequences. Our sequence-based approach, protein sequences and chemical shift correlations (PROSECCO), achieves the accuracy of the most advanced structure-based methods in the characterization of chemical shifts of folded proteins and improves the state of the art in the study of disordered proteins. Our analyses revealed fundamental insights on the structural information carried by NMR chemical shifts of structured and unstructured protein states.
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Affiliation(s)
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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13
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Chamachi NG, Chakrabarty S. Temperature-Induced Misfolding in Prion Protein: Evidence of Multiple Partially Disordered States Stabilized by Non-Native Hydrogen Bonds. Biochemistry 2017; 56:833-844. [DOI: 10.1021/acs.biochem.6b01042] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Neharika G. Chamachi
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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14
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Singh RK, Chamachi NG, Chakrabarty S, Mukherjee A. Mechanism of Unfolding of Human Prion Protein. J Phys Chem B 2017; 121:550-564. [PMID: 28030950 DOI: 10.1021/acs.jpcb.6b11416] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Misfolding and aggregation of prion proteins are associated with several neurodegenerative diseases. Therefore, understanding the mechanism of the misfolding process is of enormous interest in the scientific community. It has been speculated and widely discussed that the native cellular prion protein (PrPC) form needs to undergo substantial unfolding to a more stable PrPC* state, which may further oligomerize into the toxic scrapie (PrPSc) form. Here, we have studied the mechanism of the unfolding of the human prion protein (huPrP) using a set of extensive well-tempered metadynamics simulations. Through multiple microsecond-long metadynamics simulations, we find several possible unfolding pathways. We show that each pathway leads to an unfolded state of lower free energy than the native state. Thus, our study may point to the signature of a PrPC* form that corresponds to a global minimum on the conformational free-energy landscape. Moreover, we find that these global minima states do not involve an increased β-sheet content, as was assumed to be a signature of PrPSc formation in previous simulation studies. We have further analyzed the origin of metastability of the PrPC form through free-energy surfaces of the chopped helical segments to show that the helices, particularly H2 and H3 of the prion protein, have the tendency to form either a random coil or a β-structure. Therefore, the secondary structural elements of the prion protein are only weakly stabilized by tertiary contacts and solvation forces so that relatively weak perturbations induced by temperature, pressure, pH, and so forth can lead to substantial unfolding with characteristics of intrinsically disordered proteins.
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Affiliation(s)
- Reman K Singh
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
| | - Neharika G Chamachi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Suman Chakrabarty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Pune 411008, Maharashtra, India
| | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research , Pune 411008, Maharashtra, India
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15
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Binette V, Côté S, Mousseau N. Free-Energy Landscape of the Amino-Terminal Fragment of Huntingtin in Aqueous Solution. Biophys J 2016; 110:1075-88. [PMID: 26958885 DOI: 10.1016/j.bpj.2016.01.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 01/17/2023] Open
Abstract
The first exon of Huntingtin-a protein with multiple biological functions whose misfolding is related to Huntington's disease-modulates its localization, aggregation, and function within the cell. It is composed of a 17-amino-acid amphipathic segment (Htt17), an amyloidogenic segment of consecutive glutamines (QN), and a proline-rich segment. Htt17 is of fundamental importance: it serves as a membrane anchor to control the localization of huntingtin, it modulates huntingtin's function through posttranslational modifications, and it controls the self-assembly of the amyloidogenic QN segment into oligomers and fibrils. Experimentally, the conformational ensemble of the Htt17 monomer, as well as the impact of the polyglutamine and proline-rich segments, remains, however, mostly uncharacterized at the atomic level due to its intrinsic flexibility. Here, we unveil the free-energy landscape of Htt17, Htt17Q17, and Htt17Q17P11 using Hamiltonian replica exchange combined with well-tempered metadynamics. We characterize the free-energy landscape of these three fragments in terms of a few selected collective variables. Extensive simulations reveal that the free energy of Htt17 is dominated by a broad ensemble of configurations that agree with solution NMR chemical shifts. Addition of Q17 at its carboxy-terminus reduces the extent of the main basin to more extended configurations of Htt17 with lower helix propensity. Also, the aliphatic carbons of Q17 partially sequester the nonpolar amino acids of Htt17. For its part, addition of Q17P11 shifts the overall landscape to a more extended and helical Htt17 stabilized by interactions with Q17 and P11, which almost exclusively form a PPII-helix, as well as by intramolecular H-bonds and salt bridges. Our characterization of Huntingtin's amino-terminus provides insights into the structural origin of its ability to oligomerize and interact with phospholipid bilayers, processes closely linked to the biological functions of this protein.
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Affiliation(s)
- Vincent Binette
- Département de Physique and Groupe de Recherche sur les Protéines Membranaires (GEPROM), Université de Montréal, succursale Centre-ville, Montréal, Québec, Canada
| | - Sébastien Côté
- Département de Physique and Groupe de Recherche sur les Protéines Membranaires (GEPROM), Université de Montréal, succursale Centre-ville, Montréal, Québec, Canada
| | - Normand Mousseau
- Département de Physique and Groupe de Recherche sur les Protéines Membranaires (GEPROM), Université de Montréal, succursale Centre-ville, Montréal, Québec, Canada.
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16
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Musiani F, Giorgetti A. Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 329:49-77. [PMID: 28109331 DOI: 10.1016/bs.ircmb.2016.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Cells are extremely crowded environments, thus the use of diluted salted aqueous solutions containing a single protein is too simplistic to mimic the real situation. Macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, interactions with cognate biomolecules, and pathological aggregation. The latter phenomenon typically leads to the formation of amyloid fibrils that are linked to several lethal neurodegenerative diseases, but that can also play a functional role in certain organisms. The majority of molecular simulations performed before the last few years were conducted in diluted solutions and were restricted both in the timescales and in the system dimensions by the available computational resources. In recent years, several computational solutions were developed to get close to physiological conditions. In this review we summarize the main computational techniques used to tackle the issue of protein aggregation both in a diluted and in a crowded environment.
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Affiliation(s)
- F Musiani
- Laboratory of Bioinorganic Chemistry, University of Bologna, Bologna, Italy.
| | - A Giorgetti
- Applied Bioinformatics Group, University of Verona, Verona, Italy.
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17
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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18
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Abstract
It is now common knowledge that enzymes are mobile entities relying on complex atomic-scale dynamics and coordinated conformational events for proper ligand recognition and catalysis. However, the exact role of protein dynamics in enzyme function remains either poorly understood or difficult to interpret. This mini-review intends to reconcile biophysical observations and biological significance by first describing a number of common experimental and computational methodologies employed to characterize atomic-scale residue motions on various timescales in enzymes, and second by illustrating how the knowledge of these motions can be used to describe the functional behavior of enzymes and even act upon it. Two biologically relevant examples will be highlighted, namely the HIV-1 protease and DNA polymerase β enzyme systems.
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19
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Menon S, Sengupta N. Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrP(C): insights from atomistic simulations. MOLECULAR BIOSYSTEMS 2016; 11:1443-53. [PMID: 25855580 DOI: 10.1039/c4mb00689e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conversion of the predominantly α-helical cellular prion protein (PrP(C)) to the misfolded β-sheet enriched Scrapie form (PrP(Sc)) is a critical event in prion pathogenesis. However, the conformational triggers that lead to the isoform conversion (PrP(C) to PrP(Sc)) remain obscure, and conjectures about the role of unusually hydrophilic, short helix H1 of the C-terminal globular domain in the transition are varied. Helix H1 is anchored to helix H3 via a few stabilizing polar interactions. We have employed fully atomistic molecular dynamics simulations to study the effects triggered by a minor perturbation in the network of these non-bonded interactions in PrP(C). The elimination of just one of the key H1-H3 hydrogen bonds led to a cascade of conformational changes that are consistent with those observed in partially unfolded intermediates of PrP(C), with pathogenic mutations and in low pH environments. Our analyses reveal that the perturbation results in the enhanced conformational flexibility of the protein. The resultant enhancement in the dynamics leads to overall increased solvent exposure of the hydrophobic core residues and concomitant disruption of the H1-H3 inter-domain salt bridge network. This study lends credence to the hypothesis that perturbing the cooperativity of the stabilizing interactions in the PrP(C) globular domain can critically affect its dynamics and may lead to structural transitions of pathological relevance.
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Affiliation(s)
- Sneha Menon
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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20
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Salmon L, Blackledge M. Investigating protein conformational energy landscapes and atomic resolution dynamics from NMR dipolar couplings: a review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2015; 78:126601. [PMID: 26517337 DOI: 10.1088/0034-4885/78/12/126601] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Nuclear magnetic resonance spectroscopy is exquisitely sensitive to protein dynamics. In particular inter-nuclear dipolar couplings, that become measurable in solution when the protein is dissolved in a dilute liquid crystalline solution, report on all conformations sampled up to millisecond timescales. As such they provide the opportunity to describe the Boltzmann distribution present in solution at atomic resolution, and thereby to map the conformational energy landscape in unprecedented detail. The development of analytical methods and approaches based on numerical simulation and their application to numerous biologically important systems is presented.
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Affiliation(s)
- Loïc Salmon
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), F-38027 Grenoble, France. CEA, DSV, IBS, F-38027 Grenoble, France. CNRS, IBS, F-38027 Grenoble, France
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21
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Morriss-Andrews A, Shea JE. Computational Studies of Protein Aggregation: Methods and Applications. Annu Rev Phys Chem 2015; 66:643-66. [DOI: 10.1146/annurev-physchem-040513-103738] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Joan-Emma Shea
- Department of Physics and
- Department of Chemistry, University of California, Santa Barbara, California 93106;
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22
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De Simone A, Mote KR, Veglia G. Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations. Biophys J 2015; 106:2566-76. [PMID: 24940774 DOI: 10.1016/j.bpj.2014.03.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 03/14/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023] Open
Abstract
Solid-state NMR spectroscopy is emerging as a powerful approach to determine structure, topology, and conformational dynamics of membrane proteins at the atomic level. Conformational dynamics are often inferred and quantified from the motional averaging of the NMR parameters. However, the nature of these motions is difficult to envision based only on spectroscopic data. Here, we utilized restrained molecular dynamics simulations to probe the structural dynamics, topology and conformational transitions of regulatory membrane proteins of the calcium ATPase SERCA, namely sarcolipin and phospholamban, in explicit lipid bilayers. Specifically, we employed oriented solid-state NMR data, such as dipolar couplings and chemical shift anisotropy measured in lipid bicelles, to refine the conformational ensemble of these proteins in lipid membranes. The samplings accurately reproduced the orientations of transmembrane helices and showed a significant degree of convergence with all of the NMR parameters. Unlike the unrestrained simulations, the resulting sarcolipin structures are in agreement with distances and angles for hydrogen bonds in ideal helices. In the case of phospholamban, the restrained ensemble sampled the conformational interconversion between T (helical) and R (unfolded) states for the cytoplasmic region that could not be observed using standard structural refinements with the same experimental data set. This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes.
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Affiliation(s)
- Alfonso De Simone
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| | - Kaustubh R Mote
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota; Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota.
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23
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Krieger JM, Fusco G, Lewitzky M, Simister PC, Marchant J, Camilloni C, Feller SM, De Simone A. Conformational recognition of an intrinsically disordered protein. Biophys J 2014; 106:1771-9. [PMID: 24739176 DOI: 10.1016/j.bpj.2014.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/02/2014] [Accepted: 03/06/2014] [Indexed: 10/25/2022] Open
Abstract
There is a growing interest in understanding the properties of intrinsically disordered proteins (IDPs); however, the characterization of these states remains an open challenge. IDPs appear to have functional roles that diverge from those of folded proteins and revolve around their ability to act as hubs for protein-protein interactions. To gain a better understanding of the modes of binding of IDPs, we combined statistical mechanics, calorimetry, and NMR spectroscopy to investigate the recognition and binding of a fragment from the disordered protein Gab2 by the growth factor receptor-bound protein 2 (Grb2), a key interaction for normal cell signaling and cancer development. Structural ensemble refinement by NMR chemical shifts, thermodynamics measurements, and analysis of point mutations indicated that the population of preexisting bound conformations in the free-state ensemble of Gab2 is an essential determinant for recognition and binding by Grb2. A key role was found for transient polyproline II (PPII) structures and extended conformations. Our findings are likely to have very general implications for the biological behavior of IDPs in light of the evidence that a large fraction of these proteins possess a specific propensity to form PPII and to adopt conformations that are more extended than the typical random-coil states.
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Affiliation(s)
- James M Krieger
- Department of Life Sciences, Imperial College London, London, UK
| | - Giuliana Fusco
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Marc Lewitzky
- Department of Oncology, University of Oxford, Oxford, UK; Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | | | - Jan Marchant
- Department of Life Sciences, Imperial College London, London, UK
| | - Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Stephan M Feller
- Department of Oncology, University of Oxford, Oxford, UK; Institute of Molecular Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
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24
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Savol AJ, Chennubhotla CS. Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins. J Chem Theory Comput 2014; 10:2964-2974. [PMID: 25136267 PMCID: PMC4132847 DOI: 10.1021/ct500361w] [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: 04/24/2014] [Indexed: 11/28/2022]
Abstract
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Experiments
and atomistic simulations of polypeptides have revealed
structural intermediates that promote or inhibit conformational transitions
to the native state during folding. We invoke a concept of “kinetic
frustration” to quantify the prevalence and impact of these
behaviors on folding rates within a large set of atomistic simulation
data for 10 fast-folding proteins, where each protein’s conformational
space is represented as a Markov state model of conformational transitions.
Our graph theoretic approach addresses what conformational features
correlate with folding inhibition and therefore permits comparison
among features within a single protein network and also more generally
between proteins. Nonnative contacts and nonnative secondary structure
formation can thus be quantitatively implicated in inhibiting folding
for several of the tested peptides.
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Affiliation(s)
- Andrej J Savol
- Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States ; Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, Pennsylvania 15260, United States
| | - Chakra S Chennubhotla
- Dept. of Computational and Systems Biology, School of Medicine, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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25
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Jensen MR, Zweckstetter M, Huang JR, Blackledge M. Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy. Chem Rev 2014; 114:6632-60. [PMID: 24725176 DOI: 10.1021/cr400688u] [Citation(s) in RCA: 214] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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26
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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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27
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Camilloni C, Cavalli A, Vendruscolo M. Replica-Averaged Metadynamics. J Chem Theory Comput 2013; 9:5610-7. [DOI: 10.1021/ct4006272] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carlo Camilloni
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
| | - Andrea Cavalli
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
- Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW United Kingdom
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28
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Mercadante D, Melton LD, Jameson GB, Williams MAK, De Simone A. Substrate dynamics in enzyme action: rotations of monosaccharide subunits in the binding groove are essential for pectin methylesterase processivity. Biophys J 2013; 104:1731-9. [PMID: 23601320 DOI: 10.1016/j.bpj.2013.02.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Revised: 02/13/2013] [Accepted: 02/25/2013] [Indexed: 01/31/2023] Open
Abstract
The dynamical behavior of biomacromolecules is a fundamental property regulating a large number of biological processes. Protein dynamics have been widely shown to play a role in enzyme catalysis; however, the interplay between substrate dynamics and enzymatic activity is less understood. We report insights into the role of dynamics of substrates in the enzymatic activity of PME from Erwinia chrysanthemi, a processive enzyme that catalyzes the hydrolysis of methylester groups from the galacturonic acid residues of homogalacturonan chains, the major component of pectin. Extensive molecular dynamics simulations of this PME in complex with decameric homogalacturonan chains possessing different degrees and patterns of methylesterification show how the carbohydrate substitution pattern governs the dynamics of the substrate in the enzyme's binding cleft, such that substrate dynamics represent a key prerequisite for the PME biological activity. The analyses reveal that correlated rotations around glycosidic bonds of monosaccharide subunits at and immediately adjacent to the active site are a necessary step to ensure substrate processing. Moreover, only substrates with the optimal methylesterification pattern attain the correct dynamical behavior to facilitate processive catalysis. This investigation is one of the few reported examples of a process where the dynamics of a substrate are vitally important.
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29
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De Simone A, Stanzione F, Marasco D, Vitagliano L, Esposito L. The intrinsic stability of the human prion β-sheet region investigated by molecular dynamics. J Biomol Struct Dyn 2013; 31:441-52. [DOI: 10.1080/07391102.2012.703070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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30
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Ozbil M, Barman A, Bora RP, Prabhakar R. Computational Insights into Dynamics of Protein Aggregation and Enzyme-Substrate Interactions. J Phys Chem Lett 2012; 3:3460-3469. [PMID: 26290973 DOI: 10.1021/jz301597k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this Perspective, the roles of protein dynamics have been discussed in the aggregation of amyloid beta (Aβ) peptides and formation of enzyme-substrate complexes of beta-secretase (BACE1) and insulin-degrading enzyme (IDE). The studies regarding the influence of individual amino acid residues and specific regions on the structures and oligomerization of early Aβ aggregates and computations of their translational and rotational diffusion coefficients and order parameters exhibited that even the short-time-scale molecular dynamics simulations can reproduce certain experimental parameters with reasonable accuracy. The simulations elucidating the enzyme-substrate interactions of BACE1 and IDE successfully showed that the chemical nature and length of the substrates influence the dynamics and plasticity of both the enzyme and substrate. An atomic-level understanding of these processes will advance our efforts to develop therapeutic strategies for several deadly diseases through the design of small molecules with antiaggregation properties and substrate-specific "designer" forms of enzymes.
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Affiliation(s)
- Mehmet Ozbil
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Arghya Barman
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Ram Prasad Bora
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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31
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Michel J, Cuchillo R. The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-myc. PLoS One 2012; 7:e41070. [PMID: 22815918 PMCID: PMC3397933 DOI: 10.1371/journal.pone.0041070] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 06/18/2012] [Indexed: 11/18/2022] Open
Abstract
Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (1), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to 1 were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule 1 was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding 1 are already partially formed in the apo ensemble, suggesting that 1 binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins.
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Affiliation(s)
- Julien Michel
- EastCHEM School of Chemistry, University of Edinburgh, Edinburgh, United Kingdom.
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32
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Invernizzi G, Papaleo E, Sabate R, Ventura S. Protein aggregation: mechanisms and functional consequences. Int J Biochem Cell Biol 2012; 44:1541-54. [PMID: 22713792 DOI: 10.1016/j.biocel.2012.05.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/09/2012] [Accepted: 05/27/2012] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying protein misfolding and aggregation has become a central issue in biology and medicine. Compelling evidence show that the formation of amyloid aggregates has a negative impact in cell function and is behind the most prevalent human degenerative disorders, including Alzheimer's Parkinson's and Huntington's diseases or type 2 diabetes. Surprisingly, the same type of macromolecular assembly is used for specialized functions by different organisms, from bacteria to human. Here we address the conformational properties of these aggregates, their formation pathways, their role in human diseases, their functional properties and how bioinformatics tools might be of help to study these protein assemblies.
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Affiliation(s)
- Gaetano Invernizzi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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33
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Bemporad F, De Simone A, Chiti F, Dobson C. Characterizing intermolecular interactions that initiate native-like protein aggregation. Biophys J 2012; 102:2595-604. [PMID: 22713575 PMCID: PMC3368139 DOI: 10.1016/j.bpj.2012.03.057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 02/28/2012] [Accepted: 03/14/2012] [Indexed: 10/28/2022] Open
Abstract
Folded proteins can access aggregation-prone states without the need for transitions that cross the energy barriers for unfolding. In this study we characterized the initial steps of aggregation from a native-like state of the acylphosphatase from Sulfolobus solfataricus (Sso AcP). Using computer simulations restrained by experimental hydrogen/deuterium (H/D) exchange data, we provide direct evidence that under aggregation-promoting conditions Sso AcP populates a conformational ensemble in which native-like structure is retained throughout the sequence in the absence of local unfolding (N∗), although the protein exhibits an increase in hydrodynamic radius and dynamics. This transition leads an edge strand to experience an increased affinity for a specific unfolded segment of the protein. Direct measurements by means of H/D exchange rates, isothermal titration calorimetry, and intermolecular relaxation enhancements show that after formation of N∗, an intermolecular interaction with an antiparallel arrangement is established between the edge strand and the unfolded segment of the protein. However, under conditions that favor the fully native state of Sso AcP, such an interaction is not established. Thus, these results reveal a novel (to our knowledge) self-assembly mechanism for a folded protein that is based on the increased flexibility of highly aggregation-prone segments in the absence of local unfolding.
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Affiliation(s)
- Francesco Bemporad
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Alfonso De Simone
- Division of Molecular Biosciences, Imperial College London, London, United Kingdom
| | - Fabrizio Chiti
- Dipartimento di Scienze Biochimiche, Università degli Studi di Firenze, Firenze, Italy
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34
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Abstract
Protein molecules have evolved to adopt distinctive and well-defined functional and soluble states under physiological conditions. In some circumstances, however, proteins can self-assemble into fibrillar aggregates designated as amyloid fibrils. In vivo these processes are normally associated with severe pathological conditions but can sometimes have functional relevance. One such example is the hydrophobins, whose aggregation at air-water interfaces serves to create robust protein coats that help fungal spores to resist wetting and thus facilitate their dispersal in the air. We have performed multiscale simulations to address the molecular determinants governing the formation of functional amyloids by the class I fungal hydrophobin EAS. Extensive samplings of full-atom replica-exchange molecular dynamics and coarse-grained simulations have allowed us to identify factors that distinguish aggregation-prone from highly soluble states of EAS. As a result of unfavourable entropic terms, highly dynamical regions are shown to exert a crucial influence on the propensity of the protein to aggregate under different conditions. More generally, our findings suggest a key role that specific flexible structural elements can play to ensure the existence of soluble and functional states of proteins under physiological conditions.
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35
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Sutto L, Marsili S, Gervasio FL. New advances in metadynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2012. [DOI: 10.1002/wcms.1103] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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