1
|
Tywoniuk B, Yuan Y, McCartan S, Szydłowska BM, Tofoleanu F, Brooks BR, Buchete NV. Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments. J Phys Chem B 2018; 122:11535-11545. [PMID: 30335383 DOI: 10.1021/acs.jpcb.8b07423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nanoscale fibrils formed by amyloid peptides have a polymorphic character, adopting several types of molecular structures in similar growth conditions. As shown by experimental (e.g., solid-state NMR) and computational studies, amyloid fibril polymorphism hinders both the structural characterization of Alzheimer's Aβ amyloid protofilaments and fibrils at a molecular level, as well as the possible applications (e.g., development of drugs or biomarkers) that rely on similar, controlled molecular arrangements of the Aβ peptides in amyloid fibril structures. We have explored the use of several contact potentials for the efficient identification of minimal sequence mutations that could enhance the stability of specific fibril structures while simultaneously destabilizing competing topologies, controlling thus the amount of structural polymorphism in a rational way. We found that different types of contact potentials, while having only partial accuracy on their own, lead to similar results regarding ranking the compatibility of wild-type (WT) and mutated amyloid sequences with different fibril morphologies. This approach allows exhaustive screening and assessment of possible mutations and the identification of minimal consensus mutations that could stabilize fibrils with the desired topology at the expense of other topology types, a prediction that is further validated using atomistic molecular dynamics with explicit water molecules. We apply this two-step multiscale (i.e., residue and atomistic-level) approach to predict and validate mutations that could bias either parallel or antiparallel packing in the core Alzheimer's Aβ9-40 amyloid fibril models based on solid-state NMR experiments. Besides shedding new light on the molecular origins of structural polymorphism in WT Aβ fibrils, our study could also lead to efficient tools for assisting future experimental approaches for amyloid fibril determination, and for the development of biomarkers or drugs aimed at interfering with the stability of amyloid fibrils, as well as for the future design of amyloid fibrils with a controlled (e.g., reduced) level of structural polymorphism.
Collapse
Affiliation(s)
- Bartłomiej Tywoniuk
- School of Physics , University College Dublin , Dublin D04 V1W8 , Ireland.,Institute for Discovery , University College Dublin , Dublin D04 V1W8 , Ireland
| | - Ye Yuan
- School of Physics , University College Dublin , Dublin D04 V1W8 , Ireland.,Institute for Discovery , University College Dublin , Dublin D04 V1W8 , Ireland
| | - Sarah McCartan
- School of Physics , University College Dublin , Dublin D04 V1W8 , Ireland.,Institute for Discovery , University College Dublin , Dublin D04 V1W8 , Ireland
| | - Beata Maria Szydłowska
- Applied Physical Chemistry , Ruprecht-Karls University Heidelberg , Heidelberg 69120 , Germany.,Institute of Physics, EIT 2 , Universität der Bundeswehr München , Werner-Heisenberg-Weg 39 , 85577 Neubiberg , Germany
| | - Florentina Tofoleanu
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States.,Department of Chemistry , Yale University , New Haven , Connecticut 06520 , United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Nicolae-Viorel Buchete
- School of Physics , University College Dublin , Dublin D04 V1W8 , Ireland.,Institute for Discovery , University College Dublin , Dublin D04 V1W8 , Ireland
| |
Collapse
|
2
|
Blanco MA, Sahin E, Robinson AS, Roberts CJ. Coarse-grained model for colloidal protein interactions, B(22), and protein cluster formation. J Phys Chem B 2013; 117:16013-28. [PMID: 24289039 DOI: 10.1021/jp409300j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Reversible protein cluster formation is an important initial step in the processes of native and non-native protein aggregation, but involves relatively long time and length scales for detailed atomistic simulations and extensive mapping of free energy landscapes. A coarse-grained (CG) model is presented to semiquantitatively characterize the thermodynamics and key configurations involved in the landscape for protein oligomerization, as well as experimental measures of interactions such as the osmotic second virial coefficient (B22). Based on earlier work (Grüenberger et al., J. Phys. Chem. B 2013, 117, 763), this CG model treats proteins as rigid bodies composed of one bead per amino acid, with each amino acid having specific parameters for its size, hydrophobicity, and charge. The net interactions are a combination of steric repulsions, short-range attractions, and screened long-range charge-charge interactions. Model parametrization was done by fitting simulation results against experimental value of B22 as a function of solution ionic strength for α-chymotrypsinogen A and γD-Crystallin (gD-Crys). The CG model is applied to characterize the pairwise interactions and dimerization of gD-Crys and the dependence on temperature, protein concentration, and ionic strength. The results illustrate that at experimentally relevant conditions where stable dimers do not form, the entropic contributions are predominant in the free-energy of protein cluster formation and colloidal protein interactions, arguing against interpretations that treat B22 primarily from energetic considerations alone. Additionally, the results suggest that electrostatic interactions help to modulate the population of the different stable configurations for protein nearest-neighbor pairs, while short-range attractions determine the relative orientations of proteins within these configurations. Finally, simulation results are combined with Principal Component Analysis to identify those amino-acids/surface patches that form interprotein contacts at conditions that favor dimerization of gD-Crys. The resulting regions agree with previously found aggregation-prone sites, as well as suggesting new ones that may be important.
Collapse
Affiliation(s)
- Marco A Blanco
- Department of Chemical and Biomolecular Engineering and Center for Molecular and Engineering Thermodynamics, University of Delaware , Newark, Delaware 19176, United States
| | | | | | | |
Collapse
|
3
|
Fitzpatrick AW, Knowles TPJ, Waudby CA, Vendruscolo M, Dobson CM. Inversion of the balance between hydrophobic and hydrogen bonding interactions in protein folding and aggregation. PLoS Comput Biol 2011; 7:e1002169. [PMID: 22022239 PMCID: PMC3192805 DOI: 10.1371/journal.pcbi.1002169] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2010] [Accepted: 07/06/2011] [Indexed: 12/25/2022] Open
Abstract
Identifying the forces that drive proteins to misfold and aggregate, rather than to fold into their functional states, is fundamental to our understanding of living systems and to our ability to combat protein deposition disorders such as Alzheimer's disease and the spongiform encephalopathies. We report here the finding that the balance between hydrophobic and hydrogen bonding interactions is different for proteins in the processes of folding to their native states and misfolding to the alternative amyloid structures. We find that the minima of the protein free energy landscape for folding and misfolding tend to be respectively dominated by hydrophobic and by hydrogen bonding interactions. These results characterise the nature of the interactions that determine the competition between folding and misfolding of proteins by revealing that the stability of native proteins is primarily determined by hydrophobic interactions between side-chains, while the stability of amyloid fibrils depends more on backbone intermolecular hydrogen bonding interactions. In order to carry out their biological functions, most proteins fold into well-defined conformations known as native states. Failure to fold, or to remain folded correctly, may result in misfolding and aggregation, which are processes associated with a wide range of highly debilitating, and so far incurable, human conditions that include Alzheimer's and Parkinson's diseases and type II diabetes. In our work we investigate the nature of the fundamental interactions that are responsible for the folding and misfolding behaviour of proteins, finding that interactions between protein side-chains play a major role in stabilising native states, whilst backbone hydrogen bonding interactions are key in determining the stability of amyloid fibrils.
Collapse
Affiliation(s)
| | | | | | | | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
4
|
Ojeda-May P, Garcia ME. Electric field-driven disruption of a native beta-sheet protein conformation and generation of a helix-structure. Biophys J 2010; 99:595-9. [PMID: 20643079 DOI: 10.1016/j.bpj.2010.04.040] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 03/23/2010] [Accepted: 04/13/2010] [Indexed: 10/19/2022] Open
Abstract
We demonstrate that an external constant electric field is able to modify the secondary structure of a protein and induce a transition from a beta-sheet into a helix-like conformation. This dramatic change is driven by a global rearrangement of the dipole moments at the amide planes. We also predict electric-field-induced modifications of the intermediate states of the protein.
Collapse
Affiliation(s)
- Pedro Ojeda-May
- Theoretische Physik, Universität Kassel, Fachbereich 10, Kassel, Germany.
| | | |
Collapse
|
5
|
Bereau T, Deserno M. Generic coarse-grained model for protein folding and aggregation. J Chem Phys 2009; 130:235106. [PMID: 19548767 DOI: 10.1063/1.3152842] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A generic coarse-grained (CG) protein model is presented. The intermediate level of resolution (four beads per amino acid, implicit solvent) allows for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity. Realistic alpha/beta content is achieved by including an effective nearest-neighbor dipolar interaction. Parameters are tuned to reproduce both local conformations and tertiary structures. The thermodynamics and kinetics of a three-helix bundle are studied. We check that the CG model is able to fold proteins with tertiary structures and amino acid sequences different from the one used for parameter tuning. By studying both helical and extended conformations we make sure the force field is not biased toward any particular secondary structure. The accuracy involved in folding not only the test protein but also other ones show strong evidence for amino acid cooperativity embedded in the model. Without any further adjustments or bias a realistic oligopeptide aggregation scenario is observed.
Collapse
Affiliation(s)
- Tristan Bereau
- Department of Physics, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, Pennsylvania 15213, USA.
| | | |
Collapse
|
6
|
Ojeda P, Garcia ME, Londoño A, Chen NY. Monte Carlo simulations of proteins in cages: influence of confinement on the stability of intermediate states. Biophys J 2009; 96:1076-82. [PMID: 18849410 PMCID: PMC2716574 DOI: 10.1529/biophysj.107.125369] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 09/12/2008] [Indexed: 11/18/2022] Open
Abstract
We study the folding of small proteins inside confining potentials. Proteins are described using an effective potential model that contains the Ramachandran angles as degrees of freedom and does not need any a priori information about the native state. Hydrogen bonds, dipole-dipole-, and hydrophobic interactions are taken explicitly into account. An interesting feature displayed by this potential is the presence of metastable intermediates between the unfolded and native states. We consider different types of confining potentials to describe proteins folding inside cages with repulsive or attractive walls. Using the Wang-Landau algorithm, we determine the density of states and analyze in detail the thermodynamical properties of the confined proteins for different sizes of the cages. We show that confinement dramatically reduces the phase space available to the protein and that the presence of intermediate states can be controlled by varying the properties of the confining potential. Cages with strongly attractive walls destabilize the intermediate states and lead to a two-state folding into a configuration that is less stable than the native structure. However, cages with slightly attractive walls enhance the stability of native structure and induce a folding process, which occurs through intermediate configurations.
Collapse
Affiliation(s)
- Pedro Ojeda
- Theoretische Physik, FB 18, and Center for Interdisciplinary Nanostructure Science and Technology, Universität Kassel, Germany
| | - Martin E. Garcia
- Theoretische Physik, FB 18, and Center for Interdisciplinary Nanostructure Science and Technology, Universität Kassel, Germany
| | - Aurora Londoño
- Department of Molecular Biology, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, Mexico
| | - Nan-Yow Chen
- Institute of Physics, Academic Sinica, Nankang, Taiwan
| |
Collapse
|
7
|
Buchete NV, Straub JE, Thirumalai D. Dissecting contact potentials for proteins: relative contributions of individual amino acids. Proteins 2008; 70:119-30. [PMID: 17640067 DOI: 10.1002/prot.21538] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Knowledge-based contact potentials are routinely used in fold recognition, binding of peptides to proteins, structure prediction, and coarse-grained models to probe protein folding kinetics. The dominant physical forces embodied in the contact potentials are revealed by eigenvalue analysis of the matrices, whose elements describe the strengths of interaction between amino acid side chains. We propose a general method to rank quantitatively the importance of various inter-residue interactions represented in the currently popular pair contact potentials. Eigenvalue analysis and correlation diagrams are used to rank the inter-residue pair interactions with respect to the magnitude of their relative contributions to the contact potentials. The amino acid ranking is shown to be consistent with a mean field approximation that is used to reconstruct the original contact potentials from the most relevant amino acids for several contact potentials. By providing a general, relative ranking score for amino acids, this method permits a detailed, quantitative comparison of various contact interaction schemes. For most contact potentials, between 7 and 9 amino acids of varying chemical character are needed to accurately reconstruct the full matrix. By correlating the identified important amino acid residues in contact potentials and analysis of about 7800 structural domains in the CATH database we predict that it is important to model accurately interactions between small hydrophobic residues. In addition, only potentials that take interactions involving the protein backbone into account can predict dense packing in protein structures.
Collapse
Affiliation(s)
- N-V Buchete
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA.
| | | | | |
Collapse
|
8
|
Chen NY, Su ZY, Mou CY. Effective potentials for folding proteins. PHYSICAL REVIEW LETTERS 2006; 96:078103. [PMID: 16606145 DOI: 10.1103/physrevlett.96.078103] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Indexed: 05/08/2023]
Abstract
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding.
Collapse
Affiliation(s)
- Nan-Yow Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
| | | | | |
Collapse
|
9
|
Tarragó MEP, Rocha LFO, DaSilva RA, Caliri A. Steric constraints as folding coadjuvant. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2003; 67:031901. [PMID: 12689095 DOI: 10.1103/physreve.67.031901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Indexed: 05/24/2023]
Abstract
Through the analyses of the Miyazawa-Jernigan matrix it has been shown that the hydrophobic effect generates the dominant driving force for protein folding. By using both lattice and off-lattice models, it is shown that hydrophobic-type potentials are indeed efficient in inducing the chain through nativelike configurations, but they fail to provide sufficient stability so as to keep the chain in the native state. However, through comparative Monte Carlo simulations, it is shown that hydrophobic potentials and steric constraints are two basic ingredients for the folding process. Specifically, it is shown that suitable pairwise steric constraints introduce strong changes on the configurational activity, whose main consequence is a huge increase in the overall stability condition of the native state; detailed analysis of the effects of steric constraints on the heat capacity and configurational activity are provided. The present results support the view that the folding problem of globular proteins can be approached as a process in which the mechanism to reach the native conformation and the requirements for the globule stability are uncoupled.
Collapse
Affiliation(s)
- M E P Tarragó
- Universidade de São Paulo, FFCLRP, Departamento de Física e Matemática, Avenida Bandeirantes, 3000, 14040.000 Ribeirão Preto, São Paulo, Brazil
| | | | | | | |
Collapse
|