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Vila JA, Arnautova YA. 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information. SPRINGER SERIES ON BIO- AND NEUROSYSTEMS 2019. [PMCID: PMC7123919 DOI: 10.1007/978-3-319-95843-9_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13Cα nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13Cα chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13Cα shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13Cα-shielding computation. Finally, we illustrate how the information encoded in the 13C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined protein models.
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2
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Olsson S, Vögeli BR, Cavalli A, Boomsma W, Ferkinghoff-Borg J, Lindorff-Larsen K, Hamelryck T. Probabilistic Determination of Native State Ensembles of Proteins. J Chem Theory Comput 2014; 10:3484-91. [DOI: 10.1021/ct5001236] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simon Olsson
- Bioinformatics
Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Beat Rolf Vögeli
- Laboratory
of Physical Chemistry, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, CH-6500 Bellinzona, Switzerland
| | - Wouter Boomsma
- Structural
Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Ferkinghoff-Borg
- Cellular
Signal Integration Group, Center for Biological Sequence Analysis, Technical University of Denmark, Lyngby, Denmark
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Hamelryck
- Bioinformatics
Centre, Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
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Vila JA, Arnautova YA. 13C Chemical Shifts in Proteins: A Rich Source of Encoded Structural Information. COMPUTATIONAL METHODS TO STUDY THE STRUCTURE AND DYNAMICS OF BIOMOLECULES AND BIOMOLECULAR PROCESSES 2014. [PMCID: PMC7121069 DOI: 10.1007/978-3-642-28554-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the formidable progress in Nuclear Magnetic Resonance (NMR) spectroscopy, quality assessment of NMR-derived structures remains as an important problem. Thus, validation of protein structures is essential for the spectroscopists, since it could enable them to detect structural flaws and potentially guide their efforts in further refinement. Moreover, availability of accurate and efficient validation tools would help molecular biologists and computational chemists to evaluate quality of available experimental structures and to select a protein model which is the most suitable for a given scientific problem. The 13Cα nuclei are ubiquitous in proteins, moreover, their shieldings are easily obtainable from NMR experiments and represent a rich source of encoded structural information that makes 13Cα chemical shifts an attractive candidate for use in computational methods aimed at determination and validation of protein structures. In this chapter, the basis of a novel methodology of computing, at the quantum chemical level of theory, the 13Cα shielding for the amino acid residues in proteins is described. We also identify and examine the main factors affecting the 13Cα-shielding computation. Finally, we illustrate how the information encoded in the 13C chemical shifts can be used for a number of applications, viz., from protein structure prediction of both α-helical and β-sheet conformations, to determination of the fraction of the tautomeric forms of the imidazole ring of histidine in proteins as a function of pH or to accurate detection of structural flaws, at a residue-level, in NMR-determined protein models.
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Sieradzan AK, Liwo A, Hansmann UHE. Folding and self-assembly of a small protein complex. J Chem Theory Comput 2012; 8:3416-3422. [PMID: 24039552 DOI: 10.1021/ct300528r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthetic homotetrameric ββα (BBAT1) protein possesses a stable quaternary structure with a ββα fold. Because of its small size (a total of 84 residues), the homotetramer is an excellent model system with which to study the self-assembly and protein-protein interactions. We find from replica exchange molecular dynamics simulations with the coarse-grain UNRES force field that the folding and association pathway consists of three well-separated steps, where that association to a tetramer precedes and facilitates folding of the four chains. At room temperature the tetramer exists in an ensemble of diverse structures. The crystal structure becomes energetically favored only when the molecule is put in a dense and crystal-like environment. The observed picture of folding promoted by association may mirror the mechanism according to which intrinsically unfolded proteins assume their functional structure.
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Affiliation(s)
- Adam K Sieradzan
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland ; Department of Chemistry and Biochemistry, Oklahoma University, Norman, OK, 73019, U.S.A
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Jiang P, Hansmann UHE. Modeling Structural Flexibility of Proteins with Go-Models. J Chem Theory Comput 2012; 8:2127-2133. [PMID: 24039551 DOI: 10.1021/ct3000469] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based models are an efficient tool for folding studies of proteins since by construction their energy landscape is only minimal frustrated. However, their intrinsic drawback is a lack of structural flexibility as usually only one target structure is employed to construct the potentials. Hence, a Go-model may not capture differences in mutation-induced protein dynamics, if - as in the case of the disease-related A629P mutant of the Menkes protein ATP7A - the structural differences between mutant and wild type are small. In this work, we introduced three implementations of Go-models that take into account the flexibility of proteins in the NMR ensemble. Comparing the wild type and the mutant A629P of the 75-residue large 6th domain Menkes protein, we find that these new Go-potentials lead to broader distributions than Go-models relying on a single member of the NMR-ensemble. This allows us to detect the transient unfolding of a loosely formed β1β4-sheet in the mutant protein. Our results are consistent with previous simulations using physical force field and an explicit solvent, and suggests a mechanism by which these mutations cause Menkes disease. In addition, the improved Go-models suggest differences in the folding pathway between wild type and mutant, an observation that was not accessible to simulations of this 75-residue protein with a physical all-atom force field and explicit solvent.
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Affiliation(s)
- Ping Jiang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019-5251, USA
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Klenin K, Strodel B, Wales DJ, Wenzel W. Modelling proteins: conformational sampling and reconstruction of folding kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:977-1000. [PMID: 20851219 DOI: 10.1016/j.bbapap.2010.09.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 09/03/2010] [Accepted: 09/05/2010] [Indexed: 01/08/2023]
Abstract
In the last decades biomolecular simulation has made tremendous inroads to help elucidate biomolecular processes in-silico. Despite enormous advances in molecular dynamics techniques and the available computational power, many problems involve long time scales and large-scale molecular rearrangements that are still difficult to sample adequately. In this review we therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of the relevant family of molecular conformations by dispensing with the details of the short-term kinetics of the process. Because these methods generate thermodynamic information at best, they must be complemented by techniques to reconstruct the kinetics of the process using the ensemble of relevant conformations. Here we review recent advances for both types of methods and discuss their perspectives to permit efficient and accurate modelling of large-scale conformational changes in biomolecules. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Affiliation(s)
- Konstantin Klenin
- Steinbuch Centre for Computing, Karlsruhe Institute of Technology, P.O. Box 3640, D-76021 Karlsruhe, Germany
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Huang X, Bowman GR, Bacallado S, Pande VS. Rapid equilibrium sampling initiated from nonequilibrium data. Proc Natl Acad Sci U S A 2009; 106:19765-9. [PMID: 19805023 PMCID: PMC2785240 DOI: 10.1073/pnas.0909088106] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Indexed: 11/18/2022] Open
Abstract
Simulating the conformational dynamics of biomolecules is extremely difficult due to the rugged nature of their free energy landscapes and multiple long-lived, or metastable, states. Generalized ensemble (GE) algorithms, which have become popular in recent years, attempt to facilitate crossing between states at low temperatures by inducing a random walk in temperature space. Enthalpic barriers may be crossed more easily at high temperatures; however, entropic barriers will become more significant. This poses a problem because the dominant barriers to conformational change are entropic for many biological systems, such as the short RNA hairpin studied here. We present a new efficient algorithm for conformational sampling, called the adaptive seeding method (ASM), which uses nonequilibrium GE simulations to identify the metastable states, and seeds short simulations at constant temperature from each of them to quantitatively determine their equilibrium populations. Thus, the ASM takes advantage of the broad sampling possible with GE algorithms but generally crosses entropic barriers more efficiently during the seeding simulations at low temperature. We show that only local equilibrium is necessary for ASM, so very short seeding simulations may be used. Moreover, the ASM may be used to recover equilibrium properties from existing datasets that failed to converge, and is well suited to running on modern computer clusters.
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Affiliation(s)
| | | | | | - Vijay S. Pande
- Biophysics Program
- Department of Chemistry, Stanford University, Stanford, CA 94305
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Irbäck A, Mitternacht S, Mohanty S. An effective all-atom potential for proteins. PMC BIOPHYSICS 2009; 2:2. [PMID: 19356242 PMCID: PMC2696411 DOI: 10.1186/1757-5036-2-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Accepted: 04/08/2009] [Indexed: 11/25/2022]
Abstract
We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed α/β protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49–67-residue systems with high statistical accuracy, using only modest computational resources by today's standards. PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc
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Affiliation(s)
- Anders Irbäck
- Computational Biology & Biological Physics, Department of Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden.
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Carr JM, Wales DJ. Folding pathways and rates for the three-stranded beta-sheet peptide Beta3s using discrete path sampling. J Phys Chem B 2008; 112:8760-9. [PMID: 18588333 DOI: 10.1021/jp801777p] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The discrete path sampling method was used to investigate the folding of a three-stranded antiparallel beta-sheet peptide, Beta3s, described by an empirical potential and implicit solvent model. After application of a coarse-graining scheme that groups together sets of minima in local equilibrium, the calculated folding time was in reasonable agreement with other simulations and consistent with the experimental upper bound. The folding mechanism exhibited by the most significant discrete paths involves early formation of the C-terminal hairpin followed by docking of the N-terminal strand.
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Affiliation(s)
- Joanne M Carr
- University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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Use of 13C(alpha) chemical shifts for accurate determination of beta-sheet structures in solution. Proc Natl Acad Sci U S A 2008; 105:1891-6. [PMID: 18250334 DOI: 10.1073/pnas.0711022105] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13C(alpha) chemical shifts, is applied to determine the structure of a 20-residue all-beta peptide (BS2). The approach makes use of 13C(alpha) chemical shifts, computed at the density functional level of theory, to derive backbone and side-chain torsional constraints for all of the amino acid residues, without making use of information about residue occupancy in any region of the Ramachandran map. In addition, the torsional constraints are derived dynamically--i.e., they are redefined at each step of the algorithm. It is shown that, starting from randomly generated conformations, the final protein models are more accurate than existing NMR-derived models of the peptide, in terms of the agreement between predicted and observed 13C(beta) chemical shifts, and some stereochemical quality indicators. The accumulated evidence indicates that, for a highly flexible BS2 peptide in solution, it may not be possible to determine a single structure (or a small set of structures) that would satisfy all of the constraints exactly and simultaneously because the observed NOEs and 13C(alpha) chemical shifts correspond to a dynamic ensemble of conformations. Analysis of the structural flexibility, carried out by molecular dynamics simulations in explicit water, revealed that the whole peptide can be characterized as having liquid-like behavior, according to the Lindemann criterion. In summary, a beta-sheet structure of a highly flexible peptide in solution can be determined by a quantum-chemical-based procedure.
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Toward Reliable Simulations of Protein Folding, Misfolding and Aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2008. [DOI: 10.1016/s0079-6603(08)00402-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Zimmermann O, Hansmann UH. Understanding protein folding: small proteins in silico. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1784:252-8. [PMID: 18036571 PMCID: PMC2244683 DOI: 10.1016/j.bbapap.2007.10.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Accepted: 10/26/2007] [Indexed: 10/24/2022]
Abstract
Recent improvements in methodology and increased computer power now allow atomistic computer simulations of protein folding. We briefly review several advanced Monte Carlo algorithms that have contributed to this development. Details of folding simulations of three designed mini proteins are shown. Adding global translations and rotations has allowed us to handle multiple chains and to simulate the aggregation of six beta-amyloid fragments. In a different line of research we have developed several algorithms to predict local features from sequence. In an outlook we sketch how such biasing could extend the application spectrum of Monte Carlo simulations to structure prediction of larger proteins.
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Affiliation(s)
- Olav Zimmermann
- John von Neumann Institut für Computing, Research Centre Jülich, 52425 Jülich, Germany
| | - Ulrich H.E. Hansmann
- John von Neumann Institut für Computing, Research Centre Jülich, 52425 Jülich, Germany
- Department of Physics, Michigan Technological University, Houghton, MI 49931, U.S.A
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Abstract
Using the 28 residue betabetaalpha protein FSD-EY as a target system, we examine correction terms for the ECEPP/3 force field. We find an increased probability of formation of the native state at low temperatures resulting from a reduced propensity to form alpha helices and increased formation of beta sheets. Our analysis of the observed folding events suggests that the C-terminal helix of FSD-EY is much more stable than the N-terminal beta hairpin and forms first. The hydrophobic groups of the helix provide a template which promotes the formation of the beta hairpin that is never observed to form without the helix.
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Affiliation(s)
- Sandipan Mohanty
- John von Neumann Institut für Computing, Forschungszentrum Jülich, Jülich D-52425, Germany.
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14
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Mohanty S, Hansmann UHE. Improving an all-atom force field. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:012901. [PMID: 17677516 DOI: 10.1103/physreve.76.012901] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2007] [Indexed: 05/16/2023]
Abstract
Experimentally well-characterized proteins that are small enough to be computationally tractable provide useful information for refining existing all-atom force fields. This is used by us for reparametrizing a recently developed all-atom force field. Relying on high statistics parallel tempering simulations of a designed 20 residue beta-sheet peptide, we propose incremental changes that improve the force field's range of applicability.
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Affiliation(s)
- Sandipan Mohanty
- John von Neumann Institut für Computing, Forschungszentrum Jülich, Jülich, Germany.
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