101
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Liu H, Song D, Zhang Y, Yang S, Luo R, Chen HF. Extensive tests and evaluation of the CHARMM36IDPSFF force field for intrinsically disordered proteins and folded proteins. Phys Chem Chem Phys 2019; 21:21918-21931. [PMID: 31552948 DOI: 10.1039/c9cp03434j] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) have received increasing attention in recent studies due to their structural heterogeneity and critical biological functions. To fully understand the structural properties and determine accurate ensembles of IDPs, molecular dynamics (MD) simulation was widely used to sample diverse conformations and reveal the structural dynamics. However, the classical state-of-the-art force fields perform well for folded proteins while being unsatisfactory for the simulations of disordered proteins reported in many previous studies. Thus, improved force fields were developed to precisely describe both folded proteins and disordered proteins. Preliminary tests show that our newly developed CHARMM36IDPSFF (C36IDPSFF) force field can well reproduce the experimental observables of several disordered proteins, but more tests on different types of proteins are needed to further evaluate the performance of C36IDPSFF. Here, we extensively simulate short peptides, disordered proteins, and fast-folding proteins as well as folded proteins, and compare the simulated results with the experimental observables. The simulation results show that C36IDPSFF could substantially reproduce the experimental observables for most of the tested proteins but some limitations are also found in the radius of gyration of large disordered proteins and the stability of fast-folding proteins. This force field will facilitate large scale studies of protein structural dynamics and functions using MD simulations.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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102
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Dyson HJ, Wright PE. Perspective: the essential role of NMR in the discovery and characterization of intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:651-659. [PMID: 31617035 PMCID: PMC7043288 DOI: 10.1007/s10858-019-00280-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 09/12/2019] [Indexed: 05/13/2023]
Abstract
The 2019 ISMAR Prize recognized NMR studies of disordered proteins. Here we provide a highly personal perspective on the discovery of intrinsically disordered proteins and the development and application of NMR methods to characterize their conformational ensembles, dynamics, and interactions.
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Affiliation(s)
- H Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
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103
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Adamski W, Salvi N, Maurin D, Magnat J, Milles S, Jensen MR, Abyzov A, Moreau CJ, Blackledge M. A Unified Description of Intrinsically Disordered Protein Dynamics under Physiological Conditions Using NMR Spectroscopy. J Am Chem Soc 2019; 141:17817-17829. [PMID: 31591893 DOI: 10.1021/jacs.9b09002] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Intrinsically disordered proteins (IDPs) are flexible biomolecules whose essential functions are defined by their dynamic nature. Nuclear magnetic resonance (NMR) spectroscopy is ideally suited to the investigation of this behavior at atomic resolution. NMR relaxation is increasingly used to detect conformational dynamics in free and bound forms of IDPs under conditions approaching physiological, although a general framework providing a quantitative interpretation of these exquisitely sensitive probes as a function of experimental conditions is still lacking. Here, measuring an extensive set of relaxation rates sampling multiple-time-scale dynamics over a broad range of crowding conditions, we develop and test an integrated analytical description that accurately portrays the motion of IDPs as a function of the intrinsic properties of the crowded molecular environment. In particular we observe a strong dependence of both short-range and long-range motional time scales of the protein on the friction of the solvent. This tight coupling between the dynamic behavior of the IDP and its environment allows us to develop analytical expressions for protein motions and NMR relaxation properties that can be accurately applied over a vast range of experimental conditions. This unified dynamic description provides new insight into the physical behavior of IDPs, extending our ability to quantitatively investigate their conformational dynamics under complex environmental conditions, and accurately predicting relaxation rates reporting on motions on time scales up to tens of nanoseconds, both in vitro and in cellulo.
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Affiliation(s)
- Wiktor Adamski
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Nicola Salvi
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Damien Maurin
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Justine Magnat
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Sigrid Milles
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Anton Abyzov
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Christophe J Moreau
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
| | - Martin Blackledge
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71, Avenue des Martyrs , Grenoble , France
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104
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Kubáň V, Srb P, Štégnerová H, Padrta P, Zachrdla M, Jaseňáková Z, Šanderová H, Vítovská D, Krásný L, Koval' T, Dohnálek J, Ziemska-Legiecka J, Grynberg M, Jarnot P, Gruca A, Jensen MR, Blackledge M, Žídek L. Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase. J Am Chem Soc 2019; 141:16817-16828. [PMID: 31550880 DOI: 10.1021/jacs.9b07837] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Electrostatic interactions play important roles in the functional mechanisms exploited by intrinsically disordered proteins (IDPs). The atomic resolution description of long-range and local structural propensities that can both be crucial for the function of highly charged IDPs presents significant experimental challenges. Here, we investigate the conformational behavior of the δ subunit of RNA polymerase from Bacillus subtilis whose unfolded domain is highly charged, with 7 positively charged amino acids followed by 51 acidic amino acids. Using a specifically designed analytical strategy, we identify transient contacts between the two regions using a combination of NMR paramagnetic relaxation enhancements, residual dipolar couplings (RDCs), chemical shifts, and small-angle scattering. This strategy allows the resolution of long-range and local ensemble averaged structural contributions to the experimental RDCs, and reveals that the negatively charged segment folds back onto the positively charged strand, compacting the conformational sampling of the protein while remaining highly flexible in solution. Mutation of the positively charged region abrogates the long-range contact, leaving the disordered domain in an extended conformation, possibly due to local repulsion of like-charges along the chain. Remarkably, in vitro studies show that this mutation also has a significant effect on transcription activity, and results in diminished cell fitness of the mutated bacteria in vivo. This study highlights the importance of accurately describing electrostatic interactions for understanding the functional mechanisms of IDPs.
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Affiliation(s)
| | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , v.v.i., Flemingovo nám 2 , Prague 6 16610 , Czech Republic
| | | | | | | | | | - Hana Šanderová
- Laboratory of Microbial Genetics and Gene Expression , Institute of Microbiology of the Czech Academy of Sciences , v.v.i., Vídenská 1083 , Prague 4 14220 , Czech Republic
| | - Dragana Vítovská
- Laboratory of Microbial Genetics and Gene Expression , Institute of Microbiology of the Czech Academy of Sciences , v.v.i., Vídenská 1083 , Prague 4 14220 , Czech Republic
| | - Libor Krásný
- Laboratory of Microbial Genetics and Gene Expression , Institute of Microbiology of the Czech Academy of Sciences , v.v.i., Vídenská 1083 , Prague 4 14220 , Czech Republic
| | - Tomáš Koval'
- Laboratory of Structure and Function of Biomolecules , Institute of Biotechnology of the Czech Academy of Sciences , v.v.i., Biocev, Prumyslová 595 , Vestec 25250 , Czech Republic
| | - Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules , Institute of Biotechnology of the Czech Academy of Sciences , v.v.i., Biocev, Prumyslová 595 , Vestec 25250 , Czech Republic
| | | | - Marcin Grynberg
- Institute of Biochemistry and Biophysics PAS , Pawinskiego 5A , Warsaw 02-106 , Poland
| | - Patryk Jarnot
- Institute of Informatics , Silesian University of Technology , Akademicka 16 , Gliwice 44-100 , Poland
| | - Aleksandra Gruca
- Institute of Informatics , Silesian University of Technology , Akademicka 16 , Gliwice 44-100 , Poland
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71 avenue des Martyrs , Grenoble 38044 , France
| | - Martin Blackledge
- Institut de Biologie Structurale , Université Grenoble Alpes-CEA-CNRS , 71 avenue des Martyrs , Grenoble 38044 , France
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105
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Panova S, Cliff MJ, Macek P, Blackledge M, Jensen MR, Nissink JWM, Embrey KJ, Davies R, Waltho JP. Mapping Hidden Residual Structure within the Myc bHLH-LZ Domain Using Chemical Denaturant Titration. Structure 2019; 27:1537-1546.e4. [DOI: 10.1016/j.str.2019.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/05/2019] [Accepted: 07/17/2019] [Indexed: 12/25/2022]
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106
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Ryazantsev MN, Nikolaev DM, Struts AV, Brown MF. Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. J Membr Biol 2019; 252:425-449. [PMID: 31570961 DOI: 10.1007/s00232-019-00095-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 09/10/2019] [Indexed: 12/20/2022]
Abstract
Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
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Affiliation(s)
- Mikhail N Ryazantsev
- Institute of Chemistry, Saint Petersburg State University, 26 Universitetskii pr, Saint Petersburg, Russia, 198504
| | - Dmitrii M Nikolaev
- Saint-Petersburg Academic University - Nanotechnology Research and Education Centre RAS, Saint Petersburg, Russia, 194021
| | - Andrey V Struts
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA.,Laboratory of Biomolecular NMR, Saint Petersburg State University, Saint Petersburg, Russia, 199034
| | - Michael F Brown
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Physics, University of Arizona, Tucson, AZ, 85721, USA.
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107
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Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. Proc Natl Acad Sci U S A 2019; 116:20446-20452. [PMID: 31548393 DOI: 10.1073/pnas.1907251116] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.
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108
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Abstract
Bayesian and Maximum Entropy approaches allow for a statistically sound and systematic fitting of experimental and computational data. Unfortunately, assessing the relative confidence in these two types of data remains difficult as several steps add unknown error. Here we propose the use of a validation-set method to determine the balance, and thus the amount of fitting. We apply the method to synthetic NMR chemical shift data of an intrinsically disordered protein. We show that the method gives consistent results even when other methods to assess the amount of fitting cannot be applied. Finally, we also describe how the errors in the chemical shift predictor can lead to an incorrect fitting and how using secondary chemical shifts could alleviate this problem.
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109
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Cannon JF. Novel phosphorylation-dependent regulation in an unstructured protein. Proteins 2019; 88:366-384. [PMID: 31512287 DOI: 10.1002/prot.25812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/15/2019] [Accepted: 09/04/2019] [Indexed: 12/15/2022]
Abstract
This work explores how phosphorylation of an unstructured protein region in inhibitor-2 (I2) regulates protein phosphatase-1 (PP1) enzyme activity using molecular dynamics (MD). Free I2 is largely unstructured; however, when bound to PP1, three segments adopt a stable structure. In particular, an I2 helix (i-helix) blocks the PP1 active site and inhibits phosphatase activity. I2 phosphorylation in the PP1-I2 complex activates phosphatase activity without I2 dissociation. The I2 Thr74 regulatory phosphorylation site is in an unstructured domain in PP1-I2. PP1-I2 MD demonstrated that I2 phosphorylation promotes early steps of PP1-I2 activation in explicit solvent models. Moreover, phosphorylation-dependent activation occurred in PP1-I2 complexes derived from I2 orthologs with diverse sequences from human, yeast, worm, and protozoa. This system allowed exploration of features of the 73-residue unstructured human I2 domain critical for phosphorylation-dependent activation. These studies revealed that components of I2 unstructured domain are strategically positioned for phosphorylation responsiveness including a transient α-helix. There was no evidence that electrostatic interactions of I2 phosphothreonine74 influenced PP1-I2 activation. Instead, phosphorylation altered the conformation of residues around Thr74. Phosphorylation uncurled the distance between I2 residues Glu71 to Tyr76 to promote PP1-I2 activation, whereas reduced distances reduced activation. This I2 residue Glu71 to Tyr76 distance distribution, independently from Thr74 phosphorylation, controls I2 i-helix displacement from the PP1 active site leading to PP1-I2 activation.
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Affiliation(s)
- John F Cannon
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri
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110
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Abstract
Structural disorder is widespread in regulatory protein networks. Weak and transient interactions render disordered proteins particularly sensitive to fluctuations in solution conditions such as ion and crowder concentrations. How this sensitivity alters folding coupled binding reactions, however, has not been fully understood. Here, we demonstrate that salt jointly modulates polymer properties and binding affinities of 5 disordered proteins from a transcription factor network. A combination of single-molecule Förster resonance energy transfer experiments, polymer theory, and molecular simulations shows that all 5 proteins expand with increasing ionic strengths due to Debye-Hückel charge screening. Simultaneously, pairwise affinities between the proteins increase by an order of magnitude within physiological salt limits. A quantitative analysis shows that 50% of the affinity increase can be explained by changes in the disordered state. Disordered state properties therefore have a functional relevance even if these states are not directly involved in biological functions. Numerical solutions of coupled binding equilibria with our results show that networks of homologous disordered proteins can function surprisingly robustly in fluctuating cellular environments, despite the sensitivity of its individual proteins.
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111
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Takeuchi K, Baskaran K, Arthanari H. Structure determination using solution NMR: Is it worth the effort? JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2019; 306:195-201. [PMID: 31345771 DOI: 10.1016/j.jmr.2019.07.045] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/10/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
It has been almost 40 years since solution NMR joined X-ray crystallography as a technique for determining high-resolution structures of proteins. Since then NMR derived structure has contributed in fundamental ways to our understanding of the function of biomolecules. With the already existing mature field of X-ray crystallography and the emergence of cryo-EM as techniques to tackle high-resolution structures of large protein complexes, the role of NMR in structure determination has been questioned. However, NMR has the unique ability to recapitulate the dynamic motion of proteins in their structures, while size limitations of the biomolecular systems that can be routinely studied still present challenges. The field has continually developed methodology and instrumentation since its introduction, pushing its frontiers and redefining its limits. Here we present a brief overview of NMR-based structure determination over the past 40 years. We outline the current state of the field and look ahead to the challenges that still need to be addressed to realize the future potential of NMR as a structural technique.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery (Molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Kumaran Baskaran
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Dr, Madison, WI 53706, United States
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, United States; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, United States.
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112
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Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit. Int J Mol Sci 2019; 20:ijms20174186. [PMID: 31461845 PMCID: PMC6747279 DOI: 10.3390/ijms20174186] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 08/22/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022] Open
Abstract
Traditionally, X-ray crystallography and NMR spectroscopy represent major workhorses of structural biologists, with the lion share of protein structures reported in protein data bank (PDB) being generated by these powerful techniques. Despite their wide utilization in protein structure determination, these two techniques have logical limitations, with X-ray crystallography being unsuitable for the analysis of highly dynamic structures and with NMR spectroscopy being restricted to the analysis of relatively small proteins. In recent years, we have witnessed an explosive development of the techniques based on Cryo-electron microscopy (Cryo-EM) for structural characterization of biological molecules. In fact, single-particle Cryo-EM is a special niche as it is a technique of choice for the structural analysis of large, structurally heterogeneous, and dynamic complexes. Here, sub-nanometer atomic resolution can be achieved (i.e., resolution below 10 Å) via single-particle imaging of non-crystalline specimens, with accurate 3D reconstruction being generated based on the computational averaging of multiple 2D projection images of the same particle that was frozen rapidly in solution. We provide here a brief overview of single-particle Cryo-EM and show how Cryo-EM has revolutionized structural investigations of membrane proteins. We also show that the presence of intrinsically disordered or flexible regions in a target protein represents one of the major limitations of this promising technique.
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113
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Guseva S, Milles S, Blackledge M, Ruigrok RWH. The Nucleoprotein and Phosphoprotein of Measles Virus. Front Microbiol 2019; 10:1832. [PMID: 31496998 PMCID: PMC6713020 DOI: 10.3389/fmicb.2019.01832] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/25/2019] [Indexed: 01/04/2023] Open
Abstract
Measles virus is a negative strand virus and the genomic and antigenomic RNA binds to the nucleoprotein (N), assembling into a helical nucleocapsid. The polymerase complex comprises two proteins, the Large protein (L), that both polymerizes RNA and caps the mRNA, and the phosphoprotein (P) that co-localizes with L on the nucleocapsid. This review presents recent results about N and P, in particular concerning their intrinsically disordered domains. N is a protein of 525 residues with a 120 amino acid disordered C-terminal domain, Ntail. The first 50 residues of Ntail extricate the disordered chain from the nucleocapsid, thereby loosening the otherwise rigid structure, and the C-terminus contains a linear motif that binds P. Recent results show how the 5′ end of the viral RNA binds to N within the nucleocapsid and also show that the bases at the 3′ end of the RNA are rather accessible to the viral polymerase. P is a tetramer and most of the protein is disordered; comprising 507 residues of which around 380 are disordered. The first 37 residues of P bind N, chaperoning against non-specific interaction with cellular RNA, while a second interaction site, around residue 200 also binds N. In addition, there is another interaction between C-terminal domain of P (XD) and Ntail. These results allow us to propose a new model of how the polymerase binds to the nucleocapsid and suggests a mechanism for initiation of transcription.
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Affiliation(s)
- Serafima Guseva
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
| | - Rob W H Ruigrok
- Université Grenoble Alpes, Le Centre National de la Recherche Scientifique, Commissariatá l'Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, Grenoble, France
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114
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Rodríguez-Zamora P. Conjugation of NMR and SAXS for flexible and multidomain protein structure determination: From sample preparation to model refinement. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 150:140-144. [PMID: 31445067 DOI: 10.1016/j.pbiomolbio.2019.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 07/31/2019] [Accepted: 08/21/2019] [Indexed: 10/26/2022]
Abstract
Experimental information from small angle X-ray scattering (SAXS) is conjugated with nuclear magnetic resonance (NMR) spectroscopy data for the improvement of protein structure determination, particularly for flexible, multidomain or intrinsically disordered proteins. Individually, each of these techniques presents capabilities and limitations: NMR excels in local information, providing atomic resolution, but is limited by protein size, whereas SAXS yields a global envelope of the protein with lower resolution, but revealing domain positions. Different conjugation methodologies use the complementarity of both techniques' independent constraints to achieve comprehensive protein structure determination and resolve dynamics at a moderate computational expense.
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Affiliation(s)
- P Rodríguez-Zamora
- Instituto de Física, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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115
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Balazs AYS, Carbajo RJ, Davies NL, Dong Y, Hird AW, Johannes JW, Lamb ML, McCoull W, Raubo P, Robb GR, Packer MJ, Chiarparin E. Free Ligand 1D NMR Conformational Signatures To Enhance Structure Based Drug Design of a Mcl-1 Inhibitor (AZD5991) and Other Synthetic Macrocycles. J Med Chem 2019; 62:9418-9437. [PMID: 31361481 DOI: 10.1021/acs.jmedchem.9b00716] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The three-dimensional conformations adopted by a free ligand in solution impact bioactivity and physicochemical properties. Solution 1D NMR spectra inherently contain information on ligand conformational flexibility and three-dimensional shape, as well as the propensity of the free ligand to fully preorganize into the bioactive conformation. Herein we discuss some key learnings, distilled from our experience developing potent and selective synthetic macrocyclic inhibitors, including Mcl-1 clinical candidate AZD5991. Case studies have been selected from recent oncology research projects, demonstrating how 1D NMR conformational signatures can complement X-ray protein-ligand structural information to guide medicinal chemistry optimization. Learning to extract free ligand conformational information from routinely available 1D NMR signatures has proven to be fast enough to guide medicinal chemistry decisions within design cycles for compound optimization.
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Affiliation(s)
- Amber Y S Balazs
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Rodrigo J Carbajo
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Nichola L Davies
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Yu Dong
- Pharmaron Beijing Co., Ltd. , Beijing 100176 , China
| | - Alexander W Hird
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Jeffrey W Johannes
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - Michelle L Lamb
- Chemistry, R&D Oncology , AstraZeneca , Waltham , Massachusetts 02451 , United States
| | - William McCoull
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Piotr Raubo
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Graeme R Robb
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
| | - Martin J Packer
- Chemistry, R&D Oncology , AstraZeneca , Cambridge CB4 0QA , United Kingdom
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116
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Demerdash O, Shrestha UR, Petridis L, Smith JC, Mitchell JC, Ramanathan A. Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins. Front Mol Biosci 2019; 6:64. [PMID: 31475155 PMCID: PMC6705226 DOI: 10.3389/fmolb.2019.00064] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/16/2019] [Indexed: 12/26/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) play important roles in many aspects of normal cell physiology, such as signal transduction and transcription, as well as pathological states, including Alzheimer's, Parkinson's, and Huntington's disease. Unlike their globular counterparts that are defined by a few structures and free energy minima, IDP/IDR comprise a large ensemble of rapidly interconverting structures and a corresponding free energy landscape characterized by multiple minima. This aspect has precluded the use of structural biological techniques, such as X-ray crystallography and nuclear magnetic resonance (NMR) for resolving their structures. Instead, low-resolution techniques, such as small-angle X-ray or neutron scattering (SAXS/SANS), have become a mainstay in characterizing coarse features of the ensemble of structures. These are typically complemented with NMR data if possible or computational techniques, such as atomistic molecular dynamics, to further resolve the underlying ensemble of structures. However, over the past 10–15 years, it has become evident that the classical, pairwise-additive force fields that have enjoyed a high degree of success for globular proteins have been somewhat limited in modeling IDP/IDR structures that agree with experiment. There has thus been a significant effort to rehabilitate these models to obtain better agreement with experiment, typically done by optimizing parameters in a piecewise fashion. In this work, we take a different approach by optimizing a set of force field parameters simultaneously, using machine learning to adapt force field parameters to experimental SAXS scattering profiles. We demonstrate our approach in modeling three biologically IDP ensembles based on experimental SAXS profiles and show that our optimization approach significantly improve force field parameters that generate ensembles in better agreement with experiment.
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Affiliation(s)
- Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Utsab R Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Loukas Petridis
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, United States
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN, United States
| | - Arvind Ramanathan
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.,Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, United States
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117
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Proteasome Activation to Combat Proteotoxicity. Molecules 2019; 24:molecules24152841. [PMID: 31387243 PMCID: PMC6696185 DOI: 10.3390/molecules24152841] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 12/11/2022] Open
Abstract
Loss of proteome fidelity leads to the accumulation of non-native protein aggregates and oxidatively damaged species: hallmarks of an aged cell. These misfolded and aggregated species are often found, and suggested to be the culpable party, in numerous neurodegenerative diseases including Huntington's, Parkinson's, Amyotrophic Lateral Sclerosis (ALS), and Alzheimer's Diseases (AD). Many strategies for therapeutic intervention in proteotoxic pathologies have been put forth; one of the most promising is bolstering the efficacy of the proteasome to restore normal proteostasis. This strategy is ideal as monomeric precursors and oxidatively damaged proteins, so called "intrinsically disordered proteins" (IDPs), are targeted by the proteasome. This review will provide an overview of disorders in proteins, both intrinsic and acquired, with a focus on susceptibility to proteasomal degradation. We will then examine the proteasome with emphasis on newly published structural data and summarize current known small molecule proteasome activators.
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118
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Kolonko M, Greb-Markiewicz B. bHLH-PAS Proteins: Their Structure and Intrinsic Disorder. Int J Mol Sci 2019; 20:ijms20153653. [PMID: 31357385 PMCID: PMC6695611 DOI: 10.3390/ijms20153653] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/21/2022] Open
Abstract
The basic helix–loop–helix/Per-ARNT-SIM (bHLH–PAS) proteins are a class of transcriptional regulators, commonly occurring in living organisms and highly conserved among vertebrates and invertebrates. These proteins exhibit a relatively well-conserved domain structure: the bHLH domain located at the N-terminus, followed by PAS-A and PAS-B domains. In contrast, their C-terminal fragments present significant variability in their primary structure and are unique for individual proteins. C-termini were shown to be responsible for the specific modulation of protein action. In this review, we present the current state of knowledge, based on NMR and X-ray analysis, concerning the structural properties of bHLH–PAS proteins. It is worth noting that all determined structures comprise only selected domains (bHLH and/or PAS). At the same time, substantial parts of proteins, comprising their long C-termini, have not been structurally characterized to date. Interestingly, these regions appear to be intrinsically disordered (IDRs) and are still a challenge to research. We aim to emphasize the significance of IDRs for the flexibility and function of bHLH–PAS proteins. Finally, we propose modern NMR methods for the structural characterization of the IDRs of bHLH–PAS proteins.
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Affiliation(s)
- Marta Kolonko
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland
| | - Beata Greb-Markiewicz
- Department of Biochemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland.
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119
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Entropy and Information within Intrinsically Disordered Protein Regions. ENTROPY 2019; 21:e21070662. [PMID: 33267376 PMCID: PMC7515160 DOI: 10.3390/e21070662] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 02/06/2023]
Abstract
Bioinformatics and biophysical studies of intrinsically disordered proteins and regions (IDRs) note the high entropy at individual sequence positions and in conformations sampled in solution. This prevents application of the canonical sequence-structure-function paradigm to IDRs and motivates the development of new methods to extract information from IDR sequences. We argue that the information in IDR sequences cannot be fully revealed through positional conservation, which largely measures stable structural contacts and interaction motifs. Instead, considerations of evolutionary conservation of molecular features can reveal the full extent of information in IDRs. Experimental quantification of the large conformational entropy of IDRs is challenging but can be approximated through the extent of conformational sampling measured by a combination of NMR spectroscopy and lower-resolution structural biology techniques, which can be further interpreted with simulations. Conformational entropy and other biophysical features can be modulated by post-translational modifications that provide functional advantages to IDRs by tuning their energy landscapes and enabling a variety of functional interactions and modes of regulation. The diverse mosaic of functional states of IDRs and their conformational features within complexes demands novel metrics of information, which will reflect the complicated sequence-conformational ensemble-function relationship of IDRs.
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120
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Hartlmüller C, Spreitzer E, Göbl C, Falsone F, Madl T. NMR characterization of solvent accessibility and transient structure in intrinsically disordered proteins. JOURNAL OF BIOMOLECULAR NMR 2019; 73:305-317. [PMID: 31297688 PMCID: PMC6692294 DOI: 10.1007/s10858-019-00248-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 04/11/2019] [Indexed: 05/12/2023]
Abstract
In order to understand the conformational behavior of intrinsically disordered proteins (IDPs) and their biological interaction networks, the detection of residual structure and long-range interactions is required. However, the large number of degrees of conformational freedom of disordered proteins require the integration of extensive sets of experimental data, which are difficult to obtain. Here, we provide a straightforward approach for the detection of residual structure and long-range interactions in IDPs under near-native conditions using solvent paramagnetic relaxation enhancement (sPRE). Our data indicate that for the general case of an unfolded chain, with a local flexibility described by the overwhelming majority of available combinations, sPREs of non-exchangeable protons can be accurately predicted through an ensemble-based fragment approach. We show for the disordered protein α-synuclein and disordered regions of the proteins FOXO4 and p53 that deviation from random coil behavior can be interpreted in terms of intrinsic propensity to populate local structure in interaction sites of these proteins and to adopt transient long-range structure. The presented modification-free approach promises to be applicable to study conformational dynamics of IDPs and other dynamic biomolecules in an integrative approach.
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Affiliation(s)
- Christoph Hartlmüller
- Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 87548, Garching, Germany
| | - Emil Spreitzer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria
| | - Christoph Göbl
- The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, 610 University Avenue, Toronto, ON, M5G 2M9, Canada
| | - Fabio Falsone
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Institute of Molecular Biology & Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010, Graz, Austria.
- BioTechMed-Graz, Graz, Austria.
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121
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Salvi N, Abyzov A, Blackledge M. Solvent-dependent segmental dynamics in intrinsically disordered proteins. SCIENCE ADVANCES 2019; 5:eaax2348. [PMID: 31259246 PMCID: PMC6598773 DOI: 10.1126/sciadv.aax2348] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/22/2019] [Indexed: 05/04/2023]
Abstract
Protein and water dynamics have a synergistic relationship, which is particularly important for intrinsically disordered proteins (IDPs), although the details of this coupling remain poorly understood. Here, we combine temperature-dependent molecular dynamics simulations using different water models with extensive nuclear magnetic resonance (NMR) relaxation to examine the importance of distinct modes of solvent and solute motion for the accurate reproduction of site-specific dynamics in IDPs. We find that water dynamics play a key role in motional processes internal to "segments" of IDPs, stretches of primary sequence that share dynamic properties and behave as discrete dynamic units. We identify a relationship between the time scales of intrasegment dynamics and the lifetime of hydrogen bonds in bulk water. Correct description of these motions is essential for accurate reproduction of protein relaxation. Our findings open important perspectives for understanding the role of hydration water on the behavior and function of IDPs in solution.
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122
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Shabane PS, Izadi S, Onufriev AV. General Purpose Water Model Can Improve Atomistic Simulations of Intrinsically Disordered Proteins. J Chem Theory Comput 2019; 15:2620-2634. [PMID: 30865832 DOI: 10.1021/acs.jctc.8b01123] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP) remain a challenge: widely used, "general purpose" water models tend to favor overly compact structures relative to experiment. Here we have performed a total of 93 μs of unrestrained MD simulations to explore, in the context of IDPs, a recently developed "general-purpose" 4-point rigid water model OPC, which describes liquid state of water close to experiment. We demonstrate that OPC, together with a popular AMBER force field ff99SB, offers a noticeable improvement over TIP3P in producing more realistic structural ensembles of three common IDPs benchmarks: 55-residue apo N-terminal zinc-binding domain of HIV-1 integrase ("protein IN"), amyloid β-peptide (Aβ42) (residues 1-42), and 26-reside H4 histone tail. As a negative control, computed folding profile of a regular globular miniprotein (CLN025) in OPC water is in appreciably better agreement with experiment than that obtained in TIP3P, which tends to overstabilize the compact native state relative to the extended conformations. We employed Aβ42 peptide to investigate the possible influence of the solvent box size on simulation outcomes. We advocate a cautious approach for simulations of IDPs: we suggest that the solvent box size should be at least four times the radius of gyration of the random coil corresponding to the IDP. The computed free energy landscape of protein IN in OPC resembles a shallow "tub" - conformations with substantially different degrees of compactness that are within 2 kB T of each other. Conformations with very different secondary structure content coexist within 1 kB T of the global free energy minimum. States with higher free energy tend to have less secondary structure. Computed low helical content of the protein has virtually no correlation with its degree of compactness, which calls into question the possibility of using the helicity as a metric for assessing performance of water models for IDPs, when the helicity is low. Predicted radius of gyration ( R g) of H4 histone tail in OPC water falls in-between that of a typical globular protein and a fully denatured protein of the same size; the predicted R g is consistent with two independent predictions. In contrast, H4 tail in TIP3P water is as compact as the corresponding globular protein. The computed free energy landscape of H4 tail in OPC is relatively flat over a significant range of compactness, which, we argue, is consistent with its biological function as facilitator of internucleosome interactions.
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Affiliation(s)
| | - Saeed Izadi
- Early Stage Pharmaceutical Development , Genentech Inc. , South San Francisco , California 94080 , United States
| | - Alexey V Onufriev
- Department of Computer Science , Virginia Tech , Blacksburg , Virginia 24060 , United States.,Center for Soft Matter and Biological Physics , Virginia Tech , Blacksburg , Virginia 24061 , United States
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123
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Selenko P. Quo Vadis Biomolecular NMR Spectroscopy? Int J Mol Sci 2019; 20:ijms20061278. [PMID: 30875725 PMCID: PMC6472163 DOI: 10.3390/ijms20061278] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/06/2023] Open
Abstract
In-cell nuclear magnetic resonance (NMR) spectroscopy offers the possibility to study proteins and other biomolecules at atomic resolution directly in cells. As such, it provides compelling means to complement existing tools in cellular structural biology. Given the dominance of electron microscopy (EM)-based methods in current structure determination routines, I share my personal view about the role of biomolecular NMR spectroscopy in the aftermath of the revolution in resolution. Specifically, I focus on spin-off applications that in-cell NMR has helped to develop and how they may provide broader and more generally applicable routes for future NMR investigations. I discuss the use of ‘static’ and time-resolved solution NMR spectroscopy to detect post-translational protein modifications (PTMs) and to investigate structural consequences that occur in their response. I argue that available examples vindicate the need for collective and systematic efforts to determine post-translationally modified protein structures in the future. Furthermore, I explain my reasoning behind a Quinary Structure Assessment (QSA) initiative to interrogate cellular effects on protein dynamics and transient interactions present in physiological environments.
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Affiliation(s)
- Philipp Selenko
- Weizmann Institute of Science, Department of Biological Regulation, 234 Herzl Street, Rehovot 76100, Israel.
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124
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Bafaro EM, Maciejewski MW, Hoch JC, Dempski RE. Concomitant disorder and high-affinity zinc binding in the human zinc- and iron-regulated transport protein 4 intracellular loop. Protein Sci 2019; 28:868-880. [PMID: 30793391 DOI: 10.1002/pro.3591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/21/2019] [Accepted: 02/13/2019] [Indexed: 12/27/2022]
Abstract
The human zinc- and iron-regulated transport protein 4 (hZIP4) protein is the major plasma membrane protein responsible for the uptake of zinc in the body, and as such it plays a key role in cellular zinc homeostasis. hZIP4 plasma membrane levels are regulated through post-translational modification of its large, disordered, histidine-rich cytosolic loop (ICL2) in response to intracellular zinc concentrations. Here, structural characteristics of the isolated disordered loop region, both in the absence and presence of zinc, were investigated using nuclear magnetic resonance (NMR) spectroscopy. NMR chemical shifts, coupling constants and temperature coefficients of the apoprotein, are consistent with a random coil with minor propensities for transient polyproline Type II helices and β-strand in regions implicated in post-translational modifications. The ICL2 protein remains disordered upon zinc binding, which induces exchange broadening. Paramagnetic relaxation enhancement experiments reveal that the histidine-rich region in the apoprotein makes transient tertiary contacts with predicted post-translational modification sites. The residue-specific data presented here strengthen the relationship between hZIP4 post-translational modifications, which impact its role in cellular zinc homeostasis, and zinc sensing by the intracellular loop. Furthermore, the zinc sensing mechanism employed by the ICL2 protein demonstrates that high-affinity interactions can occur in the presence of conformational disorder.
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Affiliation(s)
- Elizabeth M Bafaro
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Mark W Maciejewski
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut 06030
| | - Jeffrey C Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, Connecticut 06030
| | - Robert E Dempski
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
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125
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Fast NMR method to probe solvent accessibility and disordered regions in proteins. Sci Rep 2019; 9:1647. [PMID: 30733478 PMCID: PMC6367444 DOI: 10.1038/s41598-018-37599-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 12/10/2018] [Indexed: 01/12/2023] Open
Abstract
Understanding protein structure and dynamics, which govern key cellular processes, is crucial for basic and applied research. Intrinsically disordered protein (IDP) regions display multifunctionality via alternative transient conformations, being key players in disease mechanisms. IDP regions are abundant, namely in small viruses, allowing a large number of functions out of a small proteome. The relation between protein function and structure is thus now seen from a different perspective: as IDP regions enable transient structural arrangements, each conformer can play different roles within the cell. However, as IDP regions are hard and time-consuming to study via classical techniques (optimized for globular proteins with unique conformations), new methods are required. Here, employing the dengue virus (DENV) capsid (C) protein and the immunoglobulin-binding domain of streptococcal protein G, we describe a straightforward NMR method to differentiate the solvent accessibility of single amino acid N-H groups in structured and IDP regions. We also gain insights into DENV C flexible fold region biological activity. The method, based on minimal pH changes, uses the well-established 1H-15N HSQC pulse sequence and is easily implementable in current protein NMR routines. The data generated are simple to interpret, with this rapid approach being an useful first-choice IDPs characterization method.
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126
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Cook EC, Sahu D, Bastidas M, Showalter SA. Solution Ensemble of the C-Terminal Domain from the Transcription Factor Pdx1 Resembles an Excluded Volume Polymer. J Phys Chem B 2018; 123:106-116. [PMID: 30525611 DOI: 10.1021/acs.jpcb.8b10051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pancreatic and duodenal homeobox 1 (Pdx1) is an essential pancreatic transcription factor. The C-terminal intrinsically disordered domain of Pdx1 (Pdx1-C) has a heavily biased amino acid composition; most notably, 18 of 83 residues are proline, including a hexaproline cluster near the middle of the chain. For these reasons, Pdx1-C is an attractive target for structure characterization, given the availability of suitable methods. To determine the solution ensembles of disordered proteins, we have developed a suite of 13C direct-detect NMR experiments that provide high spectral quality, even in the presence of strong proline enrichment. Here, we have extended our suite of NMR experiments to include four new pulse programs designed to record backbone residual dipolar couplings in a 13C,15N-CON detection format. Using our NMR strategy, in combination with small-angle X-ray scattering measurements and Monte Carlo simulations, we have determined that Pdx1-C is extended in solution, with a radius of gyration and internal scaling similar to that of an excluded volume polymer, and a subtle tendency toward a collapsed structure to the N-terminal side of the hexaproline sequence. This structure leaves Pdx1-C exposed for interactions with trans-regulatory co-factors that contribute with Pdx1 to transcription control in the cell.
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127
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Mateos B, Konrat R, Pierattelli R, Felli IC. NMR Characterization of Long-Range Contacts in Intrinsically Disordered Proteins from Paramagnetic Relaxation Enhancement in 13 C Direct-Detection Experiments. Chembiochem 2018; 20:335-339. [PMID: 30407719 DOI: 10.1002/cbic.201800539] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 12/31/2022]
Abstract
Intrinsically disordered proteins (IDPs) carry out many biological functions. They lack a stable 3D structure and are able to adopt many different conformations in dynamic equilibrium. The interplay between local dynamics and global rearrangements is key for their function. A widely used experimental NMR spectroscopy approach to study long-range contacts in IDPs exploits paramagnetic effects, and 1 H detection experiments are generally used to determine paramagnetic relaxation enhancement (PRE) for amide protons. However, under physiological conditions, exchange broadening hampers the detection of solvent-exposed amide protons, which reduces the content of information available. Herein, we present an experimental approach based on direct carbon detection of PRE that provides improved resolution, reduced sensitivity to exchange broadening, and complementary information derived from the use of different starting polarization sources.
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Affiliation(s)
- Borja Mateos
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Roberta Pierattelli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Isabella C Felli
- CERM and Department of Chemistry "Ugo Schiff", University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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128
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Xiong J, Gao M, Zhou J, Liu S, Su Z, Liu Z, Huang Y. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition. Proteins 2018; 87:265-275. [PMID: 30520528 DOI: 10.1002/prot.25646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) are extensively involved in dynamic signaling processes which require a high association rate and a high dissociation rate for rapid binding/unbinding events and at the same time a sufficient high affinity for specific recognition. Although the coupled folding-binding processes of IDPs have been extensively studied, it is still impossible to predict whether an unfolded protein is suitable for molecular signaling via coupled folding-binding. In this work, we studied the interplay between intrinsic folding mechanisms and coupled folding-binding process for unfolded proteins through molecular dynamics simulations. We first studied the folding process of three representative IDPs with different folded structures, that is, c-Myb, AF9, and E3 rRNase. We found the folding free energy landscapes of IDPs are downhill or show low barriers. To further study the influence of intrinsic folding mechanism on the binding process, we modulated the folding mechanism of barnase via circular permutation and simulated the coupled folding-binding process between unfolded barnase permutant and folded barstar. Although folding of barnase was coupled to target binding, the binding kinetics was significantly affected by the intrinsic folding free energy barrier, where reducing the folding free energy barrier enhances binding rate up to two orders of magnitude. This accelerating effect is different from previous results which reflect the effect of structure flexibility on binding kinetics. Our results suggest that coupling the folding of an unfolded protein with no/low folding free energy barrier with its target binding may provide a way to achieve high specificity and rapid binding/unbinding kinetics simultaneously.
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Affiliation(s)
- Junwen Xiong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Meng Gao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Jingjing Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Sen Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhengding Su
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, China
| | - Yongqi Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
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129
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Vymětal J, Jurásková V, Vondrášek J. AMBER and CHARMM Force Fields Inconsistently Portray the Microscopic Details of Phosphorylation. J Chem Theory Comput 2018; 15:665-679. [PMID: 30468703 DOI: 10.1021/acs.jctc.8b00715] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Phosphorylation of serine, threonine, and tyrosine is one of the most frequently occurring and crucial post-translational modifications of proteins often associated with important structural and functional changes. We investigated the direct effect of phosphorylation on the intrinsic conformational preferences of amino acids as a potential trigger of larger structural events. We conducted a comparative study of force fields on terminally capped amino acids (dipeptides) as the simplest model for phosphorylation. Our bias-exchange metadynamics simulations revealed that all model dipeptides sampled a great heterogeneity of ensembles affected by introduction of mono- and dianionic phosphate groups. However, the detected changes in populations of backbone conformers and side-chain rotamers did not reveal a strong discriminatory shift in preferences, as could be anticipated for the bulky, charged phosphate group. Furthermore, the AMBER and CHARMM force fields provided inconsistent populations of individual conformers as well as net structural trends upon phosphorylation. Detailed analysis of ensembles revealed competition between hydration and formation of internal hydrogen bonds involving amide hydrogens and the phosphate group. The observed difference in hydration free energy and potential for hydrogen bonding in individual force fields could be attributed to the different partial atomic charges used in each force field and, hence, the different parametrization strategies. Nevertheless, conformational propensities and net structural changes upon phosphorylation are difficult to extract from experimental measurements, and existing experimental data provide limited guidance for force field assessment and further development.
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Affiliation(s)
- Jiří Vymětal
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
| | - Veronika Jurásková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
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130
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Towards a Stochastic Paradigm: From Fuzzy Ensembles to Cellular Functions. Molecules 2018; 23:molecules23113008. [PMID: 30453632 PMCID: PMC6278454 DOI: 10.3390/molecules23113008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/11/2018] [Accepted: 11/16/2018] [Indexed: 01/03/2023] Open
Abstract
The deterministic sequence → structure → function relationship is not applicable to describe how proteins dynamically adapt to different cellular conditions. A stochastic model is required to capture functional promiscuity, redundant sequence motifs, dynamic interactions, or conformational heterogeneity, which facilitate the decision-making in regulatory processes, ranging from enzymes to membraneless cellular compartments. The fuzzy set theory offers a quantitative framework to address these problems. The fuzzy formalism allows the simultaneous involvement of proteins in multiple activities, the degree of which is given by the corresponding memberships. Adaptation is described via a fuzzy inference system, which relates heterogeneous conformational ensembles to different biological activities. Sequence redundancies (e.g., tandem motifs) can also be treated by fuzzy sets to characterize structural transitions affecting the heterogeneous interaction patterns (e.g., pathological fibrillization of stress granules). The proposed framework can provide quantitative protein models, under stochastic cellular conditions.
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131
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Oroz J, Chang BJ, Wysoczanski P, Lee CT, Pérez-Lara Á, Chakraborty P, Hofele RV, Baker JD, Blair LJ, Biernat J, Urlaub H, Mandelkow E, Dickey CA, Zweckstetter M. Structure and pro-toxic mechanism of the human Hsp90/PPIase/Tau complex. Nat Commun 2018; 9:4532. [PMID: 30382094 PMCID: PMC6208366 DOI: 10.1038/s41467-018-06880-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 10/03/2018] [Indexed: 02/01/2023] Open
Abstract
The molecular chaperone Hsp90 is critical for the maintenance of cellular homeostasis and represents a promising drug target. Despite increasing knowledge on the structure of Hsp90, the molecular basis of substrate recognition and pro-folding by Hsp90/co-chaperone complexes remains unknown. Here, we report the solution structures of human full-length Hsp90 in complex with the PPIase FKBP51, as well as the 280 kDa Hsp90/FKBP51 complex bound to the Alzheimer’s disease-related protein Tau. We reveal that the FKBP51/Hsp90 complex, which synergizes to promote toxic Tau oligomers in vivo, is highly dynamic and stabilizes the extended conformation of the Hsp90 dimer resulting in decreased Hsp90 ATPase activity. Within the ternary Hsp90/FKBP51/Tau complex, Hsp90 serves as a scaffold that traps the PPIase and nucleates multiple conformations of Tau’s proline-rich region next to the PPIase catalytic pocket in a phosphorylation-dependent manner. Our study defines a conceptual model for dynamic Hsp90/co-chaperone/client recognition. The chaperone Hsp90 plays a key role in maintaining cellular homeostasis. Here the authors provide structural insights into substrate recognition and the pro-folding mechanism of Hsp90/co-chaperone complexes by studying the complex of Hsp90 with its co-chaperone FKBP51 and the substrate Tau bound Hsp90/FKBP51 ternary complex using a NMR based integrative approach.
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Affiliation(s)
- Javier Oroz
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Straße 3a, 37075, Göttingen, Germany.,Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, 28006, Madrid, Spain
| | - Bliss J Chang
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Piotr Wysoczanski
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Straße 3a, 37075, Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Chung-Tien Lee
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Ángel Pérez-Lara
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Pijush Chakraborty
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Straße 3a, 37075, Göttingen, Germany
| | - Romina V Hofele
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany
| | - Jeremy D Baker
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Laura J Blair
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Jacek Biernat
- DZNE, CAESAR Research Center, Ludwig-Erhard-Alle 2, 53175, Bonn, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Eckhard Mandelkow
- DZNE, CAESAR Research Center, Ludwig-Erhard-Alle 2, 53175, Bonn, Germany
| | - Chad A Dickey
- Department of Molecular Medicine, Morsani College of Medicine, USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, FL, 33613, USA
| | - Markus Zweckstetter
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold-Straße 3a, 37075, Göttingen, Germany. .,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077, Göttingen, Germany.
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132
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Abstract
NMR spectroscopy has proven to be a key method for studying intrinsically disordered proteins (IDPs). Nonetheless, traditional NMR methods developed for solving structures of ordered protein complexes are insufficient for the full characterization of dynamic IDP complexes, where the energy landscape is broader and more rugged. Furthermore, due to their high sensitivity to environmental changes, NMR studies of IDP complexes must be conducted with extra care and the observed NMR parameters thoroughly evaluated to enable disentanglement of binding events from ensemble distribution changes. In this chapter, written for the non-NMR expert, we start out by outlining sample preparation for IDP complexes, guide through the recording and evaluation of diagnostic 1H,15N-HSQC spectra, and delineate more sophisticated NMR strategies to follow for the particular type of complex. The most relevant experiments are then described in terms of aims, needs, pitfalls, analysis, and expected outcomes, with references to recent examples.
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133
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Fuxreiter M. Fold or not to fold upon binding - does it really matter? Curr Opin Struct Biol 2018; 54:19-25. [PMID: 30340123 DOI: 10.1016/j.sbi.2018.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 12/14/2022]
Abstract
Protein interactions are usually determined by well-defined contact patterns. In this scenario, structuring of the interface is a prerequisite, which takes place prior or coupled to binding. Recent data, however, indicate plasticity of the templated folding pathway as well as considerable variations: polymorphism or dynamics in the bound-state. Conformational fluctuations in both cases are modulated by non-native, transient contacts, which complement suboptimal binding motifs to improve affinity. Here I discuss both templated folding and fuzzy binding mechanisms and propose a uniform scheme.
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Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Hungary.
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134
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Schneider R, Blackledge M, Jensen MR. Elucidating binding mechanisms and dynamics of intrinsically disordered protein complexes using NMR spectroscopy. Curr Opin Struct Biol 2018; 54:10-18. [PMID: 30316104 DOI: 10.1016/j.sbi.2018.09.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/20/2018] [Accepted: 09/21/2018] [Indexed: 01/10/2023]
Abstract
Advances in characterizing complexes of intrinsically disordered proteins (IDPs) have led to the discovery of a remarkably diverse interaction landscape that includes folding-upon-binding, highly dynamic complexes, multivalent interactions as well as regulatory switches controlled by post-translational modifications. Nuclear magnetic resonance (NMR) spectroscopy has in recent years made significant contributions to this field by describing the binding mechanisms and mapping conformational dynamics on multiple time scales. Importantly, this progress has been associated with specific methodological developments in NMR, for example in exchange techniques, allowing challenging biological systems to be studied at atomic resolution. In general, the level of dynamics observed in IDP complexes does not correlate with binding affinities, demonstrating the intricate relationship between conformational dynamics and IDP regulatory function.
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Affiliation(s)
- Robert Schneider
- Univ. Lille, CNRS, UMR 8576 - Unité de Glycobiologie Structurale et Fonctionnelle, F-59000 Lille, France
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135
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Cukier RI. Generating Intrinsically Disordered Protein Conformational Ensembles from a Database of Ramachandran Space Pair Residue Probabilities Using a Markov Chain. J Phys Chem B 2018; 122:9087-9101. [DOI: 10.1021/acs.jpcb.8b05797] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Robert I. Cukier
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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136
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Liu W, Liu X, Zhu G, Lu L, Yang D. A Method for Determining Structure Ensemble of Large Disordered Protein: Application to a Mechanosensing Protein. J Am Chem Soc 2018; 140:11276-11285. [PMID: 30124042 DOI: 10.1021/jacs.8b04792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structure characterization of intrinsically disordered proteins (IDPs) remains a key obstacle in understanding their functional mechanisms. Due to the highly dynamic feature of IDPs, structure ensembles instead of static unique structures are often derived from experimental data. Several state-of-the-art computational methods have been developed to select an optimal ensemble from a pregenerated structure pool, but they suffer from low efficiency for large IDPs. Here we present a matching pursuit genetic algorithm (MPGA) for structure ensemble determination, which takes advantages from both matching pursuit (MP) to reduce the search space and genetic algorithm (GA) to reduce the restriction on constraint types. The MPGA method is validated using a reference ensemble with predefined structures. In comparison with the conventional GA, MPGA takes much less computational time for large IDPs. The utility of the method is demonstrated by application to structure ensemble determination of a mechanosensing protein domain with 306 amino acids. The structure ensemble determined reveals that the N-terminal region 1-240 is more compact than the C-terminal region 240-306. The unique structural feature explains why only a small portion of YXXP tyrosine residues can be phosphorylated easily by kinases in the absence of extension force and why the phosphorylation is force-dependent.
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Affiliation(s)
- Wei Liu
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
| | - Xiao Liu
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
| | - Guanhua Zhu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551 , Singapore
| | - Lanyuan Lu
- School of Biological Sciences , Nanyang Technological University , 60 Nanyang Drive , Singapore 637551 , Singapore
| | - Daiwen Yang
- Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543 , Singapore
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137
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Milles S, Jensen MR, Lazert C, Guseva S, Ivashchenko S, Communie G, Maurin D, Gerlier D, Ruigrok RWH, Blackledge M. An ultraweak interaction in the intrinsically disordered replication machinery is essential for measles virus function. SCIENCE ADVANCES 2018; 4:eaat7778. [PMID: 30140745 PMCID: PMC6105297 DOI: 10.1126/sciadv.aat7778] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/18/2018] [Indexed: 05/05/2023]
Abstract
Measles virus genome encapsidation is essential for viral replication and is controlled by the intrinsically disordered phosphoprotein (P) maintaining the nucleoprotein in a monomeric form (N) before nucleocapsid assembly. All paramyxoviruses harbor highly disordered amino-terminal domains (PNTD) that are hundreds of amino acids in length and whose function remains unknown. Using nuclear magnetic resonance (NMR) spectroscopy, we describe the structure and dynamics of the 90-kDa N0PNTD complex, comprising 450 disordered amino acids, at atomic resolution. NMR relaxation dispersion reveals the existence of an ultraweak N-interaction motif, hidden within the highly disordered PNTD, that allows PNTD to rapidly associate and dissociate from a specific site on N while tightly bound at the amino terminus, thereby hindering access to the surface of N. Mutation of this linear motif quenches the long-range dynamic coupling between the two interaction sites and completely abolishes viral transcription/replication in cell-based minigenome assays comprising integral viral replication machinery. This description transforms our understanding of intrinsic conformational disorder in paramyxoviral replication. The essential mechanism appears to be conserved across Paramyxoviridae, opening unique new perspectives for drug development against this family of pathogens.
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Affiliation(s)
- Sigrid Milles
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Malene Ringkjøbing Jensen
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Carine Lazert
- International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Serafima Guseva
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Stefaniia Ivashchenko
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Guillaume Communie
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Damien Maurin
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Denis Gerlier
- International Center for Infectiology Research, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Université de Lyon, Lyon, France
| | - Rob W. H. Ruigrok
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Martin Blackledge
- Université Grenoble Alpes, CNRS, Commissariat à l’Energie Atomique et aux Energies Alternatives, Institut de Biologie Structurale, 38000 Grenoble, France
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138
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Liu H, Song D, Lu H, Luo R, Chen HF. Intrinsically disordered protein-specific force field CHARMM36IDPSFF. Chem Biol Drug Des 2018; 92:1722-1735. [DOI: 10.1111/cbdd.13342] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Dong Song
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Hui Lu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering; University of California; Irvine California
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; SJTU-Yale Joint Center for Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; School of Life Sciences and Biotechnology; Shanghai Jiao Tong University; Shanghai China
- Shanghai Center for Bioinformation Technology; Shanghai China
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139
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Orton HW, Otting G. Accurate Electron-Nucleus Distances from Paramagnetic Relaxation Enhancements. J Am Chem Soc 2018; 140:7688-7697. [PMID: 29790335 DOI: 10.1021/jacs.8b03858] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Measurements of paramagnetic relaxation enhancements (PREs) in 1H NMR spectra are an important tool to obtain long-range distance information in proteins, but quantitative interpretation is easily compromised by nonspecific intermolecular PREs. Here we show that PREs generated by lanthanides with anisotropic magnetic susceptibilities offer a route to accurate calibration-free distance measurements. As these lanthanides change 1H chemical shifts due to pseudocontact shifts, the relaxation rates in the paramagnetic and diamagnetic state can be measured with a single sample that simultaneously contains the protein labeled with a paramagnetic and a diamagnetic lanthanide ion. Nonspecific intermolecular PREs are thus automatically subtracted when calculating the PREs as the difference in nuclear relaxation rates between paramagnetic and diamagnetic protein. Although PREs from lanthanides with anisotropic magnetic susceptibilities are complicated by additional cross-correlation effects and residual dipolar couplings (RDCs) in the paramagnetic state, these effects can be controlled by the choice of lanthanide ion and experimental conditions. Using calbindin D9k with erbium, we succeeded in measuring intramolecular PREs with unprecedented accuracy, resulting in distance predictions with a root-mean-square-deviation of <0.9 Å in the range 11-24 Å.
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Affiliation(s)
- Henry W Orton
- Research School of Chemistry , Australian National University , Canberra , Australian Capital Territory 2601 , Australia
| | - Gottfried Otting
- Research School of Chemistry , Australian National University , Canberra , Australian Capital Territory 2601 , Australia
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140
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Abstract
Up to 40% of intracellular water is confined due to the dense packing of macromolecules, ions, and osmolytes. Despite the large body of work concerning the effect of additives on the biomolecular structure and stability, the role of crowding and heterogeneity in these interactions is not well understood. Here, infrared spectroscopy and molecular dynamics simulations are used to describe the mechanisms by which crowding modulates hydrogen bonding interactions between water and dimethyl sulfoxide (DMSO). Specifically, we use formamide and dimethylformamide (DMF) as molecular crowders and show that the S═O hydrogen bond populations in aqueous mixtures are increased by both amides. These additives increase the amount of water within the DMSO first solvation shell through two mechanisms: (a) directly stabilizing water-DMSO hydrogen bonds; (b) increasing water exposure by destabilizing DMSO-DMSO self-interactions. Further, we quantified the hydrogen bond enthalpies between the different components: DMSO-water (61 kJ/mol) > DMSO-formamide (32 kJ/mol) > water-water (23 kJ/mol) ≫ formamide-water (4.7 kJ/mol). Spectra of carbonyl stretching vibrations show that DMSO induces the dehydration of amides as a result of strong DMSO-water interactions, which has been suggested as the main mechanism of protein destabilization.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry , University of Texas at Austin , 105 E 24th St. Stop A5300 , Austin , TX 78712 , United States
| | - Carlos R Baiz
- Department of Chemistry , University of Texas at Austin , 105 E 24th St. Stop A5300 , Austin , TX 78712 , United States
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141
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Lanza G, Chiacchio MA. Quantum Mechanics Study on Hydrophilic and Hydrophobic Interactions in the Trivaline-Water System. J Phys Chem B 2018; 122:4289-4298. [PMID: 29584432 DOI: 10.1021/acs.jpcb.8b00833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the aim to elucidate hydrophobic effects in the unfolded state of peptides, DFT-M062X computations on the Val3H+· nH2O ( n up to 22) clusters have been accomplished. As far as the main chain is concerned, four conformers with β-strand and/or polyproline type II conformations, PPII (indicated as β-β, β-PPII, PPII-β, and PPII-PPII), have been found by changing the ϕ and ψ angles. For bare peptide, the side chain (isopropyl) of each residue can independently take on three different orientations with negligible effects on energetics. The great isopropyl spatial separations in β-β and β-PPII conformers allow for the construction of synergic and extensive water-water and water-peptide H-bonding in the minimal hydration Val3H+·22H2O models without significant steric encumbrance. Conversely, due to the proximity of the isopropyl of the central residue with the other two, some restrictions in the water shell construction around the peptide become evident for the PPII-PPII conformer and the number of energetically accessible structures decreases. This is indicative of correlated motion involving isopropyls and backbone mediated by water molecules, the origin of the nearest neighbor effects. Comparing the thermodynamic data of Ala3H+·22H2O and Val3H+·22H2O, what emerges is that both hydration enthalpy and entropy drive the β-strand stability of the latter.
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Affiliation(s)
- Giuseppe Lanza
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
| | - Maria A Chiacchio
- Dipartimento di Scienze del Farmaco , Università di Catania , Viale A. Doria 6 , Catania 95125 , Italy
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142
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Kim SS, Seffernick JT, Lindert S. Accurately Predicting Disordered Regions of Proteins Using Rosetta ResidueDisorder Application. J Phys Chem B 2018; 122:3920-3930. [PMID: 29595057 DOI: 10.1021/acs.jpcb.8b01763] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Although many proteins necessitate well-folded structures to properly instigate their biological functions, a large fraction of functioning proteins contain regions-known as intrinsically disordered protein regions-where stable structures are not likely to form. Notable functional roles of intrinsically disordered proteins are in transcriptional regulation, translation, and cellular signal transduction. Moreover, intrinsically disordered protein regions are highly abundant in many proteins associated with various human diseases, therefore these segments have become attractive drug targets for potential therapeutics. Over the past decades, numerous computational methods have been developed to accurately predict disordered regions of proteins. Here we introduce a user-friendly and reliable approach for the prediction of disordered protein regions using the structure prediction software Rosetta. Using 245 proteins from a benchmark data set (16 DisProt database proteins) and a test data set (229 proteins with NMR data), we use Rosetta to predict the global protein structures and then show that there is a statistically significant difference between Rosetta scores in disordered and ordered regions, with scores being less favorable in disordered regions. Furthermore, the difference in scores between ordered and disordered protein regions is sufficient to accurately identify disordered protein regions. As a result, our Rosetta ResidueDisorder method (benchmark data set prediction accuracy of 71.77% and independent test data set prediction accuracy of 65.37%) outperformed other established disorder prediction tools and did not exhibit a biased prediction toward either ordered or disordered regions. To facilitate usage, a Rosetta application has been developed for the Rosetta ResidueDisorder method.
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Affiliation(s)
- Stephanie S Kim
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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143
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Fuxreiter M. Fuzziness in Protein Interactions-A Historical Perspective. J Mol Biol 2018; 430:2278-2287. [PMID: 29477337 DOI: 10.1016/j.jmb.2018.02.015] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/09/2018] [Accepted: 02/16/2018] [Indexed: 12/22/2022]
Abstract
The proposal that coupled folding to binding is not an obligatory mechanism for intrinsically disordered (ID) proteins was put forward 10 years ago. The notion of fuzziness implies that conformational heterogeneity can be maintained upon interactions of ID proteins, which has a functional impact either on regulated assembly or activity of the corresponding complexes. Here I review how the concept has evolved in the past decade, via increasing experimental data providing insights into the mechanisms, pathways and regulatory modes. The effects of structural diversity and transient contacts on protein assemblies have been collected and systematically analyzed (Fuzzy Complexes Database, http://protdyn-database.org). Fuzziness has also been exploited as a framework to decipher molecular organization of higher-order protein structures. Quantification of conformational heterogeneity opens exciting future perspectives for drug discovery from small molecule-ID protein interactions to supramolecular assemblies.
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Affiliation(s)
- Monika Fuxreiter
- MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary.
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144
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Takahashi S, Yoshida A, Oikawa H. Hypothesis: structural heterogeneity of the unfolded proteins originating from the coupling of the local clusters and the long-range distance distribution. Biophys Rev 2018; 10:363-373. [PMID: 29446056 DOI: 10.1007/s12551-018-0405-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/05/2018] [Indexed: 01/22/2023] Open
Abstract
We propose a hypothesis that explains two apparently contradicting observations for the heterogeneity of the unfolded proteins. First, the line confocal method of the single-molecule Förster resonance energy transfer (sm-FRET) spectroscopy revealed that the unfolded proteins possess broad peaks in the FRET efficiency plot, implying the significant heterogeneity that lasts longer than milliseconds. Second, the fluorescence correlation method demonstrated that the unfolded proteins fluctuate in the time scale shorter than 100 ns. To formulate the hypothesis, we first summarize the recent consensus for the structure and dynamics of the unfolded proteins. We next discuss the conventional method of the sm-FRET spectroscopy and its limitations for the analysis of the unfolded proteins, followed by the advantages of the line confocal method that revealed the heterogeneity. Finally, we propose that the structural heterogeneity formed by the local clustering of hydrophobic residues modulates the distribution of the long-range distance between the labeled chromophores, resulting in the broadening of the peak in the FRET efficiency plot. A clustering of hydrophobic residues around the chromophore might further contribute to the broadening. The proposed clusters are important for the understanding of protein folding mechanism.
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Affiliation(s)
- Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan. .,Department of Chemistry, Graduate school of Science, Tohoku University, Aramaki 6-3, Aoba-ku, Sendai, 980-8578, Japan.
| | - Aya Yoshida
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate school of Science, Tohoku University, Aramaki 6-3, Aoba-ku, Sendai, 980-8578, Japan
| | - Hiroyuki Oikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan.,Department of Chemistry, Graduate school of Science, Tohoku University, Aramaki 6-3, Aoba-ku, Sendai, 980-8578, Japan
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145
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Bhattacharya S, Xu L, Thompson D. Revisiting the earliest signatures of amyloidogenesis: Roadmaps emerging from computational modeling and experiment. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Shayon Bhattacharya
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Liang Xu
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
| | - Damien Thompson
- Department of Physics, Bernal InstituteUniversity of LimerickLimerickIreland
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146
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Suárez IP, Gauto DF, Hails G, Mascali FC, Crespo R, Zhao L, Wang J, Rasia RM. Conformational sampling of the intrinsically disordered dsRBD-1 domain from Arabidopsis thaliana DCL1. Phys Chem Chem Phys 2018; 20:11237-11246. [DOI: 10.1039/c7cp07908g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Partial folding and stability of DCL1-dsRBD1.
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Affiliation(s)
- Irina P. Suárez
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Diego F. Gauto
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Guillermo Hails
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Florencia C. Mascali
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Roberta Crespo
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
| | - Lingzi Zhao
- College of Physics
- Jilin University
- Jilin
- China
| | - Jin Wang
- State University of New York at Stony Brook
- USA
| | - Rodolfo M. Rasia
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR)
- Santa Fe
- Argentina
- Área Biofísica
- Facultad de Ciencias Bioquímicas y Farmacéuticas
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147
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Salmon L, Ahlstrom LS, Bardwell JCA, Horowitz S. Selecting Conformational Ensembles Using Residual Electron and Anomalous Density (READ). Methods Mol Biol 2018; 1764:491-504. [PMID: 29605935 PMCID: PMC6148353 DOI: 10.1007/978-1-4939-7759-8_31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Heterogeneous and dynamic biomolecular complexes play a central role in many cellular processes but are poorly understood due to experimental challenges in characterizing their structural ensembles. To address these difficulties, we developed a hybrid methodology that combines X-ray crystallography with ensemble selections typically used in NMR studies to determine structural ensembles of heterogeneous biomolecular complexes. The method, termed READ, for residual electron and anomalous density, enables the visualization of heterogeneous conformational ensembles of complexes within crystals. Here we present a detailed protocol for performing the ensemble selections to construct READ ensembles. From a diverse pool of binding poses, a selection scheme is used to determine a subset of conformations that maximizes agreement with the X-ray data. Overall, READ is a general approach for obtaining a high-resolution view of dynamic protein-protein complexes.
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Affiliation(s)
- Loïc Salmon
- Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques, UMR 5280, CNRS, ENS Lyon, UCB Lyon 1, Université de Lyon, Villeurbanne, France.
| | - Logan S Ahlstrom
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Scott Horowitz
- Department of Chemistry and Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.
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148
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Huang J, MacKerell AD. Force field development and simulations of intrinsically disordered proteins. Curr Opin Struct Biol 2017; 48:40-48. [PMID: 29080468 DOI: 10.1016/j.sbi.2017.10.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/30/2017] [Accepted: 10/04/2017] [Indexed: 12/17/2022]
Abstract
Intrinsically disordered proteins (IDPs) play important roles in many physiological processes such as signal transduction and transcriptional regulation. Computer simulations that are based on empirical force fields have been increasingly used to understand the biophysics of disordered proteins. In this review, we focus on recent improvement of protein force fields, including polarizable force fields, concerning their accuracy in modeling intrinsically disordered proteins. Some recent benchmarks and applications of these force fields are also overviewed.
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Affiliation(s)
- Jing Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn St., Baltimore, MD 21201, USA; Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, 5635 Fishers Lane, Rockville, MD 20852, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn St., Baltimore, MD 21201, USA.
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149
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Salvi N, Abyzov A, Blackledge M. Atomic resolution conformational dynamics of intrinsically disordered proteins from NMR spin relaxation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:43-60. [PMID: 29157493 DOI: 10.1016/j.pnmrs.2017.06.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 05/08/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful experimental approaches for investigating the conformational behaviour of intrinsically disordered proteins (IDPs). IDPs represent a significant fraction of all proteomes, and, despite their importance for understanding fundamental biological processes, the molecular basis of their activity still remains largely unknown. The functional mechanisms exploited by IDPs in their interactions with other biomolecules are defined by their intrinsic dynamic modes and associated timescales, justifying the considerable interest over recent years in the development of technologies adapted to measure and describe this behaviour. NMR spin relaxation delivers information-rich, site-specific data reporting on conformational fluctuations occurring throughout the molecule. Here we review recent progress in the use of 15N relaxation to identify local backbone dynamics and long-range chain-like motions in unfolded proteins.
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Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Anton Abyzov
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, University Grenoble Alpes, Grenoble 38044, France.
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150
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Shen Y, Roche J, Grishaev A, Bax A. Prediction of nearest neighbor effects on backbone torsion angles and NMR scalar coupling constants in disordered proteins. Protein Sci 2017; 27:146-158. [PMID: 28884933 DOI: 10.1002/pro.3292] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/03/2017] [Accepted: 09/05/2017] [Indexed: 12/29/2022]
Abstract
Using fine-tuned hydrogen bonding criteria, a library of coiled peptide fragments has been generated from a large set of high-resolution protein X-ray structures. This library is shown to be an improved representation of ϕ/ψ torsion angles seen in intrinsically disordered proteins (IDPs). The ϕ/ψ torsion angle distribution of the library, on average, provides good agreement with experimentally observed chemical shifts and 3 JHN-Hα coupling constants for a set of five disordered proteins. Inspection of the coil library confirms that nearest-neighbor effects significantly impact the ϕ/ψ distribution of residues in the coil state. Importantly, 3 JHN-Hα coupling constants derived from the nearest-neighbor modulated backbone ϕ distribution in the coil library show improved agreement to experimental values, thereby providing a better way to predict 3 JHN-Hα coupling constants for IDPs, and for identifying locations that deviate from fully random behavior.
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Affiliation(s)
- Yang Shen
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
| | - Julien Roche
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
| | - Alexander Grishaev
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520.,National Institute of Standards and Technology and the Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850
| | - Ad Bax
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892-0520
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