1
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Qin S, Zhou HX. Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.02.526886. [PMID: 36778236 PMCID: PMC9915584 DOI: 10.1101/2023.02.02.526886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
How the sequences of intrinsically disordered proteins (IDPs) code for functions is still an enigma. Dynamics, in particular residue-specific dynamics, holds crucial clues. Enormous efforts have been spent to characterize residue-specific dynamics of IDPs, mainly through NMR spin relaxation experiments. Here we present a sequence-based method, SeqDYN, for predicting residue-specific backbone dynamics of IDPs. SeqDYN employs a mathematical model with 21 parameters: one is a correlation length and 20 are the contributions of the amino acids to slow dynamics. Training on a set of 45 IDPs reveals aromatic, Arg, and long-branched aliphatic amino acids as the most active in slow dynamics whereas Gly and short polar amino acids as the least active. SeqDYN predictions not only provide an accurate and insightful characterization of sequence-dependent IDP dynamics but may also serve as indicators in a host of biophysical processes, including the propensities of IDP sequences to undergo phase separation.
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Affiliation(s)
- Sanbo Qin
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois Chicago, Chicago, IL 60607, USA
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2
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Ceccolini I, Kauffmann C, Holzinger J, Konrat R, Zawadzka-Kazimierczuk A. A set of cross-correlated relaxation experiments to probe the correlation time of two different and complementary spin pairs. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2024; 361:107661. [PMID: 38547550 DOI: 10.1016/j.jmr.2024.107661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/20/2024]
Abstract
Intrinsically disordered proteins (IDPs) defy the conventional structure-function paradigm by lacking a well-defined tertiary structure and exhibiting inherent flexibility. This flexibility leads to distinctive spin relaxation modes, reflecting isolated and specific motions within individual peptide planes. In this work, we propose a new pulse sequence to measure the longitudinal 13C' CSA-13C'-13Cα DD CCR rate [Formula: see text] and present a novel 3D version of the transverse [Formula: see text] CCR rate, adopting the symmetrical reconversion approach. We combined these rates with the analogous ΓxyN/NH and ΓzN/NH CCR rates to derive residue-specific correlation times for both spin-pairs within the same peptide plane. The presented approach offers a straightforward and intuitive way to compare the correlation times of two different and complementary spin vectors, anticipated to be a valuable aid to determine IDPs backbone dihedral angles distributions. We performed the proposed experiments on two systems: a folded protein ubiquitin and Coturnix japonica osteopontin, a prototypical IDP. Comparative analyses of the results show that the correlation times of different residues vary more for IDPs than globular proteins, indicating that the dynamics of IDPs is largely heterogeneous and dominated by local fluctuations.
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Affiliation(s)
- Irene Ceccolini
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | | | - Julian Holzinger
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria.
| | - Anna Zawadzka-Kazimierczuk
- University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre, Żwirki i Wigury 101, 02-089 Warsaw, Poland.
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3
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Schiavina M, Bracaglia L, Rodella MA, Kümmerle R, Konrat R, Felli IC, Pierattelli R. Optimal 13C NMR investigation of intrinsically disordered proteins at 1.2 GHz. Nat Protoc 2024; 19:406-440. [PMID: 38087081 DOI: 10.1038/s41596-023-00921-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 09/20/2023] [Indexed: 02/12/2024]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for characterizing biomolecules such as proteins and nucleic acids at atomic resolution. Increased magnetic field strengths drive progress in biomolecular NMR applications, leading to improved performance, e.g., higher resolution. A new class of NMR spectrometers with a 28.2 T magnetic field (1.2 GHz 1H frequency) has been commercially available since the end of 2019. The availability of ultra-high-field NMR instrumentation makes it possible to investigate more complex systems using NMR. This is especially true for highly flexible intrinsically disordered proteins (IDPs) and highly flexible regions (IDRs) of complex multidomain proteins. Indeed, the investigation of these proteins is frequently hampered by the crowding of NMR spectra. The advantages, however, are accompanied by challenges that the user must overcome when conducting experiments at such a high field (e.g., large spectral widths, radio frequency bandwidth, performance of decoupling schemes). This protocol presents strategies and tricks for optimising high-field NMR experiments for IDPs/IDRs based on the analysis of the relaxation properties of the investigated protein. The protocol, tested on three IDPs of different molecular weight and structural complexity, focuses on 13C-detected NMR at 1.2 GHz. A set of experiments, including some multiple receiver experiments, and tips to implement versions tailored for IDPs/IDRs are described. However, the general approach and most considerations can also be applied to experiments that acquire 1H or 15N nuclei and to experiments performed at lower field strengths.
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Affiliation(s)
- Marco Schiavina
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Lorenzo Bracaglia
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | - Maria Anna Rodella
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy
| | | | - Robert Konrat
- Department of Computational and Structural Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Isabella C Felli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
| | - Roberta Pierattelli
- Department of Chemistry 'Ugo Schiff' and Magnetic Resonance Center (CERM), University of Florence, Florence, Italy.
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4
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Ueda T. [Modulation of Aggregation and Immunogenicity of a Protein: Based on the Study of Hen Lysozyme]. YAKUGAKU ZASSHI 2024; 144:299-310. [PMID: 38432940 DOI: 10.1248/yakushi.23-00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
This study focuses on the modulation of protein aggregation and immunogenicity. As a starting point for investigating long-range interactions within a non-native protein, the effects of perturbing denatured protein states on their aggregation, including the formation of amyloid fibrils, were evaluated. The effects of adducts, sugar modifications, and stabilization on protein aggregation were then examined. We also investigated how protein immunogenicity was affected by enhancing protein conformational stability and other factors.
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Affiliation(s)
- Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University
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5
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Truong HP, Koren G, Avinery R, Beck R, Saleh OA. Pincus blob elasticity in an intrinsically disordered protein. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:100. [PMID: 37847354 DOI: 10.1140/epje/s10189-023-00360-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/29/2023] [Indexed: 10/18/2023]
Abstract
Understanding the dynamic structure of intrinsically disordered proteins (IDPs) is important to deciphering their biological functions. Here, we exploit precision entropic elasticity measurements to infer the conformational behavior of a model IDP construct formed from the disordered tail of the neurofilament low molecular weight protein. The IDP construct notably displays a low-force power-law elastic regime, consistent with the Pincus blob model, which allows direct extraction of the Flory exponent, [Formula: see text], from the force-extension relationship. We find [Formula: see text] increases with added denaturant, transitioning from a nearly ideal chain to a swollen chain in a manner quantitatively consistent with measurements of IDP dimensions from other experimental techniques. We suggest that measurements of entropic elasticity could be broadly useful in the study of IDP structure.
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Affiliation(s)
- Hoang P Truong
- Materials Department, University of California, Santa Barbara, USA
| | - Gil Koren
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Ram Avinery
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Roy Beck
- The Raymond and Beverly Sackler School of Physics and Astronomy and The Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
- The Center of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel
| | - Omar A Saleh
- Materials Department, University of California, Santa Barbara, USA.
- Biomolecular Sciences and Engineering Department, University of California, Santa Barbara, USA.
- Physics Department, University of California, Santa Barbara, USA.
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6
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Yanaka S, Yagi-Utsumi M, Kato K, Kuwajima K. The B domain of protein A retains residual structures in 6 M guanidinium chloride as revealed by hydrogen/deuterium-exchange NMR spectroscopy. Protein Sci 2023; 32:e4569. [PMID: 36659853 PMCID: PMC9926473 DOI: 10.1002/pro.4569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The characterization of residual structures persistent in unfolded proteins is an important issue in studies of protein folding, because the residual structures present, if any, may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the residual structures of the isolated B domain (BDPA) of staphylococcal protein A in 6 M guanidinium chloride. BDPA is a small three-helix-bundle protein, and until recently its folding/unfolding reaction has been treated as a simple two-state process between the native and the fully unfolded states. We employed a dimethylsulfoxide (DMSO)-quenched hydrogen/deuterium (H/D)-exchange 2D NMR techniques with the use of spin desalting columns, which allowed us to investigate the H/D-exchange behavior of individually identified peptide amide (NH) protons. We obtained H/D-exchange protection factors of the 21 NH protons that form an α-helical hydrogen bond in the native structure, and the majority of these NH protons were significantly protected with a protection factor of 2.0-5.2 in 6 M guanidinium chloride, strongly suggesting that these weakly protected NH protons form much stronger hydrogen bonds under native folding conditions. The results can be used to deduce the structure of an early folding intermediate, when such an intermediate is shown by other methods. Among three native helical regions, the third helix in the C-terminal side was highly protected and stabilized by side-chain salt bridges, probably acting as the folding initiation site of BDPA. The present results are discussed in relation to previous experimental and computational findings on the folding mechanisms of BDPA.
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Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Myodaiji, Okazaki, Aichi, Japan.,Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Myodaiji, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Mizuho-ku, Nagoya, Aichi, Japan
| | - Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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7
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Structural ensembles of disordered proteins from hierarchical chain growth and simulation. Curr Opin Struct Biol 2023; 78:102501. [PMID: 36463772 DOI: 10.1016/j.sbi.2022.102501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 12/03/2022]
Abstract
Disordered proteins and nucleic acids play key roles in cellular function and disease. Here, we review recent advances in the computational exploration of the conformational dynamics of flexible biomolecules. While atomistic molecular dynamics (MD) simulation has seen a lot of improvement in recent years, large-scale computing resources and careful validation are required to simulate full-length disordered biopolymers in solution. As a computationally efficient alternative, hierarchical chain growth (HCG) combines pre-sampled chain fragments in a statistically reproducible manner into ensembles of full-length atomically detailed biomolecular structures. Experimental data can be integrated during and after chain assembly. Applications to the neurodegeneration-linked proteins α-synuclein, tau, and TDP-43, including as condensate, illustrate the use of HCG. We conclude by highlighting the emerging connections to AI-based structural modeling including AlphaFold2.
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8
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Treviño MÁ, López-Sánchez R, Moya MR, Pantoja-Uceda D, Mompeán M, Laurents DV. Insight into polyproline II helical bundle stability in an antifreeze protein denatured state. Biophys J 2022; 121:4560-4568. [PMID: 36815707 PMCID: PMC9748357 DOI: 10.1016/j.bpj.2022.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 11/02/2022] Open
Abstract
The use of polyproline II (PPII) helices in protein design is currently hindered by limitations in our understanding of their conformational stability and folding. Recent studies of the snow flea antifreeze protein (sfAFP), a useful model system composed of six PPII helices, suggested that a low denatured state entropy contributes to folding thermodynamics. Here, circular dichroism spectroscopy revealed minor populations of PPII like conformers at low temperature. To get atomic level information on the conformational ensemble and entropy of the reduced, denatured state of sfAFP, we have analyzed its chemical shifts and {1H}-15N relaxation parameters by NMR spectroscopy at four experimental conditions. No significant populations of stable secondary structure were detected. The stiffening of certain N-terminal residues at neutral versus acidic pH and shifted pKa values leads us to suggest that favorable charge-charge interactions could bias the conformational ensemble to favor the formation the C1-C28 disulfide bond during nascent folding, although no evidence for preferred contacts between these positions was detected by paramagnetic relaxation enhancement under denaturing conditions. Despite a high content of flexible glycine residues, the mobility of the sfAFP denatured ensemble is similar for denatured α/β proteins both on fast ps/ns as well as slower μs/ms timescales. These results are in line with a conformational entropy in the denatured ensemble resembling that of typical proteins and suggest that new structures based on PPII helical bundles should be amenable to protein design.
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9
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Dey S, MacAinsh M, Zhou HX. Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins. J Chem Theory Comput 2022; 18:6310-6323. [PMID: 36084347 PMCID: PMC9561007 DOI: 10.1021/acs.jctc.2c00328] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
For intrinsically disordered proteins (IDPs), a pressing question is how sequence codes for function. Dynamics serves as a crucial link, reminiscent of the role of structure in sequence-function relations of structured proteins. To define general rules governing sequence-dependent backbone dynamics, we carried out long molecular dynamics simulations of eight IDPs. Blocks of residues exhibiting large amplitudes in slow dynamics are rigidified by local inter-residue interactions or secondary structures. A long region or an entire IDP can be slowed down by long-range contacts or secondary-structure packing. On the other hand, glycines promote fast dynamics and either demarcate rigid blocks or facilitate multiple modes of local and long-range inter-residue interactions. The sequence-dependent backbone dynamics endows IDPs with versatile response to binding partners, with some blocks recalcitrant while others readily adapting to intermolecular interactions.
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Affiliation(s)
- Souvik Dey
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Matthew MacAinsh
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
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10
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Yu L, Brüschweiler R. Quantitative prediction of ensemble dynamics, shapes and contact propensities of intrinsically disordered proteins. PLoS Comput Biol 2022; 18:e1010036. [PMID: 36084124 PMCID: PMC9491582 DOI: 10.1371/journal.pcbi.1010036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 09/21/2022] [Accepted: 08/03/2022] [Indexed: 12/29/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are highly dynamic systems that play an important role in cell signaling processes and their misfunction often causes human disease. Proper understanding of IDP function not only requires the realistic characterization of their three-dimensional conformational ensembles at atomic-level resolution but also of the time scales of interconversion between their conformational substates. Large sets of experimental data are often used in combination with molecular modeling to restrain or bias models to improve agreement with experiment. It is shown here for the N-terminal transactivation domain of p53 (p53TAD) and Pup, which are two IDPs that fold upon binding to their targets, how the latest advancements in molecular dynamics (MD) simulations methodology produces native conformational ensembles by combining replica exchange with series of microsecond MD simulations. They closely reproduce experimental data at the global conformational ensemble level, in terms of the distribution properties of the radius of gyration tensor, and at the local level, in terms of NMR properties including 15N spin relaxation, without the need for reweighting. Further inspection revealed that 10-20% of the individual MD trajectories display the formation of secondary structures not observed in the experimental NMR data. The IDP ensembles were analyzed by graph theory to identify dominant inter-residue contact clusters and characteristic amino-acid contact propensities. These findings indicate that modern MD force fields with residue-specific backbone potentials can produce highly realistic IDP ensembles sampling a hierarchy of nano- and picosecond time scales providing new insights into their biological function.
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Affiliation(s)
- Lei Yu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Rafael Brüschweiler
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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11
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Szabó CL, Sebák F, Bodor A. Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations. Anal Chem 2022; 94:7885-7891. [PMID: 35617314 DOI: 10.1021/acs.analchem.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast 1H-15N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.
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Affiliation(s)
- Csenge Lilla Szabó
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary.,Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Fanni Sebák
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Andrea Bodor
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
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12
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Schweitzer-Stenner R. Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides. Int J Mol Sci 2022; 23:ijms23105643. [PMID: 35628453 PMCID: PMC9147007 DOI: 10.3390/ijms23105643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
The Flory isolated pair hypothesis (IPH) is one of the corner stones of the random coil model, which is generally invoked to describe the conformational dynamics of unfolded and intrinsically disordered proteins (IDPs). It stipulates, that individual residues sample the entire sterically allowed space of the Ramachandran plot without exhibiting any correlations with the conformational dynamics of its neighbors. However, multiple lines of computational, bioinformatic and experimental evidence suggest that nearest neighbors have a significant influence on the conformational sampling of amino acid residues. This implies that the conformational entropy of unfolded polypeptides and proteins is much less than one would expect based on the Ramachandran plots of individual residues. A further implication is that the Gibbs energies of residues in unfolded proteins or polypeptides are not additive. This review provides an overview of what is currently known and what has yet to be explored regarding nearest neighbor interactions in unfolded proteins.
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13
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Camacho-Zarco AR, Schnapka V, Guseva S, Abyzov A, Adamski W, Milles S, Jensen MR, Zidek L, Salvi N, Blackledge M. NMR Provides Unique Insight into the Functional Dynamics and Interactions of Intrinsically Disordered Proteins. Chem Rev 2022; 122:9331-9356. [PMID: 35446534 PMCID: PMC9136928 DOI: 10.1021/acs.chemrev.1c01023] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Intrinsically disordered
proteins are ubiquitous throughout all
known proteomes, playing essential roles in all aspects of cellular
and extracellular biochemistry. To understand their function, it is
necessary to determine their structural and dynamic behavior and to
describe the physical chemistry of their interaction trajectories.
Nuclear magnetic resonance is perfectly adapted to this task, providing
ensemble averaged structural and dynamic parameters that report on
each assigned resonance in the molecule, unveiling otherwise inaccessible
insight into the reaction kinetics and thermodynamics that are essential
for function. In this review, we describe recent applications of NMR-based
approaches to understanding the conformational energy landscape, the
nature and time scales of local and long-range dynamics and how they
depend on the environment, even in the cell. Finally, we illustrate
the ability of NMR to uncover the mechanistic basis of functional
disordered molecular assemblies that are important for human health.
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Affiliation(s)
| | - Vincent Schnapka
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Serafima Guseva
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Anton Abyzov
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Wiktor Adamski
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | - Sigrid Milles
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
| | | | - Lukas Zidek
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 5, 82500 Brno, Czech Republic
| | - Nicola Salvi
- Université Grenoble Alpes, CEA, CNRS, IBS, 38000 Grenoble, France
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14
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Stelzl L, Pietrek LM, Holla A, Oroz J, Sikora M, Köfinger J, Schuler B, Zweckstetter M, Hummer G. Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS AU 2022; 2:673-686. [PMID: 35373198 PMCID: PMC8970000 DOI: 10.1021/jacsau.1c00536] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 05/13/2023]
Abstract
The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the balance between functional and disease-associated conformational states, we build a structural ensemble of the tau K18 fragment containing the four pseudorepeat domains involved in both microtubule binding and amyloid fibril formation. We assemble 129-residue-long tau K18 chains with atomic detail from an extensive fragment library constructed with molecular dynamics simulations. We introduce a reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on the local structure into the assembly process in a systematic manner. By combining Bayesian ensemble refinement with importance sampling, we obtain well-defined ensembles and overcome the problem of exponentially varying weights in the integrative modeling of long-chain polymeric molecules. The resulting tau K18 ensembles capture nuclear magnetic resonance (NMR) chemical shift and J-coupling measurements. Without further fitting, we achieve very good agreement with measurements of NMR residual dipolar couplings. The good agreement with experimental measures of global structure such as single-molecule Förster resonance energy transfer (FRET) efficiencies is improved further by ensemble refinement. By comparing wild-type and mutant ensembles, we show that pathogenic single-point P301L, P301S, and P301T mutations shift the population from the turn-like conformations of the functional microtubule-bound state to the extended conformations of disease-associated tau fibrils. RHCG thus provides us with an atomically detailed view of the population equilibrium between functional and aggregation-prone states of tau K18, and demonstrates that global structural characteristics of this intrinsically disordered protein emerge from its local structure.
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Affiliation(s)
- Lukas
S. Stelzl
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Faculty
of Biology, Johannes Gutenberg University
Mainz, Gresemundweg 2, 55128 Mainz, Germany
- KOMET 1, Institute of Physics, Johannes
Gutenberg University Mainz, 55099 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Lisa M. Pietrek
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Andrea Holla
- Department
of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Javier Oroz
- German
Center for Neurodegenerative Diseases (DZNE), von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Rocasolano
Institute for Physical Chemistry, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mateusz Sikora
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Faculty
of Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, 8057 Zurich, Switzerland
| | - Markus Zweckstetter
- German
Center for Neurodegenerative Diseases (DZNE), von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department
for NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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15
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Abstract
Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.
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Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
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16
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Abyzov A, Blackledge M, Zweckstetter M. Conformational Dynamics of Intrinsically Disordered Proteins Regulate Biomolecular Condensate Chemistry. Chem Rev 2022; 122:6719-6748. [PMID: 35179885 PMCID: PMC8949871 DOI: 10.1021/acs.chemrev.1c00774] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Motions in biomolecules
are critical for biochemical reactions.
In cells, many biochemical reactions are executed inside of biomolecular
condensates formed by ultradynamic intrinsically disordered proteins.
A deep understanding of the conformational dynamics of intrinsically
disordered proteins in biomolecular condensates is therefore of utmost
importance but is complicated by diverse obstacles. Here we review
emerging data on the motions of intrinsically disordered proteins
inside of liquidlike condensates. We discuss how liquid–liquid
phase separation modulates internal motions across a wide range of
time and length scales. We further highlight the importance of intermolecular
interactions that not only drive liquid–liquid phase separation
but appear as key determinants for changes in biomolecular motions
and the aging of condensates in human diseases. The review provides
a framework for future studies to reveal the conformational dynamics
of intrinsically disordered proteins in the regulation of biomolecular
condensate chemistry.
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Affiliation(s)
- Anton Abyzov
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany
| | - Martin Blackledge
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 38044 Grenoble, France.,CEA, DSV, IBS, 38044 Grenoble, France.,CNRS, IBS, 38044 Grenoble, France
| | - Markus Zweckstetter
- Translational Structural Biology Group, German Center for Neurodegenerative Diseases (DZNE), 37075 Göttingen, Germany.,Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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17
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Maula T, Vahvelainen N, Tossavainen H, Koivunen T, T. Pöllänen M, Johansson A, Permi P, Ihalin R. Decreased temperature increases the expression of a disordered bacterial late embryogenesis abundant (LEA) protein that enhances natural transformation. Virulence 2021; 12:1239-1257. [PMID: 33939577 PMCID: PMC8096337 DOI: 10.1080/21505594.2021.1918497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/22/2021] [Accepted: 04/03/2021] [Indexed: 11/02/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins are important players in the management of responses to stressful conditions, such as drought, high salinity, and changes in temperature. Many LEA proteins do not have defined three-dimensional structures, so they are intrinsically disordered proteins (IDPs) and are often highly hydrophilic. Although LEA-like sequences have been identified in bacterial genomes, the functions of bacterial LEA proteins have been studied only recently. Sequence analysis of outer membrane interleukin receptor I (BilRI) from the oral pathogen Aggregatibacter actinomycetemcomitans indicated that it shared sequence similarity with group 3/3b/4 LEA proteins. Comprehensive nuclearcgq magnetic resonance (NMR) studies confirmed its IDP nature, and expression studies in A. actinomycetemcomitans harboring a red fluorescence reporter protein-encoding gene revealed that bilRI promoter expression was increased at decreased temperatures. The amino acid backbone of BilRI did not stimulate either the production of reactive oxygen species from human leukocytes or the production of interleukin-6 from human macrophages. Moreover, BilRI-specific IgG antibodies could not be detected in the sera of A. actinomycetemcomitans culture-positive periodontitis patients. Since the bilRI gene is located near genes involved in natural competence (i.e., genes associated with the uptake of extracellular (eDNA) and its incorporation into the genome), we also investigated the role of BilRI in these events. Compared to wild-type cells, the ΔbilRI mutants showed a lower transformation efficiency, which indicates either a direct or indirect role in natural competence. In conclusion, A. actinomycetemcomitans might express BilRI, especially outside the host, to survive under stressful conditions and improve its transmission potential.
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Affiliation(s)
- Terhi Maula
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Nelli Vahvelainen
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Helena Tossavainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Tuuli Koivunen
- Department of Life Technologies, University of Turku, Turku, Finland
| | | | - Anders Johansson
- Division of Molecular Periodontology, Department of Odontology, Umeå University, Umeå, Sweden
| | - Perttu Permi
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
- Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Riikka Ihalin
- Department of Life Technologies, University of Turku, Turku, Finland
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18
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Leavens MJ, Spang LE, Cherney MM, Bowler BE. Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues. Biochemistry 2021; 60:3071-3085. [PMID: 34606713 PMCID: PMC8751257 DOI: 10.1021/acs.biochem.1c00400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopseudomonas palustris cytochrome c', a four-helix bundle, and the second ubiquitin-associated domain, UBA(2), a three-helix bundle from the human homologue of yeast Rad23, HHR23A, deviate from random coil behavior under denaturing conditions in a fold-specific manner. The random coil deviations in each of these folds occur near interhelical turns and loops in their tertiary structures. Here, we examine an additional three-helix bundle with an identical fold to UBA(2), but a highly divergent sequence, the first ubiquitin-associated domain, UBA(1), of HHR23A. We use histidine-heme loop formation methods, employing eight single histidine variants, to probe for denatured state conformational bias of a UBA(1) domain fused to the N-terminus of iso-1-cytochrome c (iso-1-Cytc). Guanidine hydrochloride (GuHCl) denaturation shows that the iso-1-Cytc domain unfolds first, followed by the UBA(1) domain. Denatured state (4 and 6 M GuHCl) histidine-heme loop formation studies show that as the size of the histidine-heme loop increases, loop stability decreases, as expected for the Jacobson-Stockmayer relationship. However, loops formed with His35, His31, and His15, of UBA(1), are 0.6-1.1 kcal/mol more stable than expected from the Jacobson-Stockmayer relationship, confirming the importance of deviations of the denatured state from random coil behavior near interhelical turns of helical domains for facilitating folding to the correct topology. For UBA(1) and UBA(2), hydrophobic clusters on either side of the turns partially explain deviations from random coil behavior; however, helix capping also appears to be important.
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Affiliation(s)
- Moses J. Leavens
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Lisa E. Spang
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Melisa M. Cherney
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, Montana 59812, United States
- Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, Montana 59812, United States
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19
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Rösner HI, Caldarini M, Potel G, Malmodin D, Vanoni MA, Aliverti A, Broglia RA, Kragelund BB, Tiana G. The denatured state of HIV-1 protease under native conditions. Proteins 2021; 90:96-109. [PMID: 34312913 PMCID: PMC9290662 DOI: 10.1002/prot.26189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/22/2021] [Indexed: 12/01/2022]
Abstract
The denatured state of several proteins has been shown to display transient structures that are relevant for folding, stability, and aggregation. To detect them by nuclear magnetic resonance (NMR) spectroscopy, the denatured state must be stabilized by chemical agents or changes in temperature. This makes the environment different from that experienced in biologically relevant processes. Using high‐resolution heteronuclear NMR spectroscopy, we have characterized several denatured states of a monomeric variant of HIV‐1 protease, which is natively structured in water, induced by different concentrations of urea, guanidinium chloride, and acetic acid. We have extrapolated the chemical shifts and the relaxation parameters to the denaturant‐free denatured state at native conditions, showing that they converge to the same values. Subsequently, we characterized the conformational properties of this biologically relevant denatured state under native conditions by advanced molecular dynamics simulations and validated the results by comparison to experimental data. We show that the denatured state of HIV‐1 protease under native conditions displays rich patterns of transient native and non‐native structures, which could be of relevance to its guidance through a complex folding process.
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Affiliation(s)
- Heike I Rösner
- BRIC, University of Copenhagen, Copenhagen N, Denmark.,Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Martina Caldarini
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy
| | - Gregory Potel
- Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Daniel Malmodin
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Maria A Vanoni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | | | - Ricardo A Broglia
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Niels Bohr Institutet, University of Copenhagen, Copenhagen Ø, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Guido Tiana
- Department of Physics, Università degli Studi di Milano and INFN, Milan, Italy.,Center for Complexity and Biosystems, Università degli Studi di Milano, Milan, Italy
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20
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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21
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Pinet L, Wang YH, Deville C, Lescop E, Guerlesquin F, Badache A, Bontems F, Morellet N, Durand D, Assrir N, van Heijenoort C. Structural and dynamic characterization of the C-terminal tail of ErbB2: Disordered but not random. Biophys J 2021; 120:1869-1882. [PMID: 33741354 DOI: 10.1016/j.bpj.2021.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 01/23/2023] Open
Abstract
ErbB2 (or HER2) is a receptor tyrosine kinase overexpressed in some breast cancers and associated with poor prognosis. Treatments targeting the receptor extracellular and kinase domains have greatly improved disease outcome in the last 20 years. In parallel, the structures of these domains have been described, enabling better mechanistic understanding of the receptor function and targeted inhibition. However, the ErbB2 disordered C-terminal cytoplasmic tail (CtErbB2) remains very poorly characterized in terms of structure, dynamics, and detailed functional mechanism. Yet, it is where signal transduction is triggered via phosphorylation of tyrosine residues and carried out via interaction with adaptor proteins. Here, we report the first description, to our knowledge, of the ErbB2 disordered tail at atomic resolution using NMR, complemented by small-angle x-ray scattering. We show that although no part of CtErbB2 has any fully populated secondary or tertiary structure, it contains several transient α-helices and numerous transient polyproline II helices, populated up to 20 and 40%, respectively, and low but significant compaction. The presence of some structural elements suggests, along the lines of the results obtained for EGFR (ErbB1), that they may have a functional role in ErbB2's autoregulation processes. In addition, the transient formation of polyproline II helices is compliant with previously suggested interactions with SH3 domains. All in all, our in-depth structural study opens perspectives in the mechanistic understanding of ErbB2.
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Affiliation(s)
- Louise Pinet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Ying-Hui Wang
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; SGS Taiwan LTD, New Taipei City, Taiwan
| | - Célia Deville
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; IGBMC, University of Strasbourg, CNRS UMR, Illkirch, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Françoise Guerlesquin
- LISM, Institut de Microbiologie de la Méditerranée, CNRS and Aix-Marseille University, Marseille, France
| | - Ali Badache
- Centre de Recherche en Cancérologie de Marseille, Aix-Marseille Univ, INSERM, Institut Paoli-Calmettes, CNRS, Marseille, France
| | - François Bontems
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France; Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Nelly Morellet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Dominique Durand
- I2BC, Université Paris-Saclay, CNRS UMR 9198, Gif-sur-Yvette, France
| | - Nadine Assrir
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Carine van Heijenoort
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Gif-sur-Yvette, France.
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22
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Casier R, Duhamel J. The Effect of Amino Acid Size on the Internal Dynamics and Conformational Freedom of Polypeptides. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c02153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Remi Casier
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L3G1, Canada
| | - Jean Duhamel
- Institute for Polymer Research, Waterloo Institute for Nanotechnology, Department of Chemistry, University of Waterloo, Waterloo, ON N2L3G1, Canada
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23
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Yagi-Utsumi M, Chandak MS, Yanaka S, Hiranyakorn M, Nakamura T, Kato K, Kuwajima K. Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR. Biophys J 2020; 119:2029-2038. [PMID: 33142107 DOI: 10.1016/j.bpj.2020.10.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 10/07/2020] [Indexed: 12/01/2022] Open
Abstract
The characterization of residual structures persistent in unfolded proteins in concentrated denaturant solution is currently an important issue in studies of protein folding because the residual structure present, if any, in the unfolded state may form a folding initiation site and guide the subsequent folding reactions. Here, we studied the hydrogen/deuterium (H/D)-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride. We employed a dimethylsulfoxide (DMSO)-quenched H/D-exchange NMR technique with the use of spin desalting columns, which allowed us to perform a quick medium exchange from 6 M guanidinium chloride to a quenching DMSO solution. Based on the backbone resonance assignment of ubiquitin in the DMSO solution, we successfully investigated the H/D-exchange kinetics of 60 identified peptide amide groups in the ubiquitin sequence. Although a majority of these amide groups were not protected, certain amide groups involved in a middle helix (residues 23-34) and an N-terminal β-hairpin (residues 2-16) were significantly protected with a protection factor of 2.1-4.2, indicating that there were residual structures in unfolded ubiquitin and that these amide groups were more than 52% hydrogen bonded in the residual structures. We show that the hydrogen-bonded residual structures in the α-helix and the β-hairpin are formed even in 6 M guanidinium chloride, suggesting that these residual structures may function as a folding initiation site to guide the subsequent folding reactions of ubiquitin.
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Affiliation(s)
- Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Mahesh S Chandak
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Methanee Hiranyakorn
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Takashi Nakamura
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan.
| | - Kunihiro Kuwajima
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), Okazaki, Aichi, Japan; Department of Physics, Graduate School of Science, the University of Tokyo, Tokyo, Japan; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea.
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24
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Hicks A, Escobar CA, Cross TA, Zhou HX. Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ. Biomolecules 2020; 10:biom10060946. [PMID: 32585849 PMCID: PMC7355643 DOI: 10.3390/biom10060946] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022] Open
Abstract
How sequences of intrinsically disordered proteins (IDPs) code for their conformational dynamics is poorly understood. Here, we combined NMR spectroscopy, small-angle X-ray scattering (SAXS), and molecular dynamics (MD) simulations to characterize the conformations and dynamics of ChiZ1-64. MD simulations, first validated by SAXS and secondary chemical shift data, found scant α-helices or β-strands but a considerable propensity for polyproline II (PPII) torsion angles. Importantly, several blocks of residues (e.g., 11–29) emerge as “correlated segments”, identified by their frequent formation of PPII stretches, salt bridges, cation-π interactions, and sidechain-backbone hydrogen bonds. NMR relaxation experiments showed non-uniform transverse relaxation rates (R2s) and nuclear Overhauser enhancements (NOEs) along the sequence (e.g., high R2s and NOEs for residues 11–14 and 23–28). MD simulations further revealed that the extent of segmental correlation is sequence-dependent; segments where internal interactions are more prevalent manifest elevated “collective” motions on the 5–10 ns timescale and suppressed local motions on the sub-ns timescale. Amide proton exchange rates provides corroboration, with residues in the most correlated segment exhibiting the highest protection factors. We propose the correlated segment as a defining feature for the conformations and dynamics of IDPs.
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Affiliation(s)
- Alan Hicks
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; (A.H.); (C.A.E.)
- Department of Physics, Florida State University, Tallahassee, FL 32306, USA
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
| | - Cristian A. Escobar
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; (A.H.); (C.A.E.)
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
| | - Timothy A. Cross
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA; (A.H.); (C.A.E.)
- National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA
- Correspondence: (T.A.C.); (H.-X.Z.)
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL 60607, USA
- Department of Physics, University of Illinois at Chicago, Chicago, IL 60607, USA
- Correspondence: (T.A.C.); (H.-X.Z.)
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25
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Kubatova N, Pyper DJ, Jonker HRA, Saxena K, Remmel L, Richter C, Brantl S, Evguenieva‐Hackenberg E, Hess WR, Klug G, Marchfelder A, Soppa J, Streit W, Mayzel M, Orekhov VY, Fuxreiter M, Schmitz RA, Schwalbe H. Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea. Chembiochem 2020; 21:1178-1187. [PMID: 31705614 PMCID: PMC7217052 DOI: 10.1002/cbic.201900677] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Indexed: 01/08/2023]
Abstract
Proteins encoded by small open reading frames (sORFs) have a widespread occurrence in diverse microorganisms and can be of high functional importance. However, due to annotation biases and their technically challenging direct detection, these small proteins have been overlooked for a long time and were only recently rediscovered. The currently rapidly growing number of such proteins requires efficient methods to investigate their structure-function relationship. Herein, a method is presented for fast determination of the conformational properties of small proteins. Their small size makes them perfectly amenable for solution-state NMR spectroscopy. NMR spectroscopy can provide detailed information about their conformational states (folded, partially folded, and unstructured). In the context of the priority program on small proteins funded by the German research foundation (SPP2002), 27 small proteins from 9 different bacterial and archaeal organisms have been investigated. It is found that most of these small proteins are unstructured or partially folded. Bioinformatics tools predict that some of these unstructured proteins can potentially fold upon complex formation. A protocol for fast NMR spectroscopy structure elucidation is described for the small proteins that adopt a persistently folded structure by implementation of new NMR technologies, including automated resonance assignment and nonuniform sampling in combination with targeted acquisition.
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Affiliation(s)
- Nina Kubatova
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Hendrik R. A. Jonker
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Laura Remmel
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
| | - Sabine Brantl
- AG BakteriengenetikMatthias-Schleiden-InstitutPhilosophenweg 1207743JenaGermany
| | - Elena Evguenieva‐Hackenberg
- Institute for Microbiology and Molecular BiologyJustus Liebig University GiessenHeinrich-Buff-Ring 2635392GiessenGermany
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics and Experimental BioinformaticsAlbert Ludwigs University FreiburgSchänzlestrasse 179104FreiburgGermany
| | - Gabriele Klug
- Institute for Microbiology and Molecular BiologyJustus Liebig University GiessenHeinrich-Buff-Ring 2635392GiessenGermany
| | | | - Jörg Soppa
- Institute for Molecular BiosciencesJohann Wolfgang Goethe UniversityMax-von-Laue-Strasse 960438Frankfurt am MainGermany
| | - Wolfgang Streit
- Department of Microbiology and BiotechnologyUniversity of HamburgOhnhorststrasse 1822609HamburgGermany
| | - Maxim Mayzel
- Swedish NMR CentreUniversity of GothenburgP. O. Box 46540530GothenburgSweden
| | - Vladislav Y. Orekhov
- Swedish NMR CentreUniversity of GothenburgP. O. Box 46540530GothenburgSweden
- Department of Chemistry and Molecular BiologyUniversity of GothenburgKemigården 441296GothenburgSweden
| | - Monika Fuxreiter
- MTA-DE Laboratory of Protein DynamicsDepartment of Biochemistry and Molecular BiologyUniversity of DebrecenNagyerdei krt 984032DebrecenHungary
| | - Ruth A. Schmitz
- Institute for General MicrobiologyChristian Albrechts University KielAm Botanischen Garten 1–924118KielGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe UniversityMax-von-Laue-Strasse 760438Frankfurt/MainGermany
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26
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Millard PS, Bugge K, Marabini R, Boomsma W, Burow M, Kragelund BB. IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors. Protein Sci 2020; 29:169-183. [PMID: 31642121 PMCID: PMC6933863 DOI: 10.1002/pro.3754] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022]
Abstract
Protein domains constitute regions of distinct structural properties and molecular functions that are retained when removed from the rest of the protein. However, due to the lack of tertiary structure, the identification of domains has been largely neglected for long (>50 residues) intrinsically disordered regions. Here we present a sequence-based approach to assess and visualize domain organization in long intrinsically disordered regions based on compositional sequence biases. An online tool to find putative intrinsically disordered domains (IDDomainSpotter) in any protein sequence or sequence alignment using any particular sequence trait is available at http://www.bio.ku.dk/sbinlab/IDDomainSpotter. Using this tool, we have identified a putative domain enriched in hydrophilic and disorder-promoting residues (Pro, Ser, and Thr) and depleted in positive charges (Arg and Lys) bordering the folded DNA-binding domains of several transcription factors (p53, GCR, NAC46, MYB28, and MYB29). This domain, from two different MYB transcription factors, was characterized biophysically to determine its properties. Our analyses show the domain to be extended, dynamic and highly disordered. It connects the DNA-binding domain to other disordered domains and is present and conserved in several transcription factors from different families and domains of life. This example illustrates the potential of IDDomainSpotter to predict, from sequence alone, putative domains of functional interest in otherwise uncharacterized disordered proteins.
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Affiliation(s)
- Peter S. Millard
- DynaMo Center, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Katrine Bugge
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Wouter Boomsma
- Department of Computer ScienceUniversity of CopenhagenCopenhagenDenmark
| | - Meike Burow
- DynaMo Center, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Birthe B. Kragelund
- Structural Biology and NMR Laboratory, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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27
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Brillault L, Landsberg MJ. Preparation of Proteins and Macromolecular Assemblies for Cryo-electron Microscopy. Methods Mol Biol 2020; 2073:221-246. [PMID: 31612445 DOI: 10.1007/978-1-4939-9869-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Cryo-electron microscopy has become popular as the penultimate step on the road to structure determination for many proteins and macromolecular assemblies. The process of obtaining high-resolution images of a purified biomolecular complex in an electron microscope often follows a long, and in many cases exhaustive screening process in which many iterative rounds of protein purification are employed and the sample preparation procedure progressively re-evaluated in order to improve the distribution of particles visualized under the electron microscope, and thus maximize the opportunity for high-resolution structure determination. Typically, negative stain electron microscopy is employed to obtain a preliminary assessment of the sample quality, followed by cryo-EM which first requires the identification of optimal vitrification conditions. The original methods for frozen-hydrated specimen preparation developed over 40 years ago still enjoy widespread use today, although recent developments have set the scene for a future where more systematic and high-throughput approaches to the preparation of vitrified biomolecular complexes may be routinely employed. Here we summarize current approaches and ongoing innovations for the preparation of frozen-hydrated single particle specimens for cryo-EM, highlighting some of the commonly encountered problems and approaches that may help overcome these.
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Affiliation(s)
- Lou Brillault
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Michael J Landsberg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
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28
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Pietrek LM, Stelzl LS, Hummer G. Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations. J Chem Theory Comput 2019; 16:725-737. [PMID: 31809054 DOI: 10.1021/acs.jctc.9b00809] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute a large fraction of the human proteome and are critical in the regulation of cellular processes. A detailed understanding of the conformational dynamics of IDPs could help to elucidate their roles in health and disease. However, the inherent flexibility of IDPs makes structural studies and their interpretation challenging. Molecular dynamics (MD) simulations could address this challenge in principle, but inaccuracies in the simulation models and the need for long simulations have stymied progress. To overcome these limitations, we adopt a hierarchical approach that builds on the "flexible-meccano" model reported by Bernadó et al. (J. Am. Chem. Soc. 2005, 127, 17968-17969). First, we exhaustively sample small IDP fragments in all-atom simulations to capture their local structures. Then, we assemble the fragments into full-length IDPs to explore the stereochemically possible global structures of IDPs. The resulting ensembles of three-dimensional structures of full-length IDPs are highly diverse, much more so than in standard MD simulation. For the paradigmatic IDP α-synuclein, our ensemble captures both the local structure, as probed by nuclear magnetic resonance spectroscopy, and its overall dimension, as obtained from small-angle X-ray scattering in solution. By generating representative and meaningful starting ensembles, we can begin to exploit the massive parallelism afforded by current and future high-performance computing resources for atomic-resolution characterization of IDPs.
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Affiliation(s)
- Lisa M Pietrek
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany
| | - Lukas S Stelzl
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics , Max Planck Institute of Biophysics , Max-von-Laue Straße 3 , 60438 Frankfurt am Main , Germany.,Institute for Biophysics , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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29
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Rezaei-Ghaleh N, Parigi G, Zweckstetter M. Reorientational Dynamics of Amyloid-β from NMR Spin Relaxation and Molecular Simulation. J Phys Chem Lett 2019; 10:3369-3375. [PMID: 31181936 PMCID: PMC6598774 DOI: 10.1021/acs.jpclett.9b01050] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Amyloid-β (Aβ) aggregation is a hallmark of Alzheimer's disease. As an intrinsically disordered protein, Aβ undergoes extensive dynamics on multiple length and time scales. Access to a comprehensive picture of the reorientational dynamics in Aβ requires therefore the combination of complementary techniques. Here, we integrate 15N spin relaxation rates at three magnetic fields with microseconds-long molecular dynamics simulation, ensemble-based hydrodynamic calculations, and previously published nanosecond fluorescence correlation spectroscopy to investigate the reorientational dynamics of Aβ1-40 (Aβ40) at single-residue resolution. The integrative analysis shows that librational and dihedral angle fluctuations occurring at fast and intermediate time scales are not sufficient to decorrelate orientational memory in Aβ40. Instead, slow segmental motions occurring at ∼5 ns are detected throughout the Aβ40 sequence and reach up to ∼10 ns for selected residues. We propose that the modulation of time scales of reorientational dynamics with respect to intra- and intermolecular diffusion plays an important role in disease-related Aβ aggregation.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Department
of Neurology, University Medical Center
Goettingen, 37075 Goettingen, Germany
- Department
for NMR-Based Structural Biology, Max Planck
Institute for Biophysical Chemistry, 37077 Goettingen, Germany
- E-mail:
| | - Giacomo Parigi
- Magnetic
Resonance Center (CERM) and Department of Chemistry “Ugo Schiff”, University of Florence, via Sacconi 6, 50019 Sesto Fiorentino, Italy
| | - Markus Zweckstetter
- Department
of Neurology, University Medical Center
Goettingen, 37075 Goettingen, Germany
- Department
for NMR-Based Structural Biology, Max Planck
Institute for Biophysical Chemistry, 37077 Goettingen, Germany
- Research
Group for Structural Biology in Dementia, German Center for Neurodegenerative Diseases (DZNE) Goettingen, 37075 Goettingen, Germany
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30
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Maiti S, Acharya B, Boorla VS, Manna B, Ghosh A, De S. Dynamic Studies on Intrinsically Disordered Regions of Two Paralogous Transcription Factors Reveal Rigid Segments with Important Biological Functions. J Mol Biol 2019; 431:1353-1369. [PMID: 30802457 DOI: 10.1016/j.jmb.2019.02.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/31/2019] [Accepted: 02/15/2019] [Indexed: 10/27/2022]
Abstract
Long stretches of intrinsically disordered regions (IDRs) are abundantly present in eukaryotic transcription factors. Although their biological significance is well appreciated, the underlying structural and dynamic mechanisms of their function are still not clear. Using solution NMR spectroscopy, we have studied the structural and dynamic features of two paralogous HOX transcription factors, SCR and DFD, from Drosophila. Both proteins have a conserved DNA-binding homeodomain and a long stretch of functionally important IDR. Using NMR dynamics, we determined flexibility of each residue in these proteins. The flexibility of the residues in the disordered region is not uniform. In both proteins, the IDRs have short stretches of consecutive residues with relatively less flexibility, that is, higher rigidity. We show that one such rigid segment is specifically recognized by another co-transcription factor, thus highlighting the importance of these rigid segments in IDR-mediated protein-protein interactions. Using molecular dynamics simulation, we further show that the rigid segments sample less conformations compared to the rest of the residues in the disordered region. The restrained conformational sampling of these rigid residues should lower the loss in conformational entropy during their interactions with binding partners resulting in sequence specific binding. This work provides experimental evidence of a "rigid-segment" model of IDRs, where functionally important rigid segments are connected by highly flexible linkers. Furthermore, a comparative study of IDRs in paralogous proteins reveals that in spite of low-sequence conservation, the rigid and flexible segments are sequentially maintained to preserve related functions and regulations of these proteins.
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Affiliation(s)
- Snigdha Maiti
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Bidisha Acharya
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Veda Sheersh Boorla
- Department of Chemical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Bharat Manna
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Amit Ghosh
- School of Energy Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India.
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31
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Milles S, Salvi N, Blackledge M, Jensen MR. Characterization of intrinsically disordered proteins and their dynamic complexes: From in vitro to cell-like environments. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2018; 109:79-100. [PMID: 30527137 DOI: 10.1016/j.pnmrs.2018.07.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 07/16/2018] [Accepted: 07/16/2018] [Indexed: 05/08/2023]
Abstract
Over the last two decades, it has become increasingly clear that a large fraction of the human proteome is intrinsically disordered or contains disordered segments of significant length. These intrinsically disordered proteins (IDPs) play important regulatory roles throughout biology, underlining the importance of understanding their conformational behavior and interaction mechanisms at the molecular level. Here we review recent progress in the NMR characterization of the structure and dynamics of IDPs in various functional states and environments. We describe the complementarity of different NMR parameters for quantifying the conformational propensities of IDPs in their isolated and phosphorylated states, and we discuss the challenges associated with obtaining structural models of dynamic protein-protein complexes involving IDPs. In addition, we review recent progress in understanding the conformational behavior of IDPs in cell-like environments such as in the presence of crowding agents, in membrane-less organelles and in the complex environment of the human cell.
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Affiliation(s)
- Sigrid Milles
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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32
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Kämpf K, Izmailov SA, Rabdano SO, Groves AT, Podkorytov IS, Skrynnikov NR. What Drives 15N Spin Relaxation in Disordered Proteins? Combined NMR/MD Study of the H4 Histone Tail. Biophys J 2018; 115:2348-2367. [PMID: 30527335 DOI: 10.1016/j.bpj.2018.11.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/07/2018] [Accepted: 11/12/2018] [Indexed: 12/26/2022] Open
Abstract
Backbone (15N) NMR relaxation is one of the main sources of information on dynamics of disordered proteins. Yet, we do not know very well what drives 15N relaxation in such systems, i.e., how different forms of motion contribute to the measurable relaxation rates. To address this problem, we have investigated, both experimentally and via molecular dynamics simulations, the dynamics of a 26-residue peptide imitating the N-terminal portion of the histone protein H4. One part of the peptide was found to be fully flexible, whereas the other part features some transient structure (a hairpin stabilized by hydrogen bonds). The following motional modes proved relevant for 15N relaxation. 1) Sub-picosecond librations attenuate relaxation rates according to S2 ∼0.85-0.90. 2) Axial peptide-plane fluctuations along a stretch of the peptide chain contribute to relaxation-active dynamics on a fast timescale (from tens to hundreds of picoseconds). 3) φ/ψ backbone jumps contribute to relaxation-active dynamics on both fast (from tens to hundreds of picoseconds) and slow (from hundreds of picoseconds to a nanosecond) timescales. The major contribution is from polyproline II (PPII) ↔ β transitions in the Ramachandran space; in the case of glycine residues, the major contribution is from PPII ↔ (β) ↔ rPPII transitions, in which rPPII is the mirror-image (right-handed) version of the PPII geometry, whereas β geometry plays the role of an intermediate state. 4) Reorientational motion of certain (sufficiently long-lived) elements of transient structure, i.e., rotational tumbling, contributes to slow relaxation-active dynamics on ∼1-ns timescale (however, it is difficult to isolate this contribution). In conclusion, recent advances in the area of force-field development have made it possible to obtain viable Molecular Dynamics models of protein disorder. After careful validation against the experimental relaxation data, these models can provide a valuable insight into mechanistic origins of spin relaxation in disordered peptides and proteins.
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Affiliation(s)
- Kerstin Kämpf
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Sergei A Izmailov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Sevastyan O Rabdano
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Adam T Groves
- Department of Chemistry, Purdue University, West Lafayette, Indiana
| | - Ivan S Podkorytov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia
| | - Nikolai R Skrynnikov
- Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, Russia; Department of Chemistry, Purdue University, West Lafayette, Indiana.
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33
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Leavens MJ, Cherney MM, Finnegan ML, Bowler BE. Probing Denatured State Conformational Bias in a Three-Helix Bundle, UBA(2), Using a Cytochrome c Fusion Protein. Biochemistry 2018; 57:1711-1721. [PMID: 29480716 DOI: 10.1021/acs.biochem.8b00015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previous work with the four-helix-bundle protein cytochrome c' from Rhodopseudomonas palustris using histidine-heme loop formation methods revealed fold-specific deviations from random coil behavior in its denatured state ensemble. To examine the generality of this finding, we extend this work to a three-helix-bundle polypeptide, the second ubiquitin-associated domain, UBA(2), of the human DNA excision repair protein. We use yeast iso-1-cytochrome c as a scaffold, fusing the UBA(2) domain at the N-terminus of iso-1-cytochrome c. We have engineered histidine into highly solvent accessible positions of UBA(2), creating six single histidine variants. Guanidine hydrochloride denaturation studies show that the UBA(2)-cytochrome c fusion protein unfolds in a three-state process with iso-1-cytochrome c unfolding first. Furthermore, engineered histidine residues in UBA(2) strongly destabilize the iso-1-cytochrome c domain. Equilibrium and kinetic histidine-heme loop formation measurements in the denatured state at 4 and 6 M guanidine hydrochloride show that loop stability decreases as the size of the histidine-heme loop increases, in accord with the Jacobson-Stockmayer equation. However, we observe that the His27-heme loop is both more stable than expected from the Jacobson-Stockmayer relationship and breaks more slowly than expected. These results show that the sequence near His27, which is in the reverse turn between helices 2 and 3 of UBA(2), is prone to persistent interactions in the denatured state. Therefore, consistent with our results for cytochrome c', this reverse turn sequence may help to establish the topology of this fold by biasing the conformational distribution of the denatured state.
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Affiliation(s)
- Moses J Leavens
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Melisa M Cherney
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Michaela L Finnegan
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Dynamics , University of Montana , Missoula , Montana 59812 , United States
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34
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Danielson TA, Bowler BE. Helical Propensity Affects the Conformational Properties of the Denatured State of Cytochrome c'. Biophys J 2018; 114:311-322. [PMID: 29401429 DOI: 10.1016/j.bpj.2017.11.3744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022] Open
Abstract
Changing the helical propensity of a polypeptide sequence might be expected to affect the conformational properties of the denatured state of a protein. To test this hypothesis, alanines at positions 83 and 87 near the center of helix 3 of cytochrome c' from Rhodopseudomonas palustris were mutated to serine to decrease the stability of this helix. A set of 13 single histidine variants in the A83S/A87S background were prepared to permit assessment of the conformational properties of the denatured state using histidine-loop formation in 3 M guanidine hydrochloride. The data are compared with previous histidine-heme loop formation data for wild-type cytochrome c'. As expected, destabilization of helix 3 decreases the global stabilities of the histidine variants in the A83S/A87S background relative to the wild-type background. Loop stability versus loop size data yields a scaling exponent of 2.1 ± 0.2, similar to the value of 2.3 ± 0.2 obtained for wild-type cytochrome c'. However, the stabilities of all histidine-heme loops, which contain the helix 3 sequence segment, are increased in the A83S/A87S background compared to the wild-type background. Rate constants for histidine-heme loop breakage are similar for the wild-type and A83S/A87S variants. However, for histidine-heme loops that contain the helix 3 sequence segment, the rate constants for loop formation increase in the A83S/A87S background compared to the wild-type background. Thus, residual helical structure appears to stiffen the polypeptide chain slowing loop formation in the denatured state. The implications of these results for protein folding mechanisms are discussed.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry and Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana.
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35
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Danielson TA, Stine JM, Dar TA, Briknarova K, Bowler BE. Effect of an Imposed Contact on Secondary Structure in the Denatured State of Yeast Iso-1-cytochrome c. Biochemistry 2017; 56:6662-6676. [PMID: 29148740 DOI: 10.1021/acs.biochem.7b01002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is considerable evidence that long-range interactions stabilize residual protein structure under denaturing conditions. However, evaluation of the effect of a specific contact on structure in the denatured state has been difficult. Iso-1-cytochrome c variants with a Lys54 → His mutation form a particularly stable His-heme loop in the denatured state, suggestive of loop-induced residual structure. We have used multidimensional nuclear magnetic resonance methods to assign 1H and 15N backbone amide and 13C backbone and side chain chemical shifts in the denatured state of iso-1-cytochrome c carrying the Lys54 → His mutation in 3 and 6 M guanidine hydrochloride and at both pH 6.4, where the His54-heme loop is formed, and pH 3.6, where the His54-heme loop is broken. Using the secondary structure propensity score, with the 6 M guanidine hydrochloride chemical shift data as a random coil reference state for data collected in 3 M guanidine hydrochloride, we found residual helical structure in the denatured state for the 60s helix and the C-terminal helix, but not in the N-terminal helix in the presence or absence of the His54-heme loop. Non-native helical structure is observed in two regions that form Ω-loops in the native state. There is more residual helical structure in the C-terminal helix at pH 6.4 when the loop is formed. Loop formation also appears to stabilize helical structure near His54, consistent with induction of helical structure observed when His-heme bonds form in heme-peptide model systems. The results are discussed in the context of the folding mechanism of cytochrome c.
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Affiliation(s)
- Travis A Danielson
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Jessica M Stine
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Tanveer A Dar
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States
| | - Klara Briknarova
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
| | - Bruce E Bowler
- Department of Chemistry and Biochemistry, University of Montana , Missoula, Montana 59812, United States.,Center for Biomolecular Structure and Dynamics, University of Montana , Missoula, Montana 59812, United States
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36
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Grassi L, Regl C, Wildner S, Gadermaier G, Huber CG, Cabrele C, Schubert M. Complete NMR Assignment of Succinimide and Its Detection and Quantification in Peptides and Intact Proteins. Anal Chem 2017; 89:11962-11970. [PMID: 29058416 DOI: 10.1021/acs.analchem.7b01645] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Detecting and quantifying post-translational modifications (PTMs) in full-length proteins is a challenge, especially in the case of spontaneously occurring, nonenzymatic PTMs. Such a PTM is the formation of succinimide (Snn) in a protein that occurs spontaneously in prone primary sequences and leads typically to an equilibrium between Snn and its hydrolysis products isoaspartate (isoAsp) and aspartate. In order to detect these modifications in proteins by NMR spectroscopy, chemical shift assignments of reference compounds are required. We used peptide synthesis and 2D NMR spectroscopy to assign all 1H and 13C chemical shifts of Snn and isoAsp and found characteristic chemical shift correlations. To provide chemical shift reference data suitable for comparison with data of denatured proteins, we repeated the assignment in 7 M urea (pH 2.3) and in DMSO. Most characteristic of Snn are the two downfield shifted carbonyl chemical shifts, the chemical shift correlations of Cβ-Hβ of Snn and Cα-Hα of the succeeding residue which are clearly distinct from random coil chemical shift correlations. The characteristic 2D NMR fingerprints of Snn were used to detect and quantify this PTM in the model protein lysozyme, the biotherapeutic filgrastim, and the Fc part of immunoglobulin G1. Mass spectrometry (MS) was applied as an additional independent method. The orthogonality of the NMR and MS techniques allows cross-validation, which is especially important to search for subtle PTMs in proteins. Studying PTMs by NMR spectroscopy is a promising method to analyze proteins and peptides from natural sources, recombinant expression, or chemical synthesis.
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Affiliation(s)
- Luigi Grassi
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Christof Regl
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Sabrina Wildner
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Gabriele Gadermaier
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Christian G Huber
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Chiara Cabrele
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
| | - Mario Schubert
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg , Hellbrunner Strasse 34, 5020 Salzburg, Austria.,Department of Molecular Biology, University of Salzburg , Billrothstrasse 11, 5020 Salzburg, Austria
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37
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Application of Lysine-specific Labeling to Detect Transient Interactions Present During Human Lysozyme Amyloid Fibril Formation. Sci Rep 2017; 7:15018. [PMID: 29101328 PMCID: PMC5670245 DOI: 10.1038/s41598-017-14739-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/16/2017] [Indexed: 11/08/2022] Open
Abstract
Populating transient and partially unfolded species is a crucial step in the formation and accumulation of amyloid fibrils formed from pathogenic variants of human lysozyme linked with a rare but fatal hereditary systemic amyloidosis. The partially unfolded species possess an unstructured β-domain and C-helix with the rest of the α-domain remaining native-like. Here we use paramagnetic relaxation enhancement (PRE) measured by NMR spectroscopy to study the transient intermolecular interactions between such intermediate species. Nitroxide spin labels, introduced specifically at three individual lysine residues, generate distinct PRE profiles, indicating the presence of intermolecular interactions between residues within the unfolded β-domain. This study describes the applicability to PRE NMR measurements of selective lysine labeling, at different sites within a protein, as an alternative to the introduction of spin labels via engineered cysteine residues. These results reveal the importance of the β-sheet region of lysozyme for initiating self-assembly into amyloid fibrils.
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38
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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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39
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Ban D, Iconaru LI, Ramanathan A, Zuo J, Kriwacki RW. A Small Molecule Causes a Population Shift in the Conformational Landscape of an Intrinsically Disordered Protein. J Am Chem Soc 2017; 139:13692-13700. [PMID: 28885015 PMCID: PMC5962290 DOI: 10.1021/jacs.7b01380] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Intrinsically disordered proteins (IDPs) have roles in myriad biological processes and numerous human diseases. However, kinetic and amplitude information regarding their ground-state conformational fluctuations has remained elusive. We demonstrate using nuclear magnetic resonance (NMR)-based relaxation dispersion that the D2 domain of p27Kip1, a prototypical IDP, samples multiple discrete, rapidly exchanging conformational states. By combining NMR with mutagenesis and small-angle X-ray scattering (SAXS), we show that these states involve aromatic residue clustering through long-range hydrophobic interactions. Theoretical studies have proposed that small molecules bind promiscuously to IDPs, causing expansion of their conformational landscapes. However, on the basis of previous NMR-based screening results, we show here that compound binding only shifts the populations of states that existed within the ground state of apo p27-D2 without changing the barriers between states. Our results provide atomic resolution insight into how a small molecule binds an IDP and emphasize the need to examine motions on the low microsecond time scale when probing these types of interactions.
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Affiliation(s)
- David Ban
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Luigi I. Iconaru
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Arvind Ramanathan
- Computational Science and Engineering Division, Health Data Sciences Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, USA
| | - Jian Zuo
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, USA
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Sciences Center, Memphis, Tennessee 38105, USA
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40
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Salvi N, Abyzov A, Blackledge M. Analytical Description of NMR Relaxation Highlights Correlated Dynamics in Intrinsically Disordered Proteins. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale; CNRS, CEA, UGA; Grenoble France
| | - Anton Abyzov
- Institut de Biologie Structurale; CNRS, CEA, UGA; Grenoble France
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41
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Salvi N, Abyzov A, Blackledge M. Analytical Description of NMR Relaxation Highlights Correlated Dynamics in Intrinsically Disordered Proteins. Angew Chem Int Ed Engl 2017; 56:14020-14024. [PMID: 28834051 DOI: 10.1002/anie.201706740] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/06/2017] [Indexed: 12/16/2022]
Abstract
The dynamic fluctuations of intrinsically disordered proteins (IDPs) define their function. Although experimental nuclear magnetic resonance (NMR) relaxation reveals the motional complexity of these highly flexible proteins, the absence of physical models describing IDP dynamics hinders their mechanistic interpretation. Combining molecular dynamics simulation and NMR, we introduce a framework in which distinct motions are attributed to local libration, backbone dihedral angle dynamics and longer-range tumbling of one or more peptide planes. This model provides unique insight into segmental organization of dynamics in IDPs and allows us to investigate the presence and extent of the correlated motions that are essential for function.
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Affiliation(s)
- Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, Grenoble, France
| | - Anton Abyzov
- Institut de Biologie Structurale, CNRS, CEA, UGA, Grenoble, France
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42
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Schweitzer-Stenner R, Toal SE. Construction and comparison of the statistical coil states of unfolded and intrinsically disordered proteins from nearest-neighbor corrected conformational propensities of short peptides. MOLECULAR BIOSYSTEMS 2017; 12:3294-3306. [PMID: 27545097 DOI: 10.1039/c6mb00489j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Assessing the influence of nearest neighbors on the conformational ensemble of amino acid residues in unfolded and intrinsically disordered proteins and peptides is pivotal for a thorough understanding of the statistical coil state of unfolded proteins as well as of the energetics of the folding process. Research aimed at exploring nearest neighbor interactions has mostly focused on the analysis of restricted coil libraries that reflect conformational distributions in loops connecting more regular secondary structure segments. Recently, however, Toal et al. reported an experimentally based structural analysis of selected xy-pairs in GxyG tetrapeptides, which revealed quantitative information about conformational changes induced by nearest-neighbor interactions (Eur. J. Chem., 2015, 21, 5173-5192). Here, we perform analyses of Ramachandran plots of xy-pairs in GxyG and in coil libraries (Ting et al., PLOS CompBiol, 2010, 6, e1000763) using Hellinger distances as a quantitative measure of dissimilarities between Ramachandran distributions. Our analysis reveals that nearest-neighbor effects inferred from the above coil library are much less pronounced than corresponding structural changes observed for GxyG peptides. To determine whether nearest-neighbor induced conformational changes observed for GxyG can be utilized for the analysis of unfolded proteins, we analyzed sets of 3J(HHHα) coupling constants of three different unfolded proteins, namely the 130-residue fragment of the Staphylococcus aureus fibronectin-binding protein (FnBPc), denatured hen lysozyme, and the htau40 protein. For the first two proteins we found statistically meaningful correlations between predicted nearest-neighbor induced changes of 3J(HHHα) and experimentally observed deviations from corresponding coupling constants of GxG peptides in water, which we used as reference system with minimal nearest-neighbor interactions. This observation is in line with the NMR based understanding of these proteins being predominantly statistical coils. For htau40, however, which is known to exhibit residual structure and large deviations form statistical coil expectations, these correlations are weak or absent. Our results thus underscore the importance of nearest-neighbor interactions for a complete physical description of an ideal statistical coil state of a protein.
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Affiliation(s)
| | - Siobhan E Toal
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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43
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Zhang L. Different dynamics and pathway of disulfide bonds reduction of two human defensins, a molecular dynamics simulation study. Proteins 2017; 85:665-681. [PMID: 28106297 DOI: 10.1002/prot.25247] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 01/05/2017] [Accepted: 01/09/2017] [Indexed: 11/11/2022]
Abstract
Human defensins are a class of antimicrobial peptides that are crucial components of the innate immune system. Both human α defensin type 5 (HD5) and human β defensin type 3 (hBD-3) have 6 cysteine residues which form 3 pairs of disulfide bonds in oxidizing condition. Disulfide bond linking is important to the protein structure stabilization, and the disulfide bond linking and breaking order have been shown to influence protein function. In this project, microsecond long molecular dynamics simulations were performed to study the structure and dynamics of HD5 and hBD-3 wildtype and analogs which have all 3 disulfide bonds released in reducing condition. The structure of hBD-3 was found to be more dynamic and flexible than HD5, based on RMSD, RMSF, and radius of gyration calculations. The disulfide bridge breaking order of HD5 and hBD-3 in reducing condition was predicted by two kinds of methods, which gave consistent results. It was found that the disulfide bonds breaking pathways for HD5 and hBD-3 are very different. The breaking of disulfide bonds can influence the dimer interface by making the dimer structure less stable for both kinds of defensin. In order to understand the difference in dynamics and disulfide bond breaking pathway, hydrophilic and hydrophobic accessible surface areas (ASA), buried surface area between cysteine pairs, entropy of cysteine pairs, and internal energy were calculated. Comparing to the wildtype, hBD-3 analog is more hydrophobic, while HD5 is more hydrophilic. For hBD-3, the disulfide breaking is mainly entropy driven, while other factors such as the solvation effects may take the major role in controlling HD5 disulfide breaking pathway. Proteins 2017; 85:665-681. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Liqun Zhang
- Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN, 38505
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44
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Rösner HI, Caldarini M, Prestel A, Vanoni MA, Broglia RA, Aliverti A, Tiana G, Kragelund BB. Cold Denaturation of the HIV-1 Protease Monomer. Biochemistry 2017; 56:1029-1032. [DOI: 10.1021/acs.biochem.6b01141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heike I. Rösner
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
- Biotech
Research and Innovation Centre (BRIC), Faculty of Health and Medical
Sciences, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martina Caldarini
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Andreas Prestel
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maria A. Vanoni
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Ricardo A. Broglia
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
- Niels Bohr Institute, Blegdamsvej
17, 2100 Copenhagen Ø, Denmark
| | - Alessandro Aliverti
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Guido Tiana
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Birthe B. Kragelund
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
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45
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Battisti A, Ciasca G, Grottesi A, Tenenbaum A. Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors. Phys Chem Chem Phys 2017; 19:8435-8446. [DOI: 10.1039/c6cp07683a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The first quantitative assessment of the entropic, hydrophobic, and structural factors producing the thermal compaction of tau, an intrinsically disordered protein.
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Affiliation(s)
- Anna Battisti
- International School for Advanced Studies (SISSA)
- 34136 Trieste
- Italy
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46
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Piai A, Calçada EO, Tarenzi T, Grande AD, Varadi M, Tompa P, Felli IC, Pierattelli R. Just a Flexible Linker? The Structural and Dynamic Properties of CBP-ID4 Revealed by NMR Spectroscopy. Biophys J 2016; 110:372-381. [PMID: 26789760 DOI: 10.1016/j.bpj.2015.11.3516] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/12/2015] [Accepted: 11/25/2015] [Indexed: 01/01/2023] Open
Abstract
Here, we present a structural and dynamic description of CBP-ID4 at atomic resolution. ID4 is the fourth intrinsically disordered linker of CREB-binding protein (CBP). In spite of the largely disordered nature of CBP-ID4, NMR chemical shifts and relaxation measurements show a significant degree of α-helix sampling in the protein regions encompassing residues 2-25 and 101-128 (1852-1875 and 1951-1978 in full-length CBP). Proline residues are uniformly distributed along the polypeptide, except for the two α-helical regions, indicating that they play an active role in modulating the structural features of this CBP fragment. The two helical regions are lacking known functional motifs, suggesting that they represent thus-far uncharacterized functional modules of CBP. This work provides insights into the functions of this protein linker that may exploit its plasticity to modulate the relative orientations of neighboring folded domains of CBP and fine-tune its interactions with a multitude of partners.
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Affiliation(s)
- Alessandro Piai
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Eduardo O Calçada
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Thomas Tarenzi
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Alessandro Del Grande
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy
| | - Mihaly Varadi
- VIB Structural Biology Research Center, Vlaams Instituut voor Biotechnologie at Vrije Universiteit Brussel, Brussel, Belgium
| | - Peter Tompa
- VIB Structural Biology Research Center, Vlaams Instituut voor Biotechnologie at Vrije Universiteit Brussel, Brussel, Belgium; Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary
| | - Isabella C Felli
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
| | - Roberta Pierattelli
- Magnetic Resonance Center, University of Florence, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
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47
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Betancourt MR. Modeling bond correlations in denatured proteins and polypeptides. Biopolymers 2016; 105:312-323. [PMID: 26850703 DOI: 10.1002/bip.22816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
Bond-orientational correlations for finite-length homopolypeptides and a selected group of denatured proteins are obtained by numerical simulations using a polypeptide model with a potential of mean force. These correlations characterize the stiffness of the polypeptide backbone and are generally described by either an exponential or a power-law decay in the asymptotic limit. However, for finite length polypeptides and unfolded proteins the correlations significantly deviate from either single exponential or power-law behavior. A heuristic model is developed to analyze the correlations of homopolypeptides, which depends on the chain length and the side-chain properties. The model contains power-law and multi-exponential terms, the latter which could be interpreted as local persistence lengths. In the asymptotic limit, the model reduces to the expected power-law behavior. Simulations of denatured proteins show that the power-law behavior of the correlations is significantly suppressed and only the multi-exponential term is needed to model the correlations. In addition, average persistence lengths (ranging from 2.0 to 2.5 nm) are obtained from the correlations by fitting single exponentials and shown to be in general agreement with experiments, which also assume single exponential decay. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 312-323, 2016.
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Affiliation(s)
- Marcos R Betancourt
- Department of Science, BMCC - City University of New York, 199 Chambers Street, New York, NY, 10007
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48
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Zhu W, Silvers R, Schwalbe H, Keiderling TA. Reduced and mutant lysozyme refolding with lipid vesicles. Model study of disulfide impact on equilibria and dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1083-1092. [PMID: 27240304 DOI: 10.1016/j.bbapap.2016.05.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 11/26/2022]
Abstract
The recovery of secondary structure in disordered, disulfide-reduced hen egg white lysozyme (HEWL) upon interaction with lipid vesicles was studied using circular dichroism (CD), fluorescence and infrared (IR) spectroscopic techniques. Lipid vesicles having negative head groups, such as DMPG, interact with reduced HEWL to induce formation of more helical structure than in native HEWL, but no stable tertiary structure was evident. Changes in tertiary structure, as evidenced by local environment of the tryptophan residues, were monitored by fluorescence. Spectra for oxidized HEWL, reduced HEWL and mutants with no or just one disulfide bond developed variable degrees of increased helicity when added to negatively charged lipid vesicles, mostly depending on packing of tails. When mixed with zwitterionic lipid vesicles, reduced HEWL developed β-sheet structure with no change in helicity, indicating an altered interaction mechanism. Stopped flow CD and fluorescence dynamics, were fit to multi-exponential forms, consistent with refolding to metastable intermediates of increasing helicity for HEWL interacting with lipid vesicles. Formation of an intermediate after rapid interaction of the lipid vesicles and the protein is supported by the correlation of faster steps in CD and fluorescence kinetics, and largely appears driven by electrostatic interaction. In subsequent slower steps, the partially refolded intermediate further alters structure, gaining helicity and modifying tryptophan packing, as driven by hydrophobic interactions.
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Affiliation(s)
- Weiying Zhu
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., m/c 111, Chicago, IL 60607-7061, USA
| | - Robert Silvers
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt,, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt,, Max-von-Laue-Str. 7, 60438 Frankfurt/Main, Germany
| | - Timothy A Keiderling
- Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor St., m/c 111, Chicago, IL 60607-7061, USA.
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49
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Abyzov A, Salvi N, Schneider R, Maurin D, Ruigrok RWH, Jensen MR, Blackledge M. Identification of Dynamic Modes in an Intrinsically Disordered Protein Using Temperature-Dependent NMR Relaxation. J Am Chem Soc 2016; 138:6240-51. [PMID: 27112095 DOI: 10.1021/jacs.6b02424] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dynamic modes and time scales sampled by intrinsically disordered proteins (IDPs) define their function. Nuclear magnetic resonance (NMR) spin relaxation is probably the most powerful tool for investigating these motions delivering site-specific descriptions of conformational fluctuations from throughout the molecule. Despite the abundance of experimental measurement of relaxation in IDPs, the physical origin of the measured relaxation rates remains poorly understood. Here we measure an extensive range of auto- and cross-correlated spin relaxation rates at multiple magnetic field strengths on the C-terminal domain of the nucleoprotein of Sendai virus, over a large range of temperatures (268-298 K), and combine these data to describe the dynamic behavior of this archetypal IDP. An Arrhenius-type relationship is used to simultaneously analyze up to 61 relaxation rates per amino acid over the entire temperature range, allowing the measurement of local activation energies along the chain, and the assignment of physically distinct dynamic modes. Fast (τ ≤ 50 ps) components report on librational motions, a dominant mode occurs on time scales around 1 ns, apparently reporting on backbone sampling within Ramachandran substates, while a slower component (5-25 ns) reports on segmental dynamics dominated by the chain-like nature of the protein. Extending the study to three protein constructs of different lengths (59, 81, and 124 amino acids) substantiates the assignment of these contributions. The analysis is shown to be remarkably robust, accurately predicting a broad range of relaxation data measured at different magnetic field strengths and temperatures. The ability to delineate intrinsic modes and time scales from NMR spin relaxation will improve our understanding of the behavior and function of IDPs, adding a new and essential dimension to the description of this biologically important and ubiquitous class of proteins.
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Affiliation(s)
- Anton Abyzov
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Robert Schneider
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Damien Maurin
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Rob W H Ruigrok
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Malene Ringkjøbing Jensen
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
| | - Martin Blackledge
- Institut de Biologie Structurale (IBS), CEA, CNRS, Université Grenoble Alpes , 38044 Grenoble, France
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50
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Mitra M, Chaudhuri A, Patra M, Mukhopadhyay C, Chakrabarti A, Chattopadhyay A. Organization and Dynamics of Tryptophan Residues in Brain Spectrin: Novel Insight into Conformational Flexibility. J Fluoresc 2015; 25:707-17. [DOI: 10.1007/s10895-015-1556-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 03/05/2015] [Indexed: 10/23/2022]
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