1
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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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2
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Abstract
Summary Motivation. Predicting the native state of a protein has long been considered a gateway problem for understanding protein folding. Recent advances in structural modeling driven by deep learning have achieved unprecedented success at predicting a protein’s crystal structure, but it is not clear if these models are learning the physics of how proteins dynamically fold into their equilibrium structure or are just accurate knowledge-based predictors of the final state. Results. In this work, we compare the pathways generated by state-of-the-art protein structure prediction methods to experimental data about protein folding pathways. The methods considered were AlphaFold 2, RoseTTAFold, trRosetta, RaptorX, DMPfold, EVfold, SAINT2 and Rosetta. We find evidence that their simulated dynamics capture some information about the folding pathway, but their predictive ability is worse than a trivial classifier using sequence-agnostic features like chain length. The folding trajectories produced are also uncorrelated with experimental observables such as intermediate structures and the folding rate constant. These results suggest that recent advances in structure prediction do not yet provide an enhanced understanding of protein folding. Availability. The data underlying this article are available in GitHub at https://github.com/oxpig/structure-vs-folding/ Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Carlos Outeiral
- Department of Statistics, University of Oxford, Oxford OX1 3PB, UK
| | - Daniel A Nissley
- Department of Statistics, University of Oxford, Oxford OX1 3PB, UK
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3
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Bhattacharjee R, Udgaonkar JB. Structural Characterization of the Cooperativity of Unfolding of a Heterodimeric Protein using Hydrogen Exchange-Mass Spectrometry. J Mol Biol 2021; 433:167268. [PMID: 34563547 DOI: 10.1016/j.jmb.2021.167268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022]
Abstract
Little is known about how the sequence of structural changes in one chain of a heterodimeric protein is coupled to those in the other chain during protein folding and unfolding reactions, and whether individual secondary structural changes in the two chains occur in one or many coordinated steps. Here, the unfolding mechanism of a small heterodimeric protein, double chain monellin, has been characterized using hydrogen exchange-mass spectrometry. Transient structure opening, which enables HX, was found to be describable by a five state N ↔ I1 ↔ I2 ↔ I3 ↔ U mechanism. Structural changes occur gradually in the first three steps, and cooperatively in the last step. β strands 2, 4 and 5, as well as the α-helix undergo transient unfolding during all three non-cooperative steps, while β1 and the two loops on both sides of the helix undergo transient unfolding during the first two steps. In the absence of GdnHCl, only β3 in chain A of the protein unfolds during the last cooperative step, while in the presence of 1 M GdnHCl, not only β3, but also β2 in chain B unfolds cooperatively. Hence, the extent of cooperative structural change and size of the cooperative unfolding unit increase when the protein is destabilized by denaturant. The naturally evolved two-chain variant of monellin folds and unfolds in a more cooperative manner than does a single chain variant created artificially, suggesting that increasing folding cooperativity, even at the cost of decreasing stability, may be a driving force in the evolution of proteins.
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Affiliation(s)
- Rupam Bhattacharjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; Indian Institute of Science Education and Research, Pune, India. https://twitter.com/Rupam_B01
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India; Indian Institute of Science Education and Research, Pune, India.
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4
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Naganathan AN, Kannan A. A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures. Curr Res Struct Biol 2021; 3:257-267. [PMID: 34704074 PMCID: PMC8526763 DOI: 10.1016/j.crstbi.2021.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
Protein sequences and structures evolve by satisfying varied physical and biochemical constraints. This multi-level selection is enabled not just by the patterning of amino acids on the sequence, but also via coupling between residues in the native structure. Here, we employ an energetically detailed statistical mechanical model with millions of microstates to extract such long-range structural correlations, i.e. thermodynamic coupling free energies, from a diverse family of protein structures. We find that despite the intricate and anisotropic distribution of coupling patterns, the majority of residues (>70%) are only marginally coupled contributing to functional motions and catalysis. Physical origins of ‘sectors’, determinants of native ensemble heterogeneity in extant, ancient and designed proteins, and the basis for allostery emerge naturally from coupling free energies. The statistical framework highlights how evolutionary selection and optimization occur at the level of global interaction network for a given protein fold impacting folding, function, and allosteric outputs. Evolution of protein structures occurs at the level of global interaction network. More than 70% of the protein residues are weakly or marginally coupled. Functional ‘sector’ regions are a manifestation of marginal coupling. Coupling indices vary across the entire proteins in extant-ancient and natural-designed pairs. The proposed methodology can be used to understand allostery and epistasis.
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Affiliation(s)
- Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Adithi Kannan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
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5
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Llinás M. The Kringle of Life. Protein J 2021; 40:454-456. [PMID: 34131851 DOI: 10.1007/s10930-021-10009-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 11/24/2022]
Affiliation(s)
- Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Chemistry, Huck Center for Malaria Research, The Pennsylvania State University, University Park, PA, 16802, USA.
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6
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Sivaraman T, Richa T. Cryptic intermediates and metastable states of proteins as predicted by OneG computational method. J Biomol Struct Dyn 2021; 40:7899-7914. [PMID: 33764262 DOI: 10.1080/07391102.2021.1904288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Understanding structural excursions of proteins under folding conditions is crucial to map energy landscapes of proteins. In the present study, OneG computational tool has been used for analyzing possible existence of cryptic intermediates and metastable states of 26 proteins for which three prerequisite inputs of the OneG such as atomic coordinates of proteins, free energy of unfolding (ΔGU) and free energy of exchange (ΔGHX) determined in the absence of denaturant were available during the course of the study. The veraciousness of the tool on predicting the partially folded states of the proteins has been comprehensively described using experimental data available for 15 of the 26 proteins. Meanwhile, possible existence of partially structured states in the folding pathways of 11 other proteins has also been delineated as predicted by the OneG. In addition to mapping the folding pathways of proteins, the salient merits of the tool on systematically addressing the discrepancy between the ΔGU and the ΔGHX of the proteins have also been dealt.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Thirunavukkarasu Sivaraman
- Drug Design and Discovery Lab, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore, Tamil Nadu, India
| | - Tambi Richa
- Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
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7
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Bhatia S, Krishnamoorthy G, Udgaonkar JB. Mapping Distinct Sequences of Structure Formation Differentiating Multiple Folding Pathways of a Small Protein. J Am Chem Soc 2021; 143:1447-1457. [PMID: 33430589 DOI: 10.1021/jacs.0c11097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To determine experimentally how the multiple folding pathways of a protein differ, in the order in which the structural parts are assembled, has been a long-standing challenge. To resolve whether structure formation during folding can progress in multiple ways, the complex folding landscape of monellin has been characterized, structurally and temporally, using the multisite time-resolved FRET methodology. After an initial heterogeneous polypeptide chain collapse, structure formation proceeds on parallel pathways. Kinetic analysis of the population evolution data across various protein segments provides a clear structural distinction between the parallel pathways. The analysis leads to a phenomenological model that describes how and when discrete segments acquire structure independently of each other in different subensembles of protein molecules. When averaged over all molecules, structure formation is seen to progress as α-helix formation, followed by core consolidation, then β-sheet formation, and last end-to-end distance compaction. Parts of the protein that are closer in the primary sequence acquire structure before parts separated by longer sequence.
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Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560 065, India.,Indian Institute of Science Education and Research, Pune 411 008, India
| | | | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560 065, India.,Indian Institute of Science Education and Research, Pune 411 008, India
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8
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Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun 2020; 11:1231. [PMID: 32144241 PMCID: PMC7060211 DOI: 10.1038/s41467-020-14886-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2020] [Indexed: 11/23/2022] Open
Abstract
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by combining single-molecule and ensemble multiparameter fluorescence detection, EPR spectroscopy, mutagenesis, and FRET-positioning and screening, and other biochemical and biophysical tools, we characterize three short-lived conformational states over the ns-ms timescale. The use of 33 FRET-derived distance sets, to screen available T4L structures, reveal that T4L in solution mainly adopts the known open and closed states in exchange at 4 µs. A newly found minor state, undisclosed by, at present, more than 500 crystal structures of T4L and sampled at 230 µs, may be actively involved in the product release step in catalysis. The presented fluorescence spectroscopic toolkit will likely accelerate the development of dynamic structural biology by identifying transient conformational states that are highly abundant in biology and critical in enzymatic reactions. T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.
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9
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Abstract
Although many proteins possess a distinct folded structure lying at a minimum in a funneled free energy landscape, thermal energy causes any protein to continuously access lowly populated excited states. The existence of excited states is an integral part of biological function. Although transitions into the excited states may lead to protein misfolding and aggregation, little structural information is currently available for them. Here, we show how NMR spectroscopy, coupled with pressure perturbation, brings these elusive species to light. As pressure acts to favor states with lower partial molar volume, NMR follows the ensuing change in the equilibrium spectroscopically, with residue-specific resolution. For T4 lysozyme L99A, relaxation dispersion NMR was used to follow the increase in population of a previously identified "invisible" folded state with pressure, as this is driven by the reduction in cavity volume by the flipping-in of a surface aromatic group. Furthermore, multiple partly disordered excited states were detected at equilibrium using pressure-dependent H/D exchange NMR spectroscopy. Here, unfolding reduced partial molar volume by the removal of empty internal cavities and packing imperfections through subglobal and global unfolding. A close correspondence was found for the distinct pressure sensitivities of various parts of the protein and the amount of internal cavity volume that was lost in each unfolding event. The free energies and populations of excited states allowed us to determine the energetic penalty of empty internal protein cavities to be 36 cal⋅Å-3.
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10
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Vallurupalli P, Tiwari VP, Ghosh S. A Double-Resonance CEST Experiment To Study Multistate Protein Conformational Exchange: An Application to Protein Folding. J Phys Chem Lett 2019; 10:3051-3056. [PMID: 31081645 DOI: 10.1021/acs.jpclett.9b00985] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Despite the importance of protein dynamics to function, studying exchange between multiple conformational states remains a challenge because sparsely populated states are invisible to conventional techniques. CEST NMR experiments can detect minor states with lifetimes between 5 and 200 ms populated to a level of just ∼1%. However, CEST often cannot provide the exchange mechanism for processes involving three or more states, leaving the role of the detected minor states unknown. Here a double-resonance CEST experiment to determine the kinetics of multistate exchange is presented. The approach that involves irradiating resonances from two minor states simultaneously is used to study the exchange of T4 lysozyme (T4L) between the dominant native state and two minor states, the unfolded state and a second minor state (B), each populated to only ∼4%. Regular CEST does not provide the folding mechanism, but double-resonance CEST clearly shows that T4L can fold directly without going through B.
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Affiliation(s)
- Pramodh Vallurupalli
- TIFR Centre for Interdisciplinary Sciences , Tata Institute of Fundamental Research Hyderabad , 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District , Hyderabad , Telangana 500107 , India
| | - Ved Prakash Tiwari
- TIFR Centre for Interdisciplinary Sciences , Tata Institute of Fundamental Research Hyderabad , 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District , Hyderabad , Telangana 500107 , India
| | - Shamasree Ghosh
- TIFR Centre for Interdisciplinary Sciences , Tata Institute of Fundamental Research Hyderabad , 36/P, Gopanpally Village, Serilingampally Mandal, Ranga Reddy District , Hyderabad , Telangana 500107 , India
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11
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Rosemond SN, Hamadani KM, Cate JHD, Marqusee S. Modulating long-range energetics via helix stabilization: A case study using T4 lysozyme. Protein Sci 2018; 27:2084-2093. [PMID: 30284332 DOI: 10.1002/pro.3521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 11/07/2022]
Abstract
Cooperative protein folding requires distant regions of a protein to interact and provide mutual stabilization. The mechanism of this long-distance coupling remains poorly understood. Here, we use T4 lysozyme (T4L*) as a model to investigate long-range communications across two subdomains of a globular protein. T4L* is composed of two structurally distinct subdomains, although it behaves in a two-state manner at equilibrium. The subdomains of T4L* are connected via two topological connections: the N-terminal helix that is structurally part of the C-terminal subdomain (the A-helix) and a long helix that spans both subdomains (the C-helix). To understand the role that the C-helix plays in cooperative folding, we analyzed a circularly permuted version of T4L* (CP13*), whose subdomains are connected only by the C-helix. We demonstrate that when isolated as individual fragments, both subdomains of CP13* can fold autonomously into marginally stable conformations. The energetics of the N-terminal subdomain depend on the formation of a salt bridge known to be important for stability in the full-length protein. We show that the energetic contribution of the salt bridge to the stability of the N-terminal fragment increases when the C-helix is stabilized, such as occurs upon folding of the C-terminal subdomain. These results suggest a model where long-range energetic coupling is mediated by helix stabilization and not specific tertiary interactions.
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Affiliation(s)
- Sabriya N Rosemond
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720-3220
| | - Kambiz M Hamadani
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720.,California State University San Marcos, San Marcos, California, 92096
| | - Jamie H D Cate
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720-3220.,Department of Chemistry, University of California, Berkeley, California, 94720
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, University of California, Berkeley, California, 94720.,Department of Molecular and Cell Biology, University of California, Berkeley, California, 94720-3220.,Department of Chemistry, University of California, Berkeley, California, 94720.,Chan Zuckerberg Biohub, San Francisco, CA, 94158
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12
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Kitahara R, Sakuraba S, Kameda T, Okuda S, Xue M, Mulder FAA. Nuclear magnetic resonance-based determination of dioxygen binding sites in protein cavities. Protein Sci 2018; 27:769-779. [PMID: 29271012 DOI: 10.1002/pro.3371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/28/2017] [Accepted: 12/20/2017] [Indexed: 11/06/2022]
Abstract
The location and ligand accessibility of internal cavities in cysteine-free wild-type T4 lysozyme was investigated using O2 gas-pressure NMR spectroscopy and molecular dynamics (MD) simulation. Upon increasing the concentration of dissolved O2 in solvent to 8.9 mM, O2 -induced paramagnetic relaxation enhancements (PREs) to the backbone amide and side chain methyl protons were observed, specifically around two cavities in the C-terminal domain. To determine the number of O2 binding sites and their atomic coordinates from the 1/r6 distance dependence of the PREs, we established an analytical procedure using Akaike's Information Criterion, in combination with a grid-search. Two O2 -accessible sites were identified in internal cavities: One site was consistent with the xenon-binding site in the protein in crystal, and the other site was established to be a novel ligand-binding site. MD simulations performed at 10 and 100 mM O2 revealed dioxygen ingress and egress as well as rotational and translational motions of O2 in the cavities. It is therefore suggested that conformational fluctuations within the ground-state ensemble transiently develop channels for O2 association with the internal protein cavities.
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Affiliation(s)
- Ryo Kitahara
- Department of Pharmaceutical Sciences, College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Shun Sakuraba
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Tomoshi Kameda
- Computational Omics Research Team, Artificial Intelligence Research Center, Advanced Industrial Science and Technology, Koto, Tokyo, 135-0064, Japan
| | - Sanshiro Okuda
- Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577, Japan
| | - Mengjun Xue
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO), University of Aarhus, Aarhus C, DK-8000, Denmark
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13
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Malhotra P, Jethva PN, Udgaonkar JB. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding. Biochemistry 2017; 56:4053-4063. [DOI: 10.1021/acs.biochem.7b00367] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute
of Fundamental Research, Bengaluru 560065, India
| | - Prashant N. Jethva
- National Centre for Biological Sciences, Tata Institute
of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute
of Fundamental Research, Bengaluru 560065, India
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14
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Hamadani KM, Howe J, Jensen MK, Wu P, Cate JHD, Marqusee S. An in vitro tag-and-modify protein sample generation method for single-molecule fluorescence resonance energy transfer. J Biol Chem 2017; 292:15636-15648. [PMID: 28754692 DOI: 10.1074/jbc.m117.791723] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/25/2017] [Indexed: 11/06/2022] Open
Abstract
Biomolecular systems exhibit many dynamic and biologically relevant properties, such as conformational fluctuations, multistep catalysis, transient interactions, folding, and allosteric structural transitions. These properties are challenging to detect and engineer using standard ensemble-based techniques. To address this drawback, single-molecule methods offer a way to access conformational distributions, transient states, and asynchronous dynamics inaccessible to these standard techniques. Fluorescence-based single-molecule approaches are parallelizable and compatible with multiplexed detection; to date, however, they have remained limited to serial screens of small protein libraries. This stems from the current absence of methods for generating either individual dual-labeled protein samples at high throughputs or protein libraries compatible with multiplexed screening platforms. Here, we demonstrate that by combining purified and reconstituted in vitro translation, quantitative unnatural amino acid incorporation via AUG codon reassignment, and copper-catalyzed azide-alkyne cycloaddition, we can overcome these challenges for target proteins that are, or can be, methionine-depleted. We present an in vitro parallelizable approach that does not require laborious target-specific purification to generate dual-labeled proteins and ribosome-nascent chain libraries suitable for single-molecule FRET-based conformational phenotyping. We demonstrate the power of this approach by tracking the effects of mutations, C-terminal extensions, and ribosomal tethering on the structure and stability of three protein model systems: barnase, spectrin, and T4 lysozyme. Importantly, dual-labeled ribosome-nascent chain libraries enable single-molecule co-localization of genotypes with phenotypes, are well suited for multiplexed single-molecule screening of protein libraries, and should enable the in vitro directed evolution of proteins with designer single-molecule conformational phenotypes of interest.
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Affiliation(s)
- Kambiz M Hamadani
- From the California Institute for Quantitative Biosciences and .,the Department of Chemistry and Biochemistry, California State University, San Marcos, California 92096, and
| | - Jesse Howe
- the Department of Chemistry and Biochemistry, California State University, San Marcos, California 92096, and
| | | | - Peng Wu
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Jamie H D Cate
- From the California Institute for Quantitative Biosciences and .,the Departments of Molecular and Cell Biology and.,Chemistry, University of California, Berkeley, California 94720
| | - Susan Marqusee
- From the California Institute for Quantitative Biosciences and .,the Departments of Molecular and Cell Biology and
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15
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Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates. Biophys J 2016; 110:1280-90. [PMID: 27028638 DOI: 10.1016/j.bpj.2015.12.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/08/2015] [Accepted: 12/31/2015] [Indexed: 12/19/2022] Open
Abstract
Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments.
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16
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Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
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Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
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17
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Xue M, Kitahara R, Yoshimura Y, Mulder FAA. Aberrant increase of NMR signal in hydrogen exchange experiments. Observation and explanation. Biochem Biophys Res Commun 2016; 478:1185-8. [PMID: 27544032 DOI: 10.1016/j.bbrc.2016.08.092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 08/15/2016] [Indexed: 12/14/2022]
Abstract
Hydrogen exchange (HX) NMR spectroscopy is widely used for monitoring structure, stability and dynamics of proteins at the level of individual residues. The stochastic replacement of protons by deuterons typically leads to an exponential decrease of the NMR signals. However, an unusual signal increase was observed in HX of several amides for T4 lysozyme L99A. This effect can be attributed to peak sharpening as a result of reduced dipolar relaxation from proximal amide protons that experience more rapid hydrogen/deuterium (H/D) exchange. The behavior was specifically observed at the termini of secondary structure elements, where large differences in protection against H/D exchange are observed. This effect is expected to be more widespread in NMR HX studies, and is important for the accurate determination of protection factors.
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Affiliation(s)
- Mengjun Xue
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University, Shiga, Japan
| | - Yuichi Yoshimura
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, University of Aarhus, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark.
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18
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Malhotra P, Udgaonkar JB. Secondary Structural Change Can Occur Diffusely and Not Modularly during Protein Folding and Unfolding Reactions. J Am Chem Soc 2016; 138:5866-78. [DOI: 10.1021/jacs.6b03356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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19
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Lou SC, Wetzel S, Zhang H, Crone EW, Lee YT, Jackson SE, Hsu STD. The Knotted Protein UCH-L1 Exhibits Partially Unfolded Forms under Native Conditions that Share Common Structural Features with Its Kinetic Folding Intermediates. J Mol Biol 2016; 428:2507-2520. [PMID: 27067109 DOI: 10.1016/j.jmb.2016.04.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/22/2016] [Accepted: 04/02/2016] [Indexed: 10/22/2022]
Abstract
The human ubiquitin C-terminal hydrolase, UCH-L1, is an abundant neuronal deubiquitinase that is associated with Parkinson's disease. It contains a complex Gordian knot topology formed by the polypeptide chain alone. Using a combination of fluorescence-based kinetic measurements, we show that UCH-L1 has two distinct kinetic folding intermediates that are transiently populated on parallel pathways between the denatured and native states. NMR hydrogen-deuterium exchange (HDX) experiments indicate the presence of partially unfolded forms (PUFs) of UCH-L1 under native conditions. HDX measurements as a function of urea concentration were used to establish the structure of the PUFs and pulse-labelled HDX NMR was used to show that the PUFs and the folding intermediates are likely the same species. In both cases, a similar stable core encompassing most of the central β-sheet is highly structured and α-helix 3, which is partially formed, packs against it. In contrast to the stable β-sheet core, the peripheral α-helices display significant local fluctuations leading to rapid exchange. The results also suggest that the main difference between the two kinetic intermediates is structure and packing of α-helices 3 and 7 and the degree of structure in β-strand 5. Together, the fluorescence and NMR results establish that UCH-L1 neither folds through a continuum of pathways nor by a single discrete pathway. Its folding is complex, the β-sheet core forms early and is present in both intermediate states, and the rate-limiting step which is likely to involve the threading of the chain to form the 52-knot occurs late on the folding pathway.
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Affiliation(s)
- Shih-Chi Lou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan
| | - Svava Wetzel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Hongyu Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Elizabeth W Crone
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Yun-Tzai Lee
- Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Sophie E Jackson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Shang-Te Danny Hsu
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; Institute of Biological Chemistry, Academia Sinica, 128, Section 2, Academia Road, Taipei 11529, Taiwan; Institute of Biochemical Sciences, National Taiwan University, 1, Section 4, Roosevelt Road, Taipei 106, Taiwan.
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20
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Guo R, Gaffney K, Yang Z, Kim M, Sungsuwan S, Huang X, Hubbell WL, Hong H. Steric trapping reveals a cooperativity network in the intramembrane protease GlpG. Nat Chem Biol 2016; 12:353-360. [PMID: 26999782 PMCID: PMC4837050 DOI: 10.1038/nchembio.2048] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 01/22/2016] [Indexed: 12/21/2022]
Abstract
Membrane proteins are assembled through balanced interactions among protein, lipids and water. Studying their folding while maintaining the native lipid environment is necessary but challenging. Here we present methods for analyzing key elements in membrane protein folding including thermodynamic stability, compactness of the unfolded state and folding cooperativity under native conditions. The methods are based on steric trapping which couples unfolding of a doubly-biotinylated protein to binding of monovalent streptavidin (mSA). We further advanced this technology for general application by developing versatile biotin probes possessing spectroscopic reporters that are sensitized by mSA binding or protein unfolding. By applying these methods to an intramembrane protease GlpG of Escherichia coli, we elucidated a widely unraveled unfolded state, subglobal unfolding of the region encompassing the active site, and a network of cooperative and localized interactions to maintain the stability. These findings provide crucial insights into the folding energy landscape of membrane proteins.
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Affiliation(s)
- Ruiqiong Guo
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Kristen Gaffney
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Zhongyu Yang
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Miyeon Kim
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Suttipun Sungsuwan
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA
| | - Wayne L Hubbell
- Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
| | - Heedeok Hong
- Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.,Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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21
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Newcomer RL, Fraser LCR, Teschke CM, Alexandrescu AT. Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding. Biophys J 2015; 109:2666-2677. [PMID: 26682823 PMCID: PMC4699920 DOI: 10.1016/j.bpj.2015.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/13/2015] [Accepted: 11/06/2015] [Indexed: 01/30/2023] Open
Abstract
The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining (3)JNC' couplings transmitted through H-bonds, the temperature and urea-concentration dependence of (1)HN and (15)N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and (3)JNC' H-bond couplings, are identified with an accuracy of 90% by (1)HN temperature coefficients. The accuracy is improved to 95% when (15)N temperature coefficients are also included. In contrast, the urea dependence of (1)HN and (15)N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility.
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Affiliation(s)
- Rebecca L Newcomer
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - LaTasha C R Fraser
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut; Department of Chemistry, University of Connecticut, Storrs, Connecticut.
| | - Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut.
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22
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Zheng W, Glenn P. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation. J Chem Phys 2015; 142:035101. [PMID: 25612731 DOI: 10.1063/1.4905606] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant--while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York 14260, USA
| | - Paul Glenn
- Department of Physics, University at Buffalo, Buffalo, New York 14260, USA
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23
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Malhotra P, Udgaonkar JB. Tuning Cooperativity on the Free Energy Landscape of Protein Folding. Biochemistry 2015; 54:3431-41. [DOI: 10.1021/acs.biochem.5b00247] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India
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24
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Role of cavities and hydration in the pressure unfolding of T4 lysozyme. Proc Natl Acad Sci U S A 2014; 111:13846-51. [PMID: 25201963 DOI: 10.1073/pnas.1410655111] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well known that high hydrostatic pressures can induce the unfolding of proteins. The physical underpinnings of this phenomenon have been investigated extensively but remain controversial. Changes in solvation energetics have been commonly proposed as a driving force for pressure-induced unfolding. Recently, the elimination of void volumes in the native folded state has been argued to be the principal determinant. Here we use the cavity-containing L99A mutant of T4 lysozyme to examine the pressure-induced destabilization of this multidomain protein by using solution NMR spectroscopy. The cavity-containing C-terminal domain completely unfolds at moderate pressures, whereas the N-terminal domain remains largely structured to pressures as high as 2.5 kbar. The sensitivity to pressure is suppressed by the binding of benzene to the hydrophobic cavity. These results contrast to the pseudo-WT protein, which has a residual cavity volume very similar to that of the L99A-benzene complex but shows extensive subglobal reorganizations with pressure. Encapsulation of the L99A mutant in the aqueous nanoscale core of a reverse micelle is used to examine the hydration of the hydrophobic cavity. The confined space effect of encapsulation suppresses the pressure-induced unfolding transition and allows observation of the filling of the cavity with water at elevated pressures. This indicates that hydration of the hydrophobic cavity is more energetically unfavorable than global unfolding. Overall, these observations point to a range of cooperativity and energetics within the T4 lysozyme molecule and illuminate the fact that small changes in physical parameters can significantly alter the pressure sensitivity of proteins.
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25
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Richa T, Sivaraman T. OneG-Vali: a computational tool for detecting, estimating and validating cryptic intermediates of proteins under native conditions. RSC Adv 2014. [DOI: 10.1039/c4ra04642k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Unfolding pathway of T4 lysozyme under native conditions as predicted by the OneG-Vali has been illustrated. Also, structural contexts of various states (native (N), cryptic intermediates (CIs) and unfolded (U) conformations) of the protein and the population of three CIs are depicted.
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Affiliation(s)
- Tambi Richa
- Structural Biology Laboratory
- Department of Bioinformatics
- School of Chemical and Biotechnology
- SASTRA University
- , India
| | - Thirunavukkarasu Sivaraman
- Structural Biology Laboratory
- Department of Bioinformatics
- School of Chemical and Biotechnology
- SASTRA University
- , India
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26
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Radou G, Enciso M, Krivov S, Paci E. Modulation of a protein free-energy landscape by circular permutation. J Phys Chem B 2013; 117:13743-7. [PMID: 24090448 PMCID: PMC3821731 DOI: 10.1021/jp406818t] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
![]()
Circular
permutations usually retain the native structure and function
of a protein while inevitably perturbing its folding dynamics. By
using simulations with a structure-based model and a rigorous methodology
to determine free-energy surfaces from trajectories, we evaluate the
effect of a circular permutation on the free-energy landscape of the
protein T4 lysozyme. We observe changes which, although subtle, largely
affect the cooperativity between the two subdomains. Such a change
in cooperativity has been previously experimentally observed and recently
also characterized using single molecule optical tweezers and the
Crooks relation. The free-energy landscapes show that both the wild
type and circular permutant have an on-pathway intermediate, previously
experimentally characterized, in which one of the subdomains is completely
formed. The landscapes, however, differ in the position of the rate-limiting
step for folding, which occurs before the intermediate in the wild
type and after in the circular permutant. This shift of transition
state explains the observed change in the cooperativity. The underlying
free-energy landscape thus provides a microscopic description of the
folding dynamics and the connection between circular permutation and
the loss of cooperativity experimentally observed.
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Affiliation(s)
- Gaël Radou
- Astbury Centre for Structural Molecular Biology, University of Leeds , Leeds LS2 9JT, United Kingdom
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27
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Merstorf C, Maciejak O, Mathé J, Pastoriza-Gallego M, Thiebot B, Clément MJ, Pelta J, Auvray L, Curmi PA, Savarin P. Mapping the conformational stability of maltose binding protein at the residue scale using nuclear magnetic resonance hydrogen exchange experiments. Biochemistry 2012; 51:8919-30. [PMID: 23046344 DOI: 10.1021/bi3003605] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Being able to differentiate local fluctuations from global folding-unfolding dynamics of a protein is of major interest for improving our understanding of structure-function determinants. The maltose binding protein (MBP), a protein that belongs to the maltose transport system, has a structure composed of two globular domains separated by a rigid-body "hinge bending". Here we determined, by using hydrogen exchange (HX) nuclear magnetic resonance experiments, the apparent stabilization free energies of 101 residues of MBP bound to β-cyclodextrin (MBP-βCD) under native conditions. We observed that the last helix of MBP (helix α14) has a lower protection factor than the rest of the protein. Further, HX experiments were performed using guanidine hydrochloride under subdenaturing conditions to discriminate between local fluctuations and global unfolding events and to determine the MBP-βCD energy landscape. The results show that helix α4 and a part of helices α5 and α6 are clearly grouped into a subdenaturing folding unit and represent a partially folded intermediate under native conditions. In addition, we observed that amide protons located in the hinge between the two globular domains share similar ΔG(gu)(app) and m values and should unfold simultaneously. These observations provide new points of view for improving our understanding of the thermodynamic stability and the mechanisms that drive folding-unfolding dynamics of proteins.
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Affiliation(s)
- Céline Merstorf
- Centre National de la Recherche Scientifique UMR 8587, Université Evry-Val d'Essonne et Cergy Pontoise, Laboratoire d'Analyse et de modélisation pour la Biologie et l'Environnement, Evry 91025, France
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28
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Richa T, Sivaraman T. OneG: a computational tool for predicting cryptic intermediates in the unfolding kinetics of proteins under native conditions. PLoS One 2012; 7:e32465. [PMID: 22412877 PMCID: PMC3296725 DOI: 10.1371/journal.pone.0032465] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 01/31/2012] [Indexed: 11/18/2022] Open
Abstract
Understanding the relationships between conformations of proteins and their stabilities is one key to address the protein folding paradigm. The free energy change (ΔG) of unfolding reactions of proteins is measured by traditional denaturation methods and native hydrogen-deuterium (H/D) exchange methods. However, the free energy of unfolding (ΔG(U)) and the free energy of exchange (ΔG(HX)) of proteins are not in good agreement, though the experimental conditions of both methods are well matching to each other. The anomaly is due to any one or combinations of the following reasons: (i) effects of cis-trans proline isomerisation under equilibrium unfolding reactions of proteins (ii) inappropriateness in accounting the baselines of melting curves (iii) presence of cryptic intermediates, which may elude the melting curve analysis and (iv) existence of higher energy metastable states in the H/D exchange reactions of proteins. Herein, we have developed a novel computational tool, OneG, which accounts the discrepancy between ΔG(U) and ΔG(HX) of proteins by systematically accounting all the four factors mentioned above. The program is fully automated and requires four inputs: three-dimensional structures of proteins, ΔG(U), ΔG(U)(*) and residue-specific ΔG(HX) determined under EX2-exchange conditions in the absence of denaturants. The robustness of the program has been validated using experimental data available for proteins such as cytochrome c and apocytochrome b(562) and the data analyses revealed that cryptic intermediates of the proteins detected by the experimental methods and the cryptic intermediates predicted by the OneG for those proteins were in good agreement. Furthermore, using OneG, we have shown possible existence of cryptic intermediates and metastable states in the unfolding pathways of cardiotoxin III and cobrotoxin, respectively, which are homologous proteins. The unique application of the program to map the unfolding pathways of proteins under native conditions have been brought into fore and the program is publicly available at http://sblab.sastra.edu/oneg.html.
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Affiliation(s)
| | - Thirunavukkarasu Sivaraman
- Department of Bioinformatics, School of Chemical and Biotechnology, SASTRA University, Thanjavur, Tamil Nadu, India
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29
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Cossins BP, Hosseini A, Guallar V. Exploration of Protein Conformational Change with PELE and Meta-Dynamics. J Chem Theory Comput 2012; 8:959-65. [PMID: 26593358 DOI: 10.1021/ct200675g] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomistic molecular simulation methods are now able to explore complex protein or protein-ligand dynamical space in a tractable way with methods such as meta-dynamics or adaptive biasing force. However, many of these methods either require a careful selection of reaction coordinates or the knowledge of an initial pathway of some kind. Thus, it is important that effective methods are developed to produce this pathway data in an efficient fashion. PELE, a proven protein-ligand sampling code, has been developed to provide rapid protein sampling in highly flexible cases, using a reduced network model eigen problem approach. The resulting method is able to rapidly sample configuration space with very general driving information. When applied to ubiquitin, PELE was able to reproduce RMSD and average force data found in molecular dynamics simulations. PELE was also applied to explore the opening/closing transition of T4 lysozyme. A meta-dynamics exploration using a low energy pathway validated that the configurations explored by PELE represent the most populated regions of phase space. PELE and meta-dynamics explorations also discovered a low free energy region where a large cross-domain helix of T4 lysozyme is broken in two. There is previous NMR evidence for the validity of this unfolded helix region.
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Affiliation(s)
- Benjamin P Cossins
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29,08034 Barcelona, Spain
| | - Ali Hosseini
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29,08034 Barcelona, Spain
| | - Victor Guallar
- Joint BSC-IRB Research Program in Computational Biology, Barcelona Supercomputing Center, c/Jordi Girona 29,08034 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
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30
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Tjong H, Zhou HX. The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe. Biophys J 2010; 98:2273-80. [PMID: 20483336 DOI: 10.1016/j.bpj.2010.01.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 12/21/2009] [Accepted: 01/05/2010] [Indexed: 10/19/2022] Open
Abstract
The four-helix bundle protein Rd-apocyt b(562), a redesigned stable variant of apocytochrome b(562), exhibits two-state folding kinetics. Its transition-state ensemble has been characterized by Phi-value analysis. To elucidate the molecular basis of the transition-state ensemble, we have carried out high-temperature molecular dynamics simulations of the unfolding process. In six parallel simulations, unfolding started with the melting of helix I and the C-terminal half of helix IV, and followed by helix III, the N-terminal half of helix IV and helix II. This ordered melting of the helices is consistent with the conclusion from native-state hydrogen exchange, and can be rationalized by differences in intrinsic helix propensity. Guided by experimental Phi-values, a putative transition-state ensemble was extracted from the simulations. The residue helical probabilities of this transition-state ensemble show good correlation with the Phi-values. To further validate the putative transition-state ensemble, the effect of macromolecular crowding on the relative stability between the unfolded ensemble and the transition-state ensemble was calculated. The resulting effect of crowding on the folding kinetics agrees well with experimental observations. This study shows that molecular dynamics simulations combined with calculation of crowding effects provide an avenue for characterize the transition-state ensemble in atomic details.
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Affiliation(s)
- Harianto Tjong
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
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31
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Di Paolo A, Balbeur D, De Pauw E, Redfield C, Matagne A. Rapid collapse into a molten globule is followed by simple two-state kinetics in the folding of lysozyme from bacteriophage λ. Biochemistry 2010; 49:8646-57. [PMID: 20806781 DOI: 10.1021/bi101126f] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stopped-flow fluorescence and circular dichroism spectroscopy have been used in combination with quenched-flow hydrogen exchange labeling, monitored by two-dimensional NMR and electrospray ionization mass spectrometry, to investigate the folding kinetics of lysozyme from bacteriophage λ (λ lysozyme) at pH 5.6, 20 °C. The first step in the folding of λ lysozyme occurs very rapidly (τ < 1 ms) after refolding is initiated and involves both hydrophobic collapse and formation of a high content of secondary structure but only weak protection from (1)H/(2)H exchange and no fixed tertiary structure organization. This early folding step is reflected in the dead-time events observed in the far-UV CD and ANS fluorescence experiments. Following accumulation of this kinetic molten globule species, the secondary structural elements are stabilized and the majority (ca. 88%) of refolding molecules acquire native-like properties in a highly cooperative two-state process, with τ = 0.15 ± 0.03 s. This is accompanied by the acquisition of substantial native-like protection from hydrogen exchange. A double-mixing experiment and the absence of a denaturant effect reveal that slow (τ = 5 ± 1 s) folding of the remaining (ca. 12%) molecules is rate limited by the cis/trans isomerization of prolines that are trans in the folded enzyme. In addition, native state hydrogen exchange and classical denaturant unfolding experiments have been used to characterize the thermodynamic properties of the enzyme. In good agreement with previous crystallographic evidence, our results show that λ lysozyme is a highly dynamic protein, with relatively low conformational stability (ΔG°(N-U) = 25 ± 2 kJ·mol(-1)).
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Affiliation(s)
- Alexandre Di Paolo
- Laboratoire d'Enzymologie et Repliement des Protéines, Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, 4000 Liège (Sart Tilman), Belgium
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32
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The folding cooperativity of a protein is controlled by its chain topology. Nature 2010; 465:637-40. [PMID: 20495548 DOI: 10.1038/nature09021] [Citation(s) in RCA: 179] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 03/18/2010] [Indexed: 11/08/2022]
Abstract
The three-dimensional structures of proteins often show a modular architecture comprised of discrete structural regions or domains. Cooperative communication between these regions is important for catalysis, regulation and efficient folding; lack of coupling has been implicated in the formation of fibrils and other misfolding pathologies. How different structural regions of a protein communicate and contribute to a protein's overall energetics and folding, however, is still poorly understood. Here we use a single-molecule optical tweezers approach to induce the selective unfolding of particular regions of T4 lysozyme and monitor the effect on other regions not directly acted on by force. We investigate how the topological organization of a protein (the order of structural elements along the sequence) affects the coupling and folding cooperativity between its domains. To probe the status of the regions not directly subjected to force, we determine the free energy changes during mechanical unfolding using Crooks' fluctuation theorem. We pull on topological variants (circular permutants) and find that the topological organization of the polypeptide chain critically determines the folding cooperativity between domains and thus what parts of the folding/unfolding landscape are explored. We speculate that proteins may have evolved to select certain topologies that increase coupling between regions to avoid areas of the landscape that lead to kinetic trapping and misfolding.
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33
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Manson A, Whitten ST, Ferreon JC, Fox RO, Hilser VJ. Characterizing the role of ensemble modulation in mutation-induced changes in binding affinity. J Am Chem Soc 2009; 131:6785-93. [PMID: 19397330 PMCID: PMC2711448 DOI: 10.1021/ja809133u] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein conformational fluctuations are key contributors to biological function, mediating important processes such as enzyme catalysis, molecular recognition, and allosteric signaling. To better understand the role of conformational fluctuations in substrate/ligand recognition, we analyzed, experimentally and computationally, the binding reaction between an SH3 domain and the recognition peptide of its partner protein. The fluctuations in this SH3 domain were enumerated by using an algorithm based on the hard sphere collision model, and the binding energetics resulting from these fluctuations were calculated using a structure-based energy function parametrized to solvent accessible surface areas. Surprisingly, this simple model reproduced the effects of mutations on the experimentally determined SH3 binding energetics, within the uncertainties of the measurements, indicating that conformational fluctuations in SH3, and in particular the RT loop region, are structurally diverse and are well-approximated by the randomly configured states. The mutated positions in SH3 were distant to the binding site and involved Ala and Gly substitutions of solvent exposed positions in the RT loop. To characterize these fluctuations, we applied principal coordinate analysis to the computed ensembles, uncovering the principal modes of conformational variation. It is shown that the observed differences in binding affinity between each mutant, and thus the apparent coupling between the mutated sites, can be described in terms of the changes in these principal modes. These results indicate that dynamic loops in proteins can populate a broad conformational ensemble and that a quantitative understanding of molecular recognition requires consideration of the entire distribution of states.
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Affiliation(s)
- Anthony Manson
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Steven T Whitten
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
- RedStorm Scientific, Inc., Galveston, TX 77550, USA
| | - Josephine C. Ferreon
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert O Fox
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vincent J Hilser
- Department of Biochemistry and Molecular Biology, and Sealy Center for Structural Biology and Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
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34
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Brustad EM, Lemke EA, Schultz PG, Deniz AA. A general and efficient method for the site-specific dual-labeling of proteins for single molecule fluorescence resonance energy transfer. J Am Chem Soc 2009; 130:17664-5. [PMID: 19108697 DOI: 10.1021/ja807430h] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A general strategy for the site-specific dual-labeling of proteins for single-molecule fluorescence resonance energy transfer is presented. A genetically encoded unnatural ketone amino acid was labeled with a hydroxylamine-containing fluorophore with high yield (>95%) and specificity. This methodology was used to construct dual-labeled T4 lysozyme variants, allowing the study of T4 lysozyme folding at single-molecule resolution. The presented strategy is anticipated to expand the scope of single-molecule protein structure and function studies.
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Affiliation(s)
- Eric M Brustad
- Department of Molecular Biology, Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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35
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Mohan PK, Hosur RV. pH dependent unfolding characteristics of DLC8 dimer: Residue level details from NMR. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:1795-803. [DOI: 10.1016/j.bbapap.2008.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/30/2008] [Accepted: 07/04/2008] [Indexed: 10/21/2022]
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36
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Mohan PMK, Chakraborty S, Hosur RV. Residue-wise conformational stability of DLC8 dimer from native-state hydrogen exchange. Proteins 2008; 75:40-52. [PMID: 18767155 DOI: 10.1002/prot.22219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Dynein light chain (DLC8) is the smallest subunit of the dynein motor complex, which is known to act as a cargo adaptor in intracellular trafficking. The protein exists as a pure dimer at physiological pH and a completely folded monomer below pH 4. Here, we have determined the energy landscape of the dimeric protein using a combination of optical techniques and native-state hydrogen exchange of amide groups, the former giving the global features and the latter yielding the residue level details. The data indicated the presence of intermediates along the equilibrium unfolding transition. The hydrogen exchange data suggested that the molecule has differential stability in its various segments. We deduce from the free energy data that the antiparallel beta-sheets (beta4 and beta5) that form the hydrophobic core of the protein and the alpha2 helix, all of which are highly protected with regard to hydrogen exchange, contribute significantly to the initial step of the protein folding mechanism. Denaturant-dependent hydrogen exchange indicated further that some amides exchange via local fluctuations, whereas there are others which exchange via global unfolding events. Implications of these to cargo adaptability of the dimer are discussed.
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Affiliation(s)
- P M Krishna Mohan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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37
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Dong Q, Wang X, Lin L. Prediction of protein local structures and folding fragments based on building-block library. Proteins 2008; 72:353-66. [PMID: 18214964 DOI: 10.1002/prot.21931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In recent years, protein structure prediction using local structure information has made great progress. In this study, a novel and effective method is developed to predict the local structure and the folding fragments of proteins. First, the proteins with known structures are split into fragments. Second, these fragments, represented by dihedrals, are clustered to produce the building blocks (BBs). Third, an efficient machine learning method is used to predict the local structures of proteins from sequence profiles. Finally, a bi-gram model, trained by an iterated algorithm, is introduced to simulate the interactions of these BBs. For test proteins, the building-block lattice is constructed, which contains all the folding fragments of the proteins. The local structures and the optimal fragments are then obtained by the dynamic programming algorithm. The experiment is performed on a subset of the PDB database with sequence identity less than 25%. The results show that the performance of the method is better than the method that uses only sequence information. When multiple paths are returned, the average classification accuracy of local structures is 72.27% and the average prediction accuracy of local structures is 67.72%, which is a significant improvement in comparison with previous studies. The method can predict not only the local structures but also the folding fragments of proteins. This work is helpful for the ab initio protein structure prediction and especially, the understanding of the folding process of proteins.
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Affiliation(s)
- Qiwen Dong
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
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38
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Hills RD, Brooks CL. Subdomain competition, cooperativity, and topological frustration in the folding of CheY. J Mol Biol 2008; 382:485-95. [PMID: 18644380 DOI: 10.1016/j.jmb.2008.07.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Revised: 06/30/2008] [Accepted: 07/04/2008] [Indexed: 11/17/2022]
Abstract
The folding of multidomain proteins often proceeds in a hierarchical fashion with individual domains folding independent of one another. A large single-domain protein, however, can consist of multiple modules whose folding may be autonomous or interdependent in ways that are unclear. We used coarse-grained simulations to explore the folding landscape of the two-subdomain bacterial response regulator CheY. Thermodynamic and kinetic characterization shows the landscape to be highly analogous to the four-state landscape reported for another two-subdomain protein, T4 lysozyme. An on-pathway intermediate structured in the more stable nucleating subdomain was observed, as were transient states frustrated in off-pathway contacts prematurely structured in the weaker subdomain. Local unfolding, or backtracking, was observed in the frustrated state before the native conformation could be reached. Nonproductive frustration was attributable to competition for van der Waals contacts between the two subdomains. In an accompanying article, stopped-flow kinetic measurements support an off-pathway burst-phase intermediate, seemingly consistent with our prediction of early frustration in the folding landscape of CheY. Comparison of the folding mechanisms for CheY, T4 lysozyme, and interleukin-1 beta leads us to postulate that subdomain competition is a general feature of large single-domain proteins with multiple folding modules.
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Affiliation(s)
- Ronald D Hills
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, TPC6, La Jolla, CA 92037, USA
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39
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Atomic force microscopy reveals parallel mechanical unfolding pathways of T4 lysozyme: evidence for a kinetic partitioning mechanism. Proc Natl Acad Sci U S A 2008; 105:1885-90. [PMID: 18272500 DOI: 10.1073/pnas.0706775105] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Kinetic partitioning is predicted to be a general mechanism for proteins to fold into their well defined native three-dimensional structure from unfolded states following multiple folding pathways. However, experimental evidence supporting this mechanism is still limited. By using single-molecule atomic force microscopy, here we report experimental evidence supporting the kinetic partitioning mechanism for mechanical unfolding of T4 lysozyme, a small protein composed of two subdomains. We observed that on stretching from its N and C termini, T4 lysozyme unfolds by multiple distinct unfolding pathways: the majority of T4 lysozymes unfold in an all-or-none fashion by overcoming a dominant unfolding kinetic barrier; and a small fraction of T4 lysozymes unfold in three-state fashion involving unfolding intermediate states. The three-state unfolding pathways do not follow well defined routes, instead they display variability and diversity in individual unfolding pathways. The unfolding intermediate states are local energy minima along the mechanical unfolding pathways and are likely to result from the residual structures present in the two subdomains after crossing the main unfolding barrier. These results provide direct evidence for the kinetic partitioning of the mechanical unfolding pathways of T4 lysozyme, and the complex unfolding behaviors reflect the stochastic nature of kinetic barrier rupture in mechanical unfolding processes. Our results demonstrate that single-molecule atomic force microscopy is an ideal tool to investigate the folding/unfolding dynamics of complex multimodule proteins that are otherwise difficult to study using traditional methods.
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40
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Watson E, Matousek WM, Irimies EL, Alexandrescu AT. Partially folded states of staphylococcal nuclease highlight the conserved structural hierarchy of OB-fold proteins. Biochemistry 2007; 46:9484-94. [PMID: 17661445 PMCID: PMC2128864 DOI: 10.1021/bi700532j] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have been interested in whether three proteins that share a five-stranded beta-barrel "OB-fold" structural motif but no detectable sequence homology fold by similar mechanisms. Here we describe native-state hydrogen exchange experiments as a function of urea for SN (staphylococcal nuclease), a protein with an OB-fold motif and additional nonconserved elements of structure. The regions of structure with the largest stability and unfolding cooperativity are contained within the conserved OB-fold portion of SN, consistent with previous results for CspA (cold shock protein A) and LysN (anticodon binding domain of lysyl tRNA synthetase). The OB-fold also has the subset of residues with the slowest unfolding rates in the three proteins, as determined by hydrogen exchange experiments in the EX1 limit. Although the protein folding hierarchy is maintained at the level of supersecondary structure, it is not evident for individual residues as might be expected if folding depended on obligatory nucleation sites. Rather, the site-specific stability profiles appear to be linked to sequence hydrophobicity and to the density of long-range contacts at each site in the three-dimensional structures of the proteins. We discuss the implications of the correlation between stability to unfolding and conservation of structure for mechanisms of protein structure evolution.
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Affiliation(s)
| | | | | | - Andrei T. Alexandrescu
- * To whom correspondence should be addressed: Department of Molecular and Cell Biology, University of Connecticut, 91 N,. Eagleville Rd., U-3125, Storrs, CT 06269–3125., Telephone: (860) 486–4414., Fax: (860) 486–4331., E-mail:
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41
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Wu KL, Wei JH, Lai SK, Okabe Y. Energy and Enthalpy Distribution Functions for a Few Physical Systems. J Phys Chem B 2007; 111:8946-58. [PMID: 17602519 DOI: 10.1021/jp0716280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present work is devoted to extracting the energy or enthalpy distribution function of a physical system from the moments of the distribution using the maximum entropy method. This distribution theory has the salient traits that it utilizes only the experimental thermodynamic data. The calculated distribution functions provide invaluable insight into the state or phase behavior of the physical systems under study. As concrete evidence, we demonstrate the elegance of the distribution theory by studying first a test case of a two-dimensional six-state Potts model for which simulation results are available for comparison, then the biphasic behavior of the binary alloy Na-K whose excess heat capacity, experimentally observed to fall in a narrow temperature range, has yet to be clarified theoretically, and finally, the thermally induced state behavior of a collection of 16 proteins.
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Affiliation(s)
- K L Wu
- Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan
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42
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Cellitti J, Llinas M, Echols N, Shank EA, Gillespie B, Kwon E, Crowder SM, Dahlquist FW, Alber T, Marqusee S. Exploring subdomain cooperativity in T4 lysozyme I: structural and energetic studies of a circular permutant and protein fragment. Protein Sci 2007; 16:842-51. [PMID: 17400926 PMCID: PMC2206633 DOI: 10.1110/ps.062628607] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 01/07/2007] [Accepted: 01/09/2007] [Indexed: 10/23/2022]
Abstract
Small proteins are generally observed to fold in an apparent two-state manner. Recently, however, more sensitive techniques have demonstrated that even seemingly single-domain proteins are actually made up of smaller subdomains. T4 lysozyme is one such protein. We explored the relative autonomy of its two individual subdomains and their contribution to the overall stability of T4 lysozyme by examining a circular permutation (CP13*) that relocates the N-terminal A-helix, creating subdomains that are contiguous in sequence. By determining the high-resolution structure of CP13* and characterizing its energy landscape using native state hydrogen exchange (NSHX), we show that connectivity between the subdomains is an important determinant of the energetic cooperativity but not structural integrity of the protein. The circular permutation results in a protein more easily able to populate a partially unfolded form in which the C-terminal subdomain is folded and the N-terminal subdomain is unfolded. We also created a fragment model of this intermediate and demonstrate using X-ray crystallography that its structure is identical to the corresponding residues in the full-length protein with the exception of a small network of hydrophobic interactions. In sum, we conclude that the C-terminal subdomain dominates the energetics of T4 lysozyme folding, and the A-helix serves an important role in coupling the two subdomains.
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Affiliation(s)
- Jason Cellitti
- Department of Molecular and Cell Biology and QB3 Institute-Berkeley, University of California, Berkeley, Berkeley, California 94720-3206, USA
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43
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Cellitti J, Bernstein R, Marqusee S. Exploring subdomain cooperativity in T4 lysozyme II: uncovering the C-terminal subdomain as a hidden intermediate in the kinetic folding pathway. Protein Sci 2007; 16:852-62. [PMID: 17400925 PMCID: PMC2206637 DOI: 10.1110/ps.062632807] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Intermediates along a protein's folding pathway can play an important role in its biology. Previous kinetics studies have revealed an early folding intermediate for T4 lysozyme, a small, well-characterized protein composed of an N-terminal and a C-terminal subdomain. Pulse-labeling hydrogen exchange studies suggest that residues from both subdomains contribute to the structure of this intermediate. On the other hand, equilibrium native state hydrogen experiments have revealed a high-energy, partially unfolded form of the protein that has an unstructured N-terminal subdomain and a structured C-terminal subdomain. To resolve this discrepancy between kinetics and equilibrium data, we performed detailed kinetics analyses of the folding and unfolding pathways of T4 lysozyme, as well as several point mutants and large-scale variants. The data support the argument for the presence of two distinct intermediates, one present on each side of the rate-limiting transition state barrier. The effects of circular permutation and site-specific mutations in the wild-type and circular permutant background, as well as a fragment containing just the C-terminal subdomain, support a model for the unfolding intermediate with an unfolded N-terminal and a folded C-terminal subdomain. Our results suggest that the partially unfolded form identified by native state hydrogen exchange resides on the folded side of the rate-limiting transition state and is, therefore, under most conditions, a "hidden" intermediate.
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Affiliation(s)
- Jason Cellitti
- Department of Molecular and Cell Biology and QB3 Institute-Berkeley, University of California, Berkeley, Berkeley, California 94720-3206, USA
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44
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Collins MD, Quillin ML, Hummer G, Matthews BW, Gruner SM. Structural rigidity of a large cavity-containing protein revealed by high-pressure crystallography. J Mol Biol 2007; 367:752-63. [PMID: 17292912 PMCID: PMC1853337 DOI: 10.1016/j.jmb.2006.12.021] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Revised: 12/07/2006] [Accepted: 12/10/2006] [Indexed: 01/07/2023]
Abstract
Steric constraints, charged interactions and many other forces important to protein structure and function can be explored by mutagenic experiments. Research of this kind has led to a wealth of knowledge about what stabilizes proteins in their folded states. To gain a more complete picture requires that we perturb these structures in a continuous manner, something mutagenesis cannot achieve. With high pressure crystallographic methods it is now possible to explore the detailed properties of proteins while continuously varying thermodynamic parameters. Here, we detail the structural response of the cavity-containing mutant L99A of T4 lysozyme, as well as its pseudo wild-type (WT*) counterpart, to hydrostatic pressure. Surprisingly, the cavity has almost no effect on the pressure response: virtually the same changes are observed in WT* as in L99A under pressure. The cavity is most rigid, while other regions deform substantially. This implies that while some residues may increase the thermodynamic stability of a protein, they may also be structurally irrelevant. As recently shown, the cavity fills with water at pressures above 100 MPa while retaining its overall size. The resultant picture of the protein is one in which conformationally fluctuating side groups provide a liquid-like environment, but which also contribute to the rigidity of the peptide backbone.
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Affiliation(s)
- Marcus D Collins
- Department of Physics, Cornell University, Ithaca, NY 14853, USA
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45
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Ghosh A, Brinda KV, Vishveshwara S. Dynamics of lysozyme structure network: probing the process of unfolding. Biophys J 2007; 92:2523-35. [PMID: 17208969 PMCID: PMC1864820 DOI: 10.1529/biophysj.106.099903] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recently we showed that the three-dimensional structure of proteins can be investigated from a network perspective, where the amino acid residues represent the nodes in the network and the noncovalent interactions between them are considered for the edge formation. In this study, the dynamical behavior of such networks is examined by considering the example of T4 lysozyme. The equilibrium dynamics and the process of unfolding are followed by simulating the protein at 300 K and at higher temperatures (400 K and 500 K), respectively. The snapshots of the protein structure from the simulations are represented as protein structure networks in which the strength of the noncovalent interactions is considered an important criterion in the construction of edges. The profiles of the network parameters, such as the degree distribution and the size of the largest cluster (giant component), were examined as a function of interaction strength at different temperatures. Similar profiles are seen at all the temperatures. However, the critical strength of interaction (Icritical) and the size of the largest cluster at all interaction strengths shift to lower values at 500 K. Further, the folding/unfolding transition is correlated with contacts evaluated at Icritical and with the composition of the top large clusters obtained at interaction strengths greater than Icritical. Finally, the results are compared with experiments, and predictions are made about the residues, which are important for stability and folding. To summarize, the network analysis presented in this work provides insights into the details of the changes occurring in the protein tertiary structure at the level of amino acid side-chain interactions, in both the equilibrium and the unfolding simulations. The method can also be employed as a valuable tool in the analysis of molecular dynamics simulation data, since it captures the details at a global level, which may elude conventional pairwise interaction analysis.
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Affiliation(s)
- Amit Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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46
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Kato H, Feng H, Bai Y. The folding pathway of T4 lysozyme: the high-resolution structure and folding of a hidden intermediate. J Mol Biol 2006; 365:870-80. [PMID: 17109883 PMCID: PMC2494534 DOI: 10.1016/j.jmb.2006.10.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 09/03/2006] [Accepted: 10/16/2006] [Indexed: 11/21/2022]
Abstract
Folding intermediates have been detected and characterized for many proteins. However, their structures at atomic resolution have only been determined for two small single domain proteins: Rd-apocytochrome b(562) and engrailed homeo domain. T4 lysozyme has two easily distinguishable but energetically coupled domains: the N and C-terminal domains. An early native-state hydrogen exchange experiment identified an intermediate with the C-terminal domain folded and the N-terminal domain unfolded. We have used a native-state hydrogen exchange-directed protein engineering approach to populate this intermediate and demonstrated that it is on the folding pathway and exists after the rate-limiting step. Here, we determined its high-resolution structure and the backbone dynamics by multi-dimensional NMR methods. We also characterized the folding behavior of the intermediate using stopped-flow fluorescence, protein engineering, and native-state hydrogen exchange. Unlike the folding intermediates of the two single-domain proteins, which have many non-native side-chain interactions, the structure of the hidden folding intermediate of T4 lysozyme is largely native-like. It folds like many small single domain proteins. These results have implications for understanding the folding mechanism and evolution of multi-domain proteins.
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Affiliation(s)
| | | | - Yawen Bai
- *corresponding author: E-mail: , Tel: 301-594-2375, Fax: 301-402-3095
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47
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Kato H, Vu N, Feng H, Zhou Z, Bai Y. The folding pathway of T4 lysozyme: an on-pathway hidden folding intermediate. J Mol Biol 2006; 365:881-91. [PMID: 17097105 PMCID: PMC2494531 DOI: 10.1016/j.jmb.2006.10.048] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Revised: 10/10/2006] [Accepted: 10/16/2006] [Indexed: 11/15/2022]
Abstract
T4 lysozyme has two easily distinguishable but energetically coupled domains: the N and C-terminal domains. In earlier studies, an amide hydrogen/deuterium exchange pulse-labeling experiment detected a stable submillisecond intermediate that accumulates before the rate-limiting transition state. It involves the formation of structures in both the N and C-terminal regions. However, a native-state hydrogen exchange experiment subsequently detected an equilibrium intermediate that only involves the formation of the C-terminal domain. Here, using stopped-flow circular dichroism and fluorescence, amide hydrogen exchange-folding competition, and protein engineering methods, we re-examined the folding pathway of T4-lysozyme. We found no evidence for the existence of a stable folding intermediate before the rate-limiting transition state at neutral pH. In addition, using native-state hydrogen exchange-directed protein engineering, we created a mimic of the equilibrium intermediate. We found that the intermediate mimic folds with the same rate as the wild-type protein, suggesting that the equilibrium intermediate is an on-pathway intermediate that exists after the rate-limiting transition state.
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Affiliation(s)
| | | | | | | | - Yawen Bai
- *corresponding author E-mail: , Tel: 301-594-2375, Fax: 301-402-3095
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48
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Liang X, Lee GI, Van Doren SR. Partially unfolded forms and non-two-state folding of a beta-sandwich: FHA domain from Arabidopsis receptor kinase-associated protein phosphatase. J Mol Biol 2006; 364:225-40. [PMID: 17007879 PMCID: PMC2020856 DOI: 10.1016/j.jmb.2006.08.090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Accepted: 08/30/2006] [Indexed: 11/21/2022]
Abstract
FHA domains adopt a beta-sandwich fold with 11 strands. The first evidence of partially unfolded forms of a beta-sandwich is derived from native-state hydrogen exchange (NHX) of the forkhead-associated (FHA) domain from kinase-associated protein phosphatase from Arabidopsis. The folding kinetics of this FHA domain indicate that EX2 behavior prevails at pH 6.3. In the chevron plot, rollover in the folding arm and bends in the unfolding arm suggest folding intermediates. NHX of this FHA domain suggests a core of six most stable beta-strands and two loops, characterized by rare global unfolding events. Flanking this stable core are beta-strands and recognition loops with less stability, termed subglobal motifs. These suggest partially unfolded forms (near-native intermediates) with two levels of stability. The spatial separation of the subglobal motifs on the flanks suggests possible parallelism in their folding as additional beta-strands align with the stable core of six strands. Intermediates may contribute to differences in stabilities and m-values suggested by NHX or kinetics relative to chemical denaturation. Residual structure in the unfolded regime is suggested by superprotection of beta-strand 6 and by GdmCl-dependence of adjustments in amide NMR spectra and residual optical signal. The global folding stability depends strongly on pH, with at least 3 kcal/mol more stability at pH 7.3 than at pH 6.3. This FHA domain is hypothesized to fold progressively with initial hydrophobic collapse of its stable six-stranded core followed by addition of less stable flanking beta-strands and ordering of recognition loops.
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Affiliation(s)
| | | | - Steven R. Van Doren
- *To whom correspondence should be addressed. E-mail: ., Phone: 1 (573) 882-5113, FAX: 1 (573) 884-4812
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49
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Simler BR, Levy Y, Onuchic JN, Matthews CR. The folding energy landscape of the dimerization domain of Escherichia coli Trp repressor: a joint experimental and theoretical investigation. J Mol Biol 2006; 363:262-78. [PMID: 16956620 PMCID: PMC1866298 DOI: 10.1016/j.jmb.2006.07.080] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Revised: 07/27/2006] [Accepted: 07/28/2006] [Indexed: 11/25/2022]
Abstract
Enhanced structural insights into the folding energy landscape of the N-terminal dimerization domain of Escherichia coli tryptophan repressor, [2-66]2 TR, were obtained from a combined experimental and theoretical analysis of its equilibrium folding reaction. Previous studies have shown that the three intertwined helices in [2-66]2 TR are sufficient to drive the formation of a stable dimer for the full-length protein, [2-107]2 TR. The monomeric and dimeric folding intermediates that appear during the folding reactions of [2-66]2 TR have counterparts in the folding mechanism of the full-length protein. The equilibrium unfolding energy surface on which the folding and dimerization reactions occur for [2-66]2 TR was examined with a combination of native-state hydrogen exchange analysis, pepsin digestion and matrix-assisted laser/desorption mass spectrometry performed at several concentrations of protein and denaturant. Peptides corresponding to all three helices in [2-66]2 TR show multi-layered protection patterns consistent with the relative stabilities of the dimeric and monomeric folding intermediates. The observation of protection exceeding that offered by the dimeric intermediate in segments from all three helices implies that a segment-swapping mechanism may be operative in the monomeric intermediate. Protection greater than that expected from the global stability for a single amide hydrogen in a peptide from the C-helix possibly and another from the A-helix may reflect non-random structure, possibly a precursor for segment swapping, in the urea-denatured state. Native topology-based model simulations that correspond to a funnel energy landscape capture both the monomeric and dimeric intermediates suggested by the HX MS data and provide a rationale for the progressive acquisition of secondary structure in their conformational ensembles.
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Affiliation(s)
- B Robert Simler
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
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Jacobsen K, Hubbell WL, Ernst OP, Risse T. Details of the Partial Unfolding of T4 Lysozyme on Quartz Using Site-Directed Spin Labeling. Angew Chem Int Ed Engl 2006; 45:3874-7. [PMID: 16671129 DOI: 10.1002/anie.200600008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kerstin Jacobsen
- Fritz Haber Institute of the Max Planck Society, Department of Chemical Physics, Faradayweg 4-6, 14195 Berlin, Germany.
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