1
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Bandara YMNDY, Freedman KJ. Lithium Chloride Effects Field-Induced Protein Unfolding and the Transport Energetics Inside a Nanopipette. J Am Chem Soc 2024; 146:3171-3185. [PMID: 38253325 DOI: 10.1021/jacs.3c11044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The tapered geometry of nanopipettes offers a unique perspective on protein transport through nanopores since both a gradual and fast confinement are possible depending on the translocation direction. The protein capture rate, unfolding, speed of translocation, and clogging probability are studied by toggling the LiCl concentration between 2 and 4 M. Interestingly, the proteins in this study could be transported with or against electrophoresis and offer vastly different attributes of sensing. Herein, a ruleset for studying proteins is developed that prevents irreversible pore clogging and yields upward of >100,000 events/nanopore. The extended duration of experiments further revealed that the capture rate takes ∼2 h to reach a steady state, emphasizing the importance of reaching equilibrated transport for studying the energetics and kinetics of protein transport (i.e., diffusion vs barrier-limited). Even in the equilibrated transport state, improper lowpass filtering was shown to distort the classification of diffusion-limited vs barrier-limited transport. Finally, electric-field-induced protein unfolding was found to be most prominent in electroosmotic-dominant transport, whereas electrophoretic-dominant events show no evidence of unfolding. Thus, our findings showcase the optimal conditions for protein translocations and the impact on studying protein unfolding, transporting energetics, and acquiring high bandwidth data.
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Affiliation(s)
- Y M Nuwan D Y Bandara
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
| | - Kevin J Freedman
- Department of Bioengineering, University of California, Riverside, 900 University Avenue, Riverside, California 92521, United States
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2
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Bhatia S, Udgaonkar JB. Understanding the heterogeneity intrinsic to protein folding. Curr Opin Struct Biol 2024; 84:102738. [PMID: 38041993 DOI: 10.1016/j.sbi.2023.102738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 12/04/2023]
Abstract
Relating the native fold of a protein to its amino acid sequence remains a fundamental problem in biology. While computer algorithms have demonstrated recently their prowess in predicting what structure a particular amino acid sequence will fold to, an understanding of how and why a specific protein fold is achieved remains elusive. A major challenge is to define the role of conformational heterogeneity during protein folding. Recent experimental studies, utilizing time-resolved FRET, hydrogen-exchange coupled to mass spectrometry, and single-molecule force spectroscopy, often in conjunction with simulation, have begun to reveal how conformational heterogeneity evolves during folding, and whether an intermediate ensemble of defined free energy consists of different sub-populations of molecules that may differ significantly in conformation, energy and entropy.
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Affiliation(s)
- Sandhya Bhatia
- Department of Biophysics, Howard Hughes Medical Institute UT Southwestern Medical Center, Dallas 75390, United States. https://twitter.com/Sandhyabhatia_5
| | - Jayant B Udgaonkar
- Department of Biology, Indian Institute of Science Education and Research Pune, Pashan, Pune 41008, India.
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3
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Kaushik A, Udgaonkar JB. Replacement of the native cis prolines by alanine leads to simplification of the complex folding mechanism of a small globular protein. Biophys J 2023; 122:3894-3908. [PMID: 37596784 PMCID: PMC10560683 DOI: 10.1016/j.bpj.2023.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/08/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023] Open
Abstract
The folding mechanism of MNEI, a single-chain variant of naturally occurring double-chain monellin, is complex, with multiple parallel refolding channels. To determine whether its folding energy landscape could be simplified, the two native cis-prolines, Pro41 and Pro93, were mutated, singly and together, to Ala. The stability of P93A was the same as that of the wild-type protein, pWT; however, P41A and P41AP93A were destabilized by ∼0.9 kcal mol-1. The effects of the mutations on the very fast, fast, slow, and very slow phases of folding were studied. They showed that heterogeneity in the unfolded state arises due to cis to trans isomerization of the Gly92-Pro93 peptide bond. The Pro41 to Ala mutation abolished the very slow phase of folding, whereas surprisingly, the Pro93 to Ala mutation abolished the very fast phase of folding. Double-jump, interrupted folding experiments indicated that two sequential trans to cis proline isomerization steps, of the Gly92-Pro93 peptide bond followed by the Arg40-Pro41 peptide bond, lead to the formation of the native state. They also revealed the accumulation of a late native-like intermediate, N∗, which differs from the native state in the isomeric status of the Arg40-Pro41 bond, as well as in a few tertiary contacts as monitored by near-UV CD measurements. The Pro to Ala mutations not only eliminated the cis to trans Pro isomerization reaction in the unfolded state, but also the two trans to cis Pro isomerization reactions during folding. By doing so, and by differentially affecting the relative stabilities of folding intermediates, the mutations resulted in a simplification of the folding mechanism. The two Pro to Ala mutations together accelerate folding to such an extent that the native state forms more than 1000-fold faster than in the case of pWT.
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Affiliation(s)
- Anushka Kaushik
- Indian Institute of Science Education and Research, Pune, India
| | - Jayant B Udgaonkar
- Indian Institute of Science Education and Research, Pune, India; National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.
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4
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Bhattacharjee R, Udgaonkar JB. Differentiating between the sequence of structural events on alternative pathways of folding of a heterodimeric protein. Protein Sci 2022; 31:e4513. [PMID: 36382901 PMCID: PMC9703597 DOI: 10.1002/pro.4513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
Distinguishing between competing pathways of folding of a protein, on the basis of how they differ in their progress of structure acquisition, remains an important challenge in protein folding studies. A previous study had shown that the heterodimeric protein, double chain monellin (dcMN) switches between alternative folding pathways upon a change in guanidine hydrochloride (GdnHCl) concentration. In the current study, the folding of dcMN has been characterized by the pulsed hydrogen exchange (HX) labeling methodology used in conjunction with mass spectrometry. Quantification of the extent to which folding intermediates accumulate and then disappear with time of folding at both low and high GdnHCl concentrations, where the folding pathways are known to be different, shows that the folding mechanism is describable by a triangular three-state mechanism. Structural characterization of the productive folding intermediates populated on the alternative pathways has enabled the pathways to be differentiated on the basis of the progress of structure acquisition that occurs on them. The intermediates on the two pathways differ in the extent to which the α-helix and the rest of the β-sheet have acquired structure that is protective against HX. The major difference is, however, that β2 has not acquired any protective structure in the intermediate formed on one pathway, but it has acquired significant protective structure in the intermediate formed on the alternative pathway. Hence, the sequence of structural events is different on the two alternative pathways.
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Affiliation(s)
- Rupam Bhattacharjee
- National Centre for Biological Sciences, Tata Institute of Fundamental ResearchBengaluruKarnatakaIndia
- Indian Institute of Science Education and ResearchPuneMaharashtraIndia
| | - Jayant B. Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental ResearchBengaluruKarnatakaIndia
- Indian Institute of Science Education and ResearchPuneMaharashtraIndia
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5
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Acharya N, Jha SK. Dry Molten Globule-Like Intermediates in Protein Folding, Function, and Disease. J Phys Chem B 2022; 126:8614-8622. [PMID: 36286394 DOI: 10.1021/acs.jpcb.2c04991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The performance of a protein depends on its correct folding to the final functional native form. Hence, understanding the process of protein folding has remained an important field of research for the scientific community for the past five decades. Two important intermediate states, namely, wet molten globule (WMG) and dry molten globule (DMG), have emerged as critical milestones during protein folding-unfolding reactions. While much has been discussed about WMGs as a common unfolding intermediate, the evidence for DMGs has remained elusive owing to their near-native features, which makes them difficult to probe using global structural probes. This Review puts together the available literature and new evidence on DMGs to give a broader perspective on the universality of DMGs and discuss their significance in protein folding, function, and disease.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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6
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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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7
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Site-directed fluorescence approaches to monitor the structural dynamics of proteins using intrinsic Trp and labeled with extrinsic fluorophores. STAR Protoc 2022; 3:101200. [PMID: 35252885 PMCID: PMC8889417 DOI: 10.1016/j.xpro.2022.101200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Comprehensive understanding of a protein’s function depends on having reliable, sophisticated tools to study protein structural dynamics in physiologically-relevant conditions. Here, we present an effective, robust step-by-step protocol to monitor the structural dynamics (including hydration dynamics) of a protein utilizing various site-directed fluorescence (SDFL) approaches. This protocol should be widely applicable for studying soluble proteins, intrinsically-disordered proteins, and membrane proteins. For complete details on the use and execution of this protocol, please refer to Das et al. (2020), Das and Raghuraman (2021), and Chatterjee et al. (2021). A step-by-step protocol to monitor the structural dynamics of proteins using SDFL Applicable to proteins with intrinsic Trp and labeled with extrinsic fluorophores This protocol should be widely applicable for soluble and membrane proteins
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8
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The native state conformational heterogeneity in the energy landscape of protein folding. Biophys Chem 2022; 283:106761. [DOI: 10.1016/j.bpc.2022.106761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 11/18/2022]
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9
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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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10
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Bhatia S, Krishnamoorthy G, Udgaonkar JB. Resolving Site-Specific Heterogeneity of the Unfolded State under Folding Conditions. J Phys Chem Lett 2021; 12:3295-3302. [PMID: 33764778 DOI: 10.1021/acs.jpclett.1c00098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the properties of the unfolded state under folding conditions is of fundamental importance for gaining mechanistic insight into folding as well as misfolding reactions. Toward achieving this objective, the folding reaction of a small protein, monellin, has been resolved structurally and temporally, with the use of the multisite time-resolved FRET methodology. The present study establishes that the initial polypeptide chain collapse is not only heterogeneous but also structurally asymmetric and nonuniform. The population-averaged size for the segments spanning parts of the β-sheet decreases much more than that for the α-helix. Multisite measurements enabled specific and nonspecific components of the initial chain collapse to be discerned. The expanded and compact intermediate subensembles have the properties of a nonspecifically collapsed (hence, random-coil-like) and specifically collapsed (hence, globular) polymer, respectively. During subsequent folding, both the subensembles underwent contraction to varying extents at the four monitored segments, which was close to gradual in nature. The expanded intermediate subensemble exhibited an additional very slow contraction, suggestive of the presence of non-native interactions that result in a higher effective viscosity slowing down intrachain motions under folding conditions.
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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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11
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Aupič J, Strmšek Ž, Lapenta F, Pahovnik D, Pisanski T, Drobnak I, Ljubetič A, Jerala R. Designed folding pathway of modular coiled-coil-based proteins. Nat Commun 2021; 12:940. [PMID: 33574262 PMCID: PMC7878764 DOI: 10.1038/s41467-021-21185-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/13/2021] [Indexed: 12/02/2022] Open
Abstract
Natural proteins are characterised by a complex folding pathway defined uniquely for each fold. Designed coiled-coil protein origami (CCPO) cages are distinct from natural compact proteins, since their fold is prescribed by discrete long-range interactions between orthogonal pairwise-interacting coiled-coil (CC) modules within a single polypeptide chain. Here, we demonstrate that CCPO proteins fold in a stepwise sequential pathway. Molecular dynamics simulations and stopped-flow Förster resonance energy transfer (FRET) measurements reveal that CCPO folding is dominated by the effective intra-chain distance between CC modules in the primary sequence and subsequent folding intermediates, allowing identical CC modules to be employed for multiple cage edges and thus relaxing CCPO cage design requirements. The number of orthogonal modules required for constructing a CCPO tetrahedron can be reduced from six to as little as three different CC modules. The stepwise modular nature of the folding pathway offers insights into the folding of tandem repeat proteins and can be exploited for the design of modular protein structures based on a given set of orthogonal modules.
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Affiliation(s)
- Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Žiga Strmšek
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- Interdisciplinary Doctoral Programme in Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
- EN-FIST Centre of Excellence, Ljubljana, Slovenia
| | - David Pahovnik
- Department of Polymer Chemistry and Technology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tomaž Pisanski
- FAMNIT, University of Primorska, Koper, Slovenia
- Institute of Mathematics, Physics and Mechanics, Ljubljana, Slovenia
| | - Igor Drobnak
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia.
- EN-FIST Centre of Excellence, Ljubljana, Slovenia.
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12
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Das A, Raghuraman H. Conformational heterogeneity of the voltage sensor loop of KvAP in micelles and membranes: A fluorescence approach. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2021; 1863:183568. [PMID: 33529577 DOI: 10.1016/j.bbamem.2021.183568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 01/06/2021] [Accepted: 01/27/2021] [Indexed: 12/14/2022]
Abstract
KvAP is a tetrameric voltage-gated potassium channel that is composed of a pore domain and a voltage-sensing domain (VSD). The VSD is crucial for sensing transmembrane potential and gating. At 0 mV, the VSD adopts an activated conformation in both n-octylglucoside (OG) micelles and phospholipid membranes. Importantly, gating-modifier toxins that bind at S3b-S4 loop of KvAP-VSD exhibit pronounced differences in binding affinity in these membrane-mimetic systems. However, the conformational heterogeneity of this functionally-important sensor loop in membrane mimetics is poorly understood, and is the focus of this work. In this paper, we establish, using intrinsic fluorescence of the uniquely positioned W70 in KvAP-VSD and environment-sensitive NBD (7-nitrobenz-2-oxa-1,3-diazol-4-yl-ethylenediamine) fluorescence of the labelled S3b-S4 loop, that the surface charge of the membrane does not significantly affect the topology and structural dynamics of the sensor loop in membranes. Importantly, the dynamic variability of the sensor loop is preserved in both zwitterionic (POPC) and anionic (POPC/POPG) membranes. Further, the lifetime distribution analysis for the NBD-labelled residues by maximum entropy method (MEM) demonstrates that, in contrast to micelles, the membrane environment not only reduces the relative discrete population of sensor loop conformations, but also broadens the lifetime distribution peaks. Overall, our results strongly suggest that the conformational heterogeneity of the sensor loop is significantly altered in membranes and this correlates well with its environmental heterogeneity. This constitutes the first report demonstrating that MEM-lifetime distribution could be a powerful tool to distinguish changes in conformational heterogeneity in potassium channels with similar architecture and topology.
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Affiliation(s)
- Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India.
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13
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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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14
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Chatterjee S, Brahma R, Raghuraman H. Gating-related Structural Dynamics of the MgtE Magnesium Channel in Membrane-Mimetics Utilizing Site-Directed Tryptophan Fluorescence. J Mol Biol 2020; 433:166691. [PMID: 33203509 DOI: 10.1016/j.jmb.2020.10.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 12/25/2022]
Abstract
Magnesium is the most abundant divalent cation present in the cell, and an abnormal Mg2+ homeostasis is associated with several diseases in humans. However, among ion channels, the mechanisms of intracellular regulation and transport of Mg2+ are poorly understood. MgtE is a homodimeric Mg2+-selective channel and is negatively regulated by high intracellular Mg2+ concentration where the cytoplasmic domain of MgtE acts as a Mg2+ sensor. Most of the previous biophysical studies on MgtE have been carried out in detergent micelles and the information regarding gating-related structural dynamics of MgtE in physiologically-relevant membrane environment is scarce. In this work, we monitored the changes in gating-related structural dynamics, hydration dynamics and conformational heterogeneity of MgtE in micelles and membranes using the intrinsic site-directed Trp fluorescence. For this purpose, we have engineered six single-Trp mutants in the functional Trp-less background of MgtE to obtain site-specific information on the gating-related structural dynamics of MgtE in membrane-mimetic systems. Our results indicate that Mg2+-induced gating might involve the possibility of a 'conformational wave' from the cytosolic N-domain to transmembrane domain of MgtE. Although MgtE is responsive to Mg2+-induced gating in both micelles and membranes, the organization and dynamics of MgtE is substantially altered in physiologically important phospholipid membranes compared to micelles. This is accompanied by significant changes in hydration dynamics and conformational heterogeneity. Overall, our results highlight the importance of lipid-protein interactions and are relevant for understanding gating mechanism of magnesium channels in general, and MgtE in particular.
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Affiliation(s)
- Satyaki Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - Rupasree Brahma
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, India.
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15
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Mirdha L, Chakraborty H. Fluorescence quenching by ionic liquid as a potent tool to study protein unfolding intermediates. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113408] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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16
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Kachlishvili K, Korneev A, Maisuradze L, Liu J, Scheraga HA, Molochkov A, Senet P, Niemi AJ, Maisuradze GG. New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain. J Phys Chem B 2020; 124:3855-3872. [PMID: 32271570 DOI: 10.1021/acs.jpcb.0c00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Intermediate states in protein folding are associated with formation of amyloid fibrils, which are responsible for a number of neurodegenerative diseases. Therefore, prevention of the aggregation of folding intermediates is one of the most important problems to overcome. Recently, we studied the origins and prevention of formation of intermediate states with the example of the Formin binding protein 28 (FBP28) WW domain. We demonstrated that the replacement of Leu26 by Asp26 or Trp26 (in ∼15% of the folding trajectories) can alter the folding scenario from three-state folding, a major folding scenario for the FBP28 WW domain (WT) and its mutants, toward two-state or downhill folding at temperatures below the melting point. Here, for a better understanding of the physics of the formation/elimination of intermediates, (i) the dynamics and energetics of formation of β-strands in folding, misfolding, and nonfolding trajectories of these mutants (L26D and L26W) is investigated; (ii) the experimental structures of WT, L26D, and L26W are analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger equation. We show that the formation of each β-strand in folding trajectories is accompanied by the emergence of kinks in internal coordinate space as well as a decrease in local free energy. In particular, the decrease in downhill folding trajectory is ∼7 kcal/mol, while it varies between 31 and 48 kcal/mol for the three-state folding trajectory. The kink analyses of the experimental structures give new insights into formation of intermediates, which may become a useful tool for preventing aggregation.
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Affiliation(s)
- Khatuna Kachlishvili
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States
| | - Anatolii Korneev
- Laboratory of Physics of Living Matter, Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia
| | - Luka Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States.,Biochemistry, Quantitative Biology, Biophysics, and Structural Biology (BQBS) Track, Yale University, New Haven 06520-8084, ConnecticutUnited States
| | - Jiaojiao Liu
- School of Physics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Harold A Scheraga
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States
| | - Alexander Molochkov
- Laboratory of Physics of Living Matter, Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia
| | - Patrick Senet
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States.,Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303 CNRS-Univ. de Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, Dijon Cedex F-21078, France
| | - Antti J Niemi
- Laboratory of Physics of Living Matter, Far Eastern Federal University, Sukhanova 8, Vladivostok 690950, Russia.,School of Physics, Beijing Institute of Technology, Beijing 100081, P. R. China.,Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, Tours F37200, France.,Nordita, Stockholm University, Roslagstullsbacken 23, Stockholm SE-106 91, Sweden
| | - Gia G Maisuradze
- Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States
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17
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Structure of an Unfolding Intermediate of an RRM Domain of ETR-3 Reveals Its Native-like Fold. Biophys J 2020; 118:352-365. [PMID: 31866002 DOI: 10.1016/j.bpj.2019.11.3392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/24/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022] Open
Abstract
Prevalence of one or more partially folded intermediates during protein unfolding with different secondary and ternary conformations has been identified as an integral character of protein unfolding. These transition-state species need to be characterized structurally for elucidation of their folding pathways. We have determined the three-dimensional structure of an intermediate state with increased conformational space sampling under urea-denaturing condition. The protein unfolds completely at 10 M urea but retains residual secondary structural propensities with restricted motion. Here, we describe the native state, observable intermediate state, and unfolded state for ETR-3 RRM-3, which has canonical RRM fold. These observations can shed more light on unfolding events for RRM-containing proteins.
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18
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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19
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Observation of Continuous Contraction and a Metastable Misfolded State during the Collapse and Folding of a Small Protein. J Mol Biol 2019; 431:3814-3826. [DOI: 10.1016/j.jmb.2019.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/22/2023]
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20
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Krishnamoorthy G. Intramolecular Distance Distribution Reveals Mechanisms in Protein Folding and Dynamics. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES INDIA SECTION A-PHYSICAL SCIENCES 2018. [DOI: 10.1007/s40010-018-0525-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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21
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Narayan A, Naganathan AN. Switching Protein Conformational Substates by Protonation and Mutation. J Phys Chem B 2018; 122:11039-11047. [PMID: 30048131 DOI: 10.1021/acs.jpcb.8b05108] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein modules that regulate the availability and conformational status of transcription factors determine the rapidity, duration, and magnitude of cellular response to changing conditions. One such system is the single-gene product Cnu, a four-helix bundle transcription co-repressor, which acts as a molecular thermosensor regulating the expression of virulence genes in enterobacteriaceae through modulation of its native conformational ensemble. Cnu and related genes have also been implicated in pH-dependent expression of virulence genes. We hypothesize that protonation of a conserved buried histidine (H45) in Cnu promotes large electrostatic frustration, thus disturbing the H-NS, a transcription factor, binding face. Spectroscopic and calorimetric methods reveal that H45 exhibits a suppressed p Ka of ∼5.1, the protonation of which switches the conformation to an alternate native ensemble in which the fourth helix is disordered. The population redistribution can also be achieved through a mutation H45V, which does not display any switching behavior at pH values greater than 4. The Wako-Saitô-Muñoz-Eaton (WSME) statistical mechanical model predicts specific differences in the conformations and fluctuations of the fourth and first helices of Cnu determining the observed pH response. We validate these predictions through fluorescence lifetime measurements of a sole tryptophan, highlighting the presence of both native and non-native interactions in the regions adjoining the binding face of Cnu. Our combined experimental-computational study thus shows that Cnu acts both as a thermo- and pH-sensor orchestrated via a subtle but quantifiable balance between the weak packing of a structural element and protonation of a buried histidine that promotes electrostatic frustration.
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Affiliation(s)
- Abhishek Narayan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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22
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Leone S, Fonderico J, Melchiorre C, Carpentieri A, Picone D. Structural effects of methylglyoxal glycation, a study on the model protein MNEI. Mol Cell Biochem 2018; 451:165-171. [PMID: 30014221 DOI: 10.1007/s11010-018-3403-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/12/2018] [Indexed: 12/23/2022]
Abstract
The reaction of free amino groups in proteins with reactive carbonyl species, known as glycation, leads to the formation of mixtures of products, collectively referred to as advanced glycation endproducts (AGEs). These compounds have been implicated in several important diseases, but their role in pathogenesis and clinical symptoms' development is still debated. Particularly, AGEs are often associated to the formation of amyloid deposits in conformational diseases, such as Alzheimer's and Parkinson's disease, and it has been suggested that they might influence the mechanisms and kinetics of protein aggregation. We here present the characterization of the products of glycation of the model protein MNEI with methylglyoxal and their effect on the protein structure. We demonstrate that, despite being an uncontrolled process, glycation occurs only at specific residues of the protein. Moreover, while not affecting the protein fold, it alters its shape and hydrodynamic properties and increases its tendency to fibrillar aggregation. Our study opens the way to in deep structural investigations to shed light on the complex link between protein post-translational modifications, structure, and stability.
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Affiliation(s)
- Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy.
| | - Jole Fonderico
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy
| | - Chiara Melchiorre
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy
| | - Andrea Carpentieri
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cintia, 80126, Naples, Italy.
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23
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Krishnamoorthy G. Fluorescence spectroscopy for revealing mechanisms in biology: Strengths and pitfalls. J Biosci 2018; 43:555-567. [PMID: 30002272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This article describes the basic principles of steady-state and time-resolved fluorescence. The formal equivalence of the two methodologies is described first, followed by the extra advantages of time-resolved methods in revealing population heterogeneity in complex systems encountered in biology. Several examples from the author's work are described in support of the above contention. Finally, several misinterpretations and pitfalls in the interpretation of fluorescence data and their remedy are described.
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Affiliation(s)
- G Krishnamoorthy
- Department of Biotechnology, Anna University, Chennai 600 025, India,
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24
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25
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Bhatia S, Krishnamoorthy G, Udgaonkar JB. Site-specific time-resolved FRET reveals local variations in the unfolding mechanism in an apparently two-state protein unfolding transition. Phys Chem Chem Phys 2018; 20:3216-3232. [DOI: 10.1039/c7cp06214a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Using multi-site time-resolved FRET, it is shown that equilibrium unfolding of monellin is not only heterogeneous, but that the degree of non-cooperativity differs between the sole α-helix and different parts of the β-sheet.
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Affiliation(s)
- Sandhya Bhatia
- 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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26
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Fluorescence Lifetime Distribution Brings Out Mechanisms Involving Biomolecules While Quantifying Population Heterogeneity. REVIEWS IN FLUORESCENCE 2017 2018. [DOI: 10.1007/978-3-030-01569-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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27
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Mishra P, Jha SK. An Alternatively Packed Dry Molten Globule-like Intermediate in the Native State Ensemble of a Multidomain Protein. J Phys Chem B 2017; 121:9336-9347. [DOI: 10.1021/acs.jpcb.7b07032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Prajna Mishra
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, Maharashtra 411008, India
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28
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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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29
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Aghera N, Udgaonkar JB. Stepwise Assembly of β-Sheet Structure during the Folding of an SH3 Domain Revealed by a Pulsed Hydrogen Exchange Mass Spectrometry Study. Biochemistry 2017; 56:3754-3769. [DOI: 10.1021/acs.biochem.7b00374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nilesh Aghera
- 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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30
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Narayan A, Naganathan AN. Tuning the Continuum of Structural States in the Native Ensemble of a Regulatory Protein. J Phys Chem Lett 2017; 8:1683-1687. [PMID: 28345920 PMCID: PMC5464678 DOI: 10.1021/acs.jpclett.7b00475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The mesoscale nature of proteins allows for an efficient coupling between environmental cues and conformational changes, enabling their function as molecular transducers. Delineating the precise structural origins of such a connection and the expected spectroscopic response has, however, been challenging. In this work, we perform a combination of urea-temperature double perturbation experiments and theoretical modeling to probe the conformational landscape of Cnu, a natural thermosensor protein. We observe unique ensemble signatures that point to a continuum of conformational substates in the native ensemble and that respond intricately to perturbations upon monitoring secondary and tertiary structures, distances between an intrinsic FRET pair, and hydrodynamic volumes. Binding assays further reveal a weakening of the Cnu functional complex with temperature, highlighting the molecular origins of signal transduction critical for pathogenic response in enterobacteriaceae.
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31
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Acharya N, Mishra P, Jha SK. A dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein. Phys Chem Chem Phys 2017; 19:30207-30216. [DOI: 10.1039/c7cp06614g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An early intermediate during the base-induced unfolding of a multidomain protein resembles a dry molten globule state in which the structure is expanded without core hydration.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Prajna Mishra
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
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32
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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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33
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Spadaccini R, Leone S, Rega MF, Richter C, Picone D. Influence of pH on the structure and stability of the sweet protein MNEI. FEBS Lett 2016; 590:3681-3689. [DOI: 10.1002/1873-3468.12437] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Scienze e Tecnologie; Università del Sannio; Benevento Italy
| | - Serena Leone
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II; Naples Italy
| | | | | | - Delia Picone
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II; Naples Italy
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34
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Goluguri RR, Udgaonkar JB. Microsecond Rearrangements of Hydrophobic Clusters in an Initially Collapsed Globule Prime Structure Formation during the Folding of a Small Protein. J Mol Biol 2016; 428:3102-17. [PMID: 27370109 DOI: 10.1016/j.jmb.2016.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/17/2016] [Accepted: 06/19/2016] [Indexed: 12/14/2022]
Abstract
Determining how polypeptide chain collapse initiates structure formation during protein folding is a long standing goal. It has been challenging to characterize experimentally the dynamics of the polypeptide chain, which lead to the formation of a compact kinetic molten globule (MG) in about a millisecond. In this study, the sub-millisecond events that occur early during the folding of monellin from the guanidine hydrochloride-unfolded state have been characterized using multiple fluorescence and fluorescence resonance energy transfer probes. The kinetic MG is shown to form in a noncooperative manner from the unfolded (U) state as a result of at least three different processes happening during the first millisecond of folding. Initial chain compaction completes within the first 37μs, and further compaction occurs only after structure formation commences at a few milliseconds of folding. The transient nonnative and native-like hydrophobic clusters with side chains of certain residues buried form during the initial chain collapse and the nonnative clusters quickly disassemble. Subsequently, partial chain desolvation occurs, leading to the formation of a kinetic MG. The initial chain compaction and subsequent chain rearrangement appear to be barrierless processes. The two structural rearrangements within the collapsed globule appear to prime the protein for the actual folding transition.
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Affiliation(s)
- Rama Reddy Goluguri
- 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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35
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Leone S, Picone D. Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein. PLoS One 2016; 11:e0158372. [PMID: 27340829 PMCID: PMC4920389 DOI: 10.1371/journal.pone.0158372] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022] Open
Abstract
MNEI is a single chain derivative of monellin, a plant protein that can interact with the human sweet taste receptor, being therefore perceived as sweet. This unusual physiological activity makes MNEI a potential template for the design of new sugar replacers for the food and beverage industry. Unfortunately, applications of MNEI have been so far limited by its intrinsic sensitivity to some pH and temperature conditions, which could occur in industrial processes. Changes in physical parameters can, in fact, lead to irreversible protein denaturation, as well as aggregation and precipitation. It has been previously shown that the correlation between pH and stability in MNEI derives from the presence of a single glutamic residue in a hydrophobic pocket of the protein. We have used molecular dynamics to study the consequences, at the atomic level, of the protonation state of such residue and have identified the network of intramolecular interactions responsible for MNEI stability at acidic pH. Based on this information, we have designed a pH-independent, stabilized mutant of MNEI and confirmed its increased stability by both molecular modeling and experimental techniques.
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Affiliation(s)
- Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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36
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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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37
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Limited cooperativity in protein folding. Curr Opin Struct Biol 2016; 36:58-66. [DOI: 10.1016/j.sbi.2015.12.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/09/2015] [Indexed: 01/07/2023]
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38
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Acharya N, Mishra P, Jha SK. Evidence for Dry Molten Globule-Like Domains in the pH-Induced Equilibrium Folding Intermediate of a Multidomain Protein. J Phys Chem Lett 2016; 7:173-179. [PMID: 26700266 DOI: 10.1021/acs.jpclett.5b02545] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The role of van der Waals (vdW) packing interactions compared to the hydrophobic effect in stabilizing the functional structure of proteins is poorly understood. Here we show, using fluorescence resonance energy transfer, dynamic fluorescence quenching, red-edge excitation shift, and near- and far-UV circular dichroism, that the pH-induced structural perturbation of a multidomain protein leads to the formation of a state in which two out of the three domains have characteristics of dry molten globules, that is, the domains are expanded compared to the native protein with disrupted packing interactions but have dry cores. We quantitatively estimate the energetic contribution of vdW interactions and show that they play an important role in the stability of the native state and cooperativity of its structural transition, in addition to the hydrophobic effect. Our results also indicate that during the pH-induced unfolding, side-chain unlocking and hydrophobic solvation occur in two distinct steps and not in a concerted manner, as commonly believed.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Prajna Mishra
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory , Dr. Homi Bhabha Road, Pune 411008, Maharashtra, India
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39
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Effects of PEG molecular weight on its interaction with albumin. CHINESE JOURNAL OF POLYMER SCIENCE 2015. [DOI: 10.1007/s10118-015-1687-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Goluguri RR, Udgaonkar JB. Rise of the Helix from a Collapsed Globule during the Folding of Monellin. Biochemistry 2015; 54:5356-65. [DOI: 10.1021/acs.biochem.5b00730] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rama Reddy Goluguri
- 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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41
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Lindhoud S, Pirchi M, Westphal AH, Haran G, van Mierlo CPM. Gradual Folding of an Off-Pathway Molten Globule Detected at the Single-Molecule Level. J Mol Biol 2015; 427:3148-57. [PMID: 26163276 DOI: 10.1016/j.jmb.2015.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 05/27/2015] [Accepted: 07/01/2015] [Indexed: 10/23/2022]
Abstract
Molten globules (MGs) are compact, partially folded intermediates that are transiently present during folding of many proteins. These intermediates reside on or off the folding pathway to native protein. Conformational evolution during folding of off-pathway MGs is largely unexplored. Here, we characterize the denaturant-dependent structure of apoflavodoxin's off-pathway MG. Using single-molecule fluorescence resonance energy transfer (smFRET), we follow conversion of unfolded species into MG down to denaturant concentrations that favor formation of native protein. Under strongly denaturing conditions, fluorescence resonance energy transfer histograms show a single peak, arising from unfolded protein. The smFRET efficiency distribution shifts to higher value upon decreasing denaturant concentration because the MG folds. Strikingly, upon approaching native conditions, the fluorescence resonance energy transfer efficiency of the MG rises above that of native protein. Thus, smFRET exposes the misfolded nature of apoflavodoxin's off-pathway MG. We show that conversion of unfolded into MG protein is a gradual, second-order-like process that simultaneously involves separate regions within the polypeptide.
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Affiliation(s)
- Simon Lindhoud
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Menahem Pirchi
- Chemical Physics Department, Weizmann Institute of Science, Herzl St 234, Rehovot 76100, Israel
| | - Adrie H Westphal
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Gilad Haran
- Chemical Physics Department, Weizmann Institute of Science, Herzl St 234, Rehovot 76100, Israel.
| | - Carlo P M van Mierlo
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands.
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42
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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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43
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Jiang L, Zeng Y, Sun Q, Sun Y, Guo Z, Qu JY, Yao S. Microsecond protein folding events revealed by time-resolved fluorescence resonance energy transfer in a microfluidic mixer. Anal Chem 2015; 87:5589-95. [PMID: 25938953 DOI: 10.1021/acs.analchem.5b00366] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We demonstrate the combination of the time-resolved fluorescence resonance energy transfer (tr-FRET) measurement and the ultrarapid hydrodynamic focusing microfluidic mixer. The combined technique is capable of probing the intermolecular distance change with temporal resolution at microsecond level and structural resolution at Angstrom level, and the use of two-photon excitation enables a broader exploration of FRET with spectrum from near-ultraviolet to visible wavelength. As a proof of principle, we used the coupled microfluidic laminar flow and time-resolved two-photon excitation microscopy to investigate the early folding states of Cytochrome c (cyt c) by monitoring the distance between the tryptophan (Trp-59)-heme donor-acceptor (D-A) pair. The transformation of folding states of cyt c in the early 500 μs of refolding was revealed on the microsecond time scale. For the first time, we clearly resolved the early transient state of cyt c, which is populated within the dead time of the mixer (<10 μs) and has a characteristic Trp-59-heme distance of ∼31 Å. We believe this tool can find more applications in studying the early stages of biological processes with FRET as the probe.
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Affiliation(s)
- Liguo Jiang
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Yan Zeng
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Qiqi Sun
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Yueru Sun
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Zhihong Guo
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Jianan Y Qu
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - Shuhuai Yao
- †HKUST Jockey Club Institute for Advanced Study, ‡Department of Electronic and Computer Engineering, §Department of Chemistry, ⊥Department of Mechanical and Aerospace Engineering, and ∇Division of Biomedical Engineering, Hong Kong University of Science and Technology, Hong Kong
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44
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Higher impact energy in traumatic brain injury interferes with noncovalent and covalent bonds resulting in cytotoxic brain tissue edema as measured with computational simulation. Acta Neurochir (Wien) 2015; 157:639-48; discussion 648. [PMID: 25686919 DOI: 10.1007/s00701-015-2368-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/29/2015] [Indexed: 10/24/2022]
Abstract
BACKGROUND Cytotoxic brain tissue edema is a complicated secondary consequence of ischemic injury following cerebral diseases such as traumatic brain injury and stroke. To some extent the pathophysiological mechanisms are known, but far from completely. In this study, a hypothesis is proposed in which protein unfolding and perturbation of nucleotide structures participate in the development of cytotoxic edema following traumatic brain injury (TBI). METHODS An advanced computational simulation model of the human head was used to simulate TBI. The consequences of kinetic energy transfer following an external dynamic impact were analyzed including the intracranial pressure (ICP), strain level, and their potential influences on the noncovalent and covalent bonds in folded protein structures. RESULTS The result shows that although most of the transferred kinetic energy is absorbed in the skin and three bone layers, there is a substantial amount of energy reaching the gray and white matter. The kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent but also covalent bonds when high enough. The induced mechanical strain and pressure may further interfere with the proteins, which accumulate water molecules into the interior of the hydrophobic structures of unfolded proteins. Simultaneously, the noncovalent energy-rich bonds in nucleotide adenosine-triphosphates may be perturbed as well. CONCLUSIONS Based on the analysis of the numerical simulation data, the kinetic energy from an external dynamic impact has the theoretical potential to interfere not only with noncovalent, but also with covalent bonds when high enough. The subsequent attraction of increased water molecules into the unfolded protein structures and disruption of adenosine-triphosphate bonds could to some extent explain the etiology to cytotoxic edema.
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45
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Rosen LE, Marqusee S. Autonomously folding protein fragments reveal differences in the energy landscapes of homologous RNases H. PLoS One 2015; 10:e0119640. [PMID: 25803034 PMCID: PMC4372590 DOI: 10.1371/journal.pone.0119640] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/02/2015] [Indexed: 11/19/2022] Open
Abstract
An important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. In this work, we compare E. coli and T. thermophilus homologs of the protein RNase H. Using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (I(core) and I(core+1)) hypothesized to be present on the energy landscapes of these two proteins. We observe that both T. thermophilus RNase H (ttRNH) fragments are folded and have distinct stabilities, indicating that both regions are capable of autonomous folding and that both intermediates are present as local minima on the ttRNH energy landscape. In contrast, the two E. coli RNase H (ecRNH) fragments have very similar stabilities, suggesting that the presence of additional residues in the I(core+1) fragment does not affect the folding or structure as compared to I(core). NMR experiments provide additional evidence that only the I(core) intermediate is populated by ecRNH. This is one of the biggest differences that has been observed between the energy landscapes of these two proteins. Additionally, we used a FRET experiment in the background of full-length ttRNH to specifically monitor the formation of the I(core+1) intermediate. We determine that the ttRNH I(core+1) intermediate is likely the intermediate populated prior to the rate-limiting barrier to global folding, in contrast to E. coli RNase H for which I(core) is the folding intermediate. This result provides new insight into the nature of the rate-limiting barrier for the folding of RNase H.
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Affiliation(s)
- Laura E. Rosen
- Biophysics Graduate Group, University of California, Berkeley, CA, United States of America
- California Institute for Quantitative Biosciences – Berkeley, Berkeley, CA, United States of America
| | - Susan Marqusee
- Biophysics Graduate Group, University of California, Berkeley, CA, United States of America
- California Institute for Quantitative Biosciences – Berkeley, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- * E-mail:
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46
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Sarkar SS, Udgaonkar JB, Krishnamoorthy G. Unfolding of a small protein proceeds via dry and wet globules and a solvated transition state. Biophys J 2014; 105:2392-402. [PMID: 24268151 DOI: 10.1016/j.bpj.2013.09.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/31/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022] Open
Abstract
Dissecting a protein unfolding process into individual steps can provide valuable information on the forces that maintain the integrity of the folded structure. Solvation of the protein core determines stability, but it is not clear when such solvation occurs during unfolding. In this study, far-UV circular dichroism measurements suggest a simplistic two-state view of the unfolding of barstar, but the use of multiple other probes brings out the complexity of the unfolding reaction. Near-UV circular dichroism measurements show that unfolding commences with the loosening of tertiary interactions in a native-like intermediate, N(∗). Fluorescence resonance energy transfer measurements show that N(∗) then expands rapidly but partially to form an early unfolding intermediate IE. Fluorescence spectral measurements indicate that both N(∗) and IE have retained native-like solvent accessibility of the core, suggesting that they are dry molten globules. Dynamic quenching measurements at the single tryptophan buried in the core suggest that the core becomes solvated only later in a late wet molten globule, IL, which precedes the unfolded form. Fluorescence anisotropy decay measurements show that tight packing around the core tryptophan is lost when IL forms. Of importance, the slowest step is unfolding of the wet molten globule and involves a solvated transition state.
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Affiliation(s)
- Saswata Sankar Sarkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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47
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Malhotra P, Udgaonkar JB. High-Energy Intermediates in Protein Unfolding Characterized by Thiol Labeling under Nativelike Conditions. Biochemistry 2014; 53:3608-20. [DOI: 10.1021/bi401493t] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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48
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Dasgupta A, Udgaonkar JB, Das P. Multistage Unfolding of an SH3 Domain: An Initial Urea-Filled Dry Molten Globule Precedes a Wet Molten Globule with Non-Native Structure. J Phys Chem B 2014; 118:6380-92. [DOI: 10.1021/jp410019f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amrita Dasgupta
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Jayant B. Udgaonkar
- National
Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Payel Das
- Computational
Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan
Road, Yorktown Heights, New
York 10598, United States
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49
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Jha SK, Marqusee S. Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride. Proc Natl Acad Sci U S A 2014; 111:4856-61. [PMID: 24639503 PMCID: PMC3977270 DOI: 10.1073/pnas.1315453111] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).
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Affiliation(s)
| | - Susan Marqusee
- California Institute for Quantitative Biosciences and
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720-3220
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50
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von Holst H, Li X. Numerical impact simulation of gradually increased kinetic energy transfer has the potential to break up folded protein structures resulting in cytotoxic brain tissue edema. J Neurotrauma 2014; 30:1192-9. [PMID: 23384662 DOI: 10.1089/neu.2012.2730] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although the consequences of traumatic brain injury (TBI) and its treatment have been improved, there is still a substantial lack of understanding the mechanisms. Numerical simulation of the impact can throw further lights on site and mechanism of action. A finite element model of the human head and brain tissue was used to simulate TBI. The consequences of gradually increased kinetic energy transfer was analyzed by evaluating the impact intracranial pressure (ICP), strain level, and their potential influences on binding forces in folded protein structures. The gradually increased kinetic energy was found to have the potential to break apart bonds of Van der Waals in all impacts and hydrogen bonds at simulated impacts from 6 m/s and higher, thereby superseding the energy in folded protein structures. Further, impacts below 6 m/s showed none or very slight increase in impact ICP and strain levels, whereas impacts of 6 m/s or higher showed a gradual increase of the impact ICP and strain levels reaching over 1000 KPa and over 30%, respectively. The present simulation study shows that the free kinetic energy transfer, impact ICP, and strain levels all have the potential to initiate cytotoxic brain tissue edema by unfolding protein structures. The definition of mild, moderate, and severe TBI should thus be looked upon as the same condition and separated only by a gradual severity of impact.
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Affiliation(s)
- Hans von Holst
- Section of Neurosurgery, Division of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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