1
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Hossain M, Huda N, Bhuyan AK. A three-state mechanism for trifluoroethanol denaturation of an intrinsically disordered protein (IDP). J Biochem 2023; 174:519-531. [PMID: 37709541 DOI: 10.1093/jb/mvad067] [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: 04/27/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023] Open
Abstract
Relating the amino acid composition and sequence to chain folding and binding preferences of intrinsically disordered proteins (IDPs) has emerged as a huge challenge. While globular proteins have respective 3D structures that are unique to their individual functions, IDPs violate this structure-function paradigm because rather than having a well-defined structure an ensemble of rapidly interconverting disordered structures characterize an IDP. This work measures 2,2,2-trifluoroethanol (TFE)-induced equilibrium transitions of an IDP called AtPP16-1 (Arabidopsis thaliana phloem protein type 16-1) by using fluorescence, circular dichroism, infrared and nuclear magnetic resonance (NMR) methods at pH 4, 298 K. Low TFE reversibly removes the tertiary structure to produce an ensemble of obligate intermediate ($\mathrm{I}$) retaining the native-state ($\mathrm{N}$) secondary structure. The intermediate $\mathrm{I}$ is preceded by a non-obligate tryptophan-specific intermediate ${\mathrm{I}}_{\mathrm{w}}$ whose population is detectable for AtPP16-1 specifically. Accumulation of such non-obligate intermediates is discriminated according to the sequence composition of the protein. In all cases, however, a tertiary structure-unfolded general obligate intermediate $\mathrm{I}$ is indispensable. The $\mathrm{I}$ ensemble has higher helical propensity conducive to the acquisition of an exceedingly large level of α-helices by a reversible denaturation transition of $\mathrm{I}$ to the denatured state $\mathrm{D}$ as the TFE level is increased. Strikingly, it is the same $\mathrm{N}\rightleftharpoons \mathrm{I}\rightleftharpoons \mathrm{D}$ scheme typifying the TFE transitions of globular proteins. The high-energy state $\mathrm{I}$ characterized by increased helical propensity is called a universal intermediate encountered in both genera of globular and disordered proteins. Neither $\mathrm{I}$ nor $\mathrm{D}$ strictly show molten globule (MG)-like properties, dismissing the belief that TFE promotes MGs.
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Affiliation(s)
- Mujahid Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Noorul Huda
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Abani K Bhuyan
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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2
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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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3
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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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4
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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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5
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Sadat A, Tiwari S, Mapa K. Protocol for Spontaneous and Chaperonin-assisted in vitro Refolding of a Slow-folding Mutant of GFP, sGFP. Bio Protoc 2021; 11:e4099. [PMID: 34395735 DOI: 10.21769/bioprotoc.4099] [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: 12/16/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/02/2022] Open
Abstract
Understanding the folding pathway of any protein is of utmost importance for deciphering the folding problems under adverse conditions. We can obtain important information about the folding pathway by monitoring the folding of any protein from its unfolded state. It is usually very difficult to monitor the folding process in real time as the process is generally very fast, and we need a suitable read out. In this protocol, we have solved this issue by using a protein that is non-fluorescent in its unfolded state but fluoresces in its native state after folding. The kinetics of refolding can be monitored by following the increase in fluorescence in real time. Previously, this was generally achieved by either monitoring a protein's enzymatic activity or measuring the tryptophan fluorescence, where the signal output depends on well-described enzymatic activity or the frequency of tryptophan residues present in the proteins, respectively. Here, we describe a simple and real-time assay to monitor the refolding of sGFP, a recently described slow-folding mutant of yeGFP (yeast enhanced GFP). We unfold this protein using chemical denaturant and refold in a suitable buffer, monitoring the increase in fluorescence over time. GFP is fluorescent only when correctly folded; thus, using this technique, we can measure the true rate of protein refolding by following the increase in fluorescence over time. Therefore, sGFP can be used as an ideal model to study the in vitro protein folding process. Accordingly, the effects of different conditions and molecules on the protein folding pathway can be efficiently studied using sGFP as a model protein. Graphical abstract: Schematic of the steps involved in the sGFP refolding pathway. Native sGFP is unfolded by chemical denaturation using 6 M GuHCl at 25°C for 1 hour and then refolded in refolding buffer by 100-fold dilution.
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Affiliation(s)
- Anwar Sadat
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh 201002, India.,CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Satyam Tiwari
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh 201002, India.,CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Koyeli Mapa
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh 201002, India.,Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Greater Noida, Gautam Buddha Nagar, Uttar Pradesh 201314, India
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6
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Donnarumma F, Leone S, Delfi M, Emendato A, Ami D, Laurents DV, Natalello A, Spadaccini R, Picone D. Probing structural changes during amyloid aggregation of the sweet protein MNEI. FEBS J 2019; 287:2808-2822. [DOI: 10.1111/febs.15168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Federica Donnarumma
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Serena Leone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Masoud Delfi
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Alessandro Emendato
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Douglas V. Laurents
- Institute of Physical Chemistry ‘Rocasolano’ Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Antonino Natalello
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Roberta Spadaccini
- Department of Science and Technology Università degli Studi del Sannio Benevento Italy
| | - Delia Picone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
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7
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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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8
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Dahiya V, Buchner J. Functional principles and regulation of molecular chaperones. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:1-60. [PMID: 30635079 DOI: 10.1016/bs.apcsb.2018.10.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To be able to perform their biological function, a protein needs to be correctly folded into its three dimensional structure. The protein folding process is spontaneous and does not require the input of energy. However, in the crowded cellular environment where there is high risk of inter-molecular interactions that may lead to protein molecules sticking to each other, hence forming aggregates, protein folding is assisted. Cells have evolved robust machinery called molecular chaperones to deal with the protein folding problem and to maintain proteins in their functional state. Molecular chaperones promote efficient folding of newly synthesized proteins, prevent their aggregation and ensure protein homeostasis in cells. There are different classes of molecular chaperones functioning in a complex interplay. In this review, we discuss the principal characteristics of different classes of molecular chaperones, their structure-function relationships, their mode of regulation and their involvement in human disorders.
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Affiliation(s)
- Vinay Dahiya
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany
| | - Johannes Buchner
- Center for Integrated Protein Science Munich CIPSM at the Department Chemie, Technische Universität München, Garching, Germany.
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9
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Jethva PN, Udgaonkar JB. The Osmolyte TMAO Modulates Protein Folding Cooperativity by Altering Global Protein Stability. Biochemistry 2018; 57:5851-5863. [DOI: 10.1021/acs.biochem.8b00698] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- 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
- Indian Institute of Science Education and Research, Pune 411008, India
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10
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11
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pH driven fibrillar aggregation of the super-sweet protein Y65R-MNEI: A step-by-step structural analysis. Biochim Biophys Acta Gen Subj 2018; 1862:808-815. [DOI: 10.1016/j.bbagen.2017.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 12/14/2017] [Accepted: 12/22/2017] [Indexed: 11/22/2022]
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12
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Mascarenhas NM, Terse VL, Gosavi S. Intrinsic Disorder in a Well-Folded Globular Protein. J Phys Chem B 2018; 122:1876-1884. [PMID: 29304275 DOI: 10.1021/acs.jpcb.7b12546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The folded structure of the heterodimeric sweet protein monellin mimics single-chain proteins with topology β1-α1-β2-β3-β4-β5 (chain A: β3-β4-β5; chain B: β1-α1-β2). Furthermore, like naturally occurring single-chain proteins of a similar size, monellin folds cooperatively with no detectable intermediates. However, the two monellin chains, A and B, are marginally structured in isolation and fold only upon binding to each other. Thus, monellin presents a unique opportunity to understand the design of intrinsically disordered proteins that fold upon binding. Here, we study the folding of a single-chain variant of monellin (scMn) using simulations of an all heavy-atom structure-based model. These simulations can explain mechanistic details derived from scMn experiments performed using several different structural probes. scMn folds cooperatively in our structure-based simulations, as is also seen in experiments. We find that structure formation near the transition-state ensemble of scMn is not uniformly distributed but is localized to a hairpin-like structure which contains one strand from each chain (β2, β3). Thus, the sequence and the underlying energetics of heterodimeric monellin promote the early formation of the interchain interface (β2-β3). By studying computational scMn mutants whose "interchain" interactions are deleted, we infer that this energy distribution allows the two protein chains to remain largely disordered when this interface is not folded. From these results, we suggest that cutting the protein backbone of a globular protein between residues which lie within its folding nucleus may be one way to construct two disordered fragments which fold upon binding.
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Affiliation(s)
| | - Vishram L Terse
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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13
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Maity H, Reddy G. Thermodynamics and Kinetics of Single-Chain Monellin Folding with Structural Insights into Specific Collapse in the Denatured State Ensemble. J Mol Biol 2018; 430:465-478. [DOI: 10.1016/j.jmb.2017.09.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 08/28/2017] [Accepted: 09/09/2017] [Indexed: 01/21/2023]
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14
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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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15
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Jethva PN, Udgaonkar JB. Modulation of the Extent of Cooperative Structural Change During Protein Folding by Chemical Denaturant. J Phys Chem B 2017; 121:8263-8275. [DOI: 10.1021/acs.jpcb.7b04473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- 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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16
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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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17
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Moulick R, Udgaonkar JB. Identification and Structural Characterization of the Precursor Conformation of the Prion Protein which Directly Initiates Misfolding and Oligomerization. J Mol Biol 2017; 429:886-899. [DOI: 10.1016/j.jmb.2017.01.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/19/2017] [Accepted: 01/19/2017] [Indexed: 12/11/2022]
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18
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Shah R, Ohashi T, Erickson HP, Oas TG. Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange: THERMODYNAMIC STABILITY CORRELATES WITH RATES OF UNFOLDING RATHER THAN FOLDING. J Biol Chem 2016; 292:955-966. [PMID: 27909052 DOI: 10.1074/jbc.m116.760371] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/29/2016] [Indexed: 11/06/2022] Open
Abstract
Globular proteins are not permanently folded but spontaneously unfold and refold on time scales that can span orders of magnitude for different proteins. A longstanding debate in the protein-folding field is whether unfolding rates or folding rates correlate to the stability of a protein. In the present study, we have determined the unfolding and folding kinetics of 10 FNIII domains. FNIII domains are one of the most common protein folds and are present in 2% of animal proteins. FNIII domains are ideal for this study because they have an identical seven-strand β-sandwich structure, but they vary widely in sequence and thermodynamic stability. We assayed thermodynamic stability of each domain by equilibrium denaturation in urea. We then assayed the kinetics of domain opening and closing by a technique known as thiol exchange. For this we introduced a buried Cys at the identical location in each FNIII domain and measured the kinetics of labeling with DTNB over a range of urea concentrations. A global fit of the kinetics data gave the kinetics of spontaneous unfolding and refolding in zero urea. We found that the folding rates were relatively similar, ∼0.1-1 s-1, for the different domains. The unfolding rates varied widely and correlated with thermodynamic stability. Our study is the first to address this question using a set of domains that are structurally homologous but evolved with widely varying sequence identity and thermodynamic stability. These data add new evidence that thermodynamic stability correlates primarily with unfolding rate rather than folding rate. The study also has implications for the question of whether opening of FNIII domains contributes to the stretching of fibronectin matrix fibrils.
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Affiliation(s)
| | - Tomoo Ohashi
- Cell Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Harold P Erickson
- From the Departments of Biochemistry and .,Cell Biology, Duke University Medical Center, Durham, North Carolina 27710
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19
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Mascarenhas NM, Gosavi S. Understanding protein domain-swapping using structure-based models of protein folding. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 128:113-120. [PMID: 27867057 PMCID: PMC7127520 DOI: 10.1016/j.pbiomolbio.2016.09.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Revised: 09/05/2016] [Accepted: 09/26/2016] [Indexed: 02/05/2023]
Abstract
In domain-swapping, two or more identical protein monomers exchange structural elements and fold into dimers or multimers whose units are structurally similar to the original monomer. Domain-swapping is of biotechnological interest because inhibiting domain-swapping can reduce disease-causing fibrillar protein aggregation. To achieve such inhibition, it is important to understand both the energetics that stabilize the domain-swapped structure and the protein dynamics that enable the swapping. Structure-based models (SBMs) encode the folded structure of the protein in their potential energy functions. SBMs have been successfully used to understand diverse aspects of monomer folding. Symmetrized SBMs model interactions between two identical protein chains using only intra-monomer interactions. Molecular dynamics simulations of such symmetrized SBMs have been used to correctly predict the domain-swapped structure and to understand the mechanism of domain-swapping. Here, we review such models and illustrate that monomer topology determines key aspects of domain-swapping. However, in some proteins, specifics of local energetic interactions modulate domain-swapping and these need to be added to the symmetrized SBMs. We then summarize some general principles of the mechanism of domain-swapping that emerge from the symmetrized SBM simulations. Finally, using our own results, we explore how symmetrized SBMs could be used to design domain-swapping in proteins.
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Affiliation(s)
- Nahren Manuel Mascarenhas
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India.
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20
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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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21
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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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22
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Frank AT, Law SM, Ahlstrom LS, Brooks CL. Predicting protein backbone chemical shifts from Cα coordinates: extracting high resolution experimental observables from low resolution models. J Chem Theory Comput 2016; 11:325-31. [PMID: 25620895 PMCID: PMC4295808 DOI: 10.1021/ct5009125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Indexed: 12/18/2022]
Abstract
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Given
the demonstrated utility of coarse-grained modeling and simulations
approaches in studying protein structure and dynamics, developing
methods that allow experimental observables to be directly recovered from coarse-grained models is of great importance. In
this work, we develop one such method that enables protein backbone
chemical shifts (1HN, 1Hα, 13Cα, 13C, 13Cβ, and 15N) to be predicted from Cα coordinates. We show that our Cα-based
method, LARMORCα, predicts backbone chemical shifts
with comparable accuracy to some all-atom approaches. More importantly,
we demonstrate that LARMORCα predicted chemical shifts
are able to resolve native structure from decoy pools that contain
both native and non-native models, and so it is sensitive to protein
structure. As an application, we use LARMORCα to
characterize the transient state of the fast-folding protein gpW using
recently published NMR relaxation dispersion derived backbone chemical
shifts. The model we obtain is consistent with the previously proposed
model based on independent analysis of the chemical shift dispersion
pattern of the transient state. We anticipate that LARMORCα will find utility as a tool that enables important protein conformational
substates to be identified by “parsing” trajectories
and ensembles generated using coarse-grained modeling and simulations.
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Affiliation(s)
- Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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23
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Mascarenhas NM, Gosavi S. Protein Domain-Swapping Can Be a Consequence of Functional Residues. J Phys Chem B 2016; 120:6929-38. [PMID: 27331242 DOI: 10.1021/acs.jpcb.6b03968] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Monomer topology has been implicated in domain-swapping, a potential first step on the route to disease-causing protein aggregation. Despite having the same topology (β1-α1-β2-β3-β4-β5), the cysteine protease inhibitor stefin-B domain swaps more readily than a single-chain variant of the heterodimeric sweet protein monellin (scMn). Here, we computationally study the folding of stefin-B and scMn in order to understand the molecular basis for the difference in their domain-swapping propensities. In agreement with experiments, our structure-based simulations show that scMn folds cooperatively without the population of an intermediate while stefin-B populates an equilibrium intermediate state. Since the simulation intermediate has only one domain structured (β3-β4-β5), it can directly lead to domain-swapping. Using computational variants of stefin-B, we show that the population of this intermediate is caused by regions of stefin-B that have been implicated in protease inhibition. We also find that the protease-binding regions are located on two structural elements and localized in space. In contrast, the residues that contribute to the sweetness of monellin are not localized to a few structural elements but are distributed over the protein fold. We conclude that the distributed functional residues of monellin do not induce large local perturbations in the protein structure, eliminating the formation of folding intermediates and in turn domain-swapping. On the other hand, the localized protease-binding regions of stefin-B promote the formation of a folding intermediate which can lead to domain-swapping. Thus, domain-swapping can be a direct consequence of the constraints that function imposes on the protein structure.
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Affiliation(s)
- Nahren Manuel Mascarenhas
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research , Bangalore 560065, India
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24
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Surana P, Das R. Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR. Protein Sci 2016; 25:1438-50. [PMID: 27111887 DOI: 10.1002/pro.2940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 04/20/2016] [Indexed: 01/29/2023]
Abstract
The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly-Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process.
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Affiliation(s)
- Parag Surana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India
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25
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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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26
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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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27
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Singh J, Udgaonkar JB. Molecular Mechanism of the Misfolding and Oligomerization of the Prion Protein: Current Understanding and Its Implications. Biochemistry 2015; 54:4431-42. [PMID: 26171558 DOI: 10.1021/acs.biochem.5b00605] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Prion diseases, also known as transmissible spongiform encephalopathies, make up a group of fatal neurodegenerative disorders linked with the misfolding and aggregation of the prion protein (PrP). Although it is not yet understood how the misfolding of PrP induces neurodegeneration, it is widely accepted that the formation of misfolded prion protein (termed PrP(Sc)) is both the triggering event in the disease and the main component of the infectious agent responsible for disease transmission. Despite the clear involvement of PrP(Sc) in prion diseases, the exact composition of PrP(Sc) is not yet well-known. Recent studies show that misfolded oligomers of PrP could, however, be responsible for neurotoxicity and/or infectivity in the prion diseases. Hence, understanding the molecular mechanism of formation of the misfolded oligomers of PrP is critical for developing an understanding about the prion diseases and for developing anti-prion therapeutics. This review discusses recent advances in understanding the molecular mechanism of misfolded oligomer formation by PrP and its implications for the development of anti-prion therapeutics.
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Affiliation(s)
- Jogender Singh
- 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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28
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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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