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Abstract
Proteins have dynamic structures that undergo chain motions on time scales spanning from picoseconds to seconds. Resolving the resultant conformational heterogeneity is essential for gaining accurate insight into fundamental mechanistic aspects of the protein folding reaction. The use of high-resolution structural probes, sensitive to population distributions, has begun to enable the resolution of site-specific conformational heterogeneity at different stages of the folding reaction. Different states populated during protein folding, including the unfolded state, collapsed intermediate states, and even the native state, are found to possess significant conformational heterogeneity. Heterogeneity in protein folding and unfolding reactions originates from the reduced cooperativity of various kinds of physicochemical interactions between various structural elements of a protein, and between a protein and solvent. Heterogeneity may arise because of functional or evolutionary constraints. Conformational substates within the unfolded state and the collapsed intermediates that exchange at rates slower than the subsequent folding steps give rise to heterogeneity on the protein folding pathways. Multiple folding pathways are likely to represent distinct sequences of structure formation. Insight into the nature of the energy barriers separating different conformational states populated during (un)folding can also be obtained by resolving heterogeneity.
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Affiliation(s)
- Sandhya Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru 560065, India.,Indian Institute of Science Education and Research, Pune 411008, India
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2
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Zhuravlev PI, Hinczewski M, Thirumalai D. Low Force Unfolding of a Single-Domain Protein by Parallel Pathways. J Phys Chem B 2021; 125:1799-1805. [DOI: 10.1021/acs.jpcb.0c11308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Pavel I. Zhuravlev
- Biophysics Program, Institute for Physical Science and Technology, Department of Chemistry & Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Michael Hinczewski
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - D. Thirumalai
- Department of Chemistry, The University of Texas, Austin, Texas 78712, United States
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3
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Delfi M, Leone S, Emendato A, Ami D, Borriello M, Natalello A, Iannuzzi C, Picone D. Understanding the self-assembly pathways of a single chain variant of monellin: A first step towards the design of sweet nanomaterials. Int J Biol Macromol 2020; 152:21-29. [PMID: 32088237 DOI: 10.1016/j.ijbiomac.2020.02.229] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/20/2022]
Abstract
Peptides and proteins possess an inherent tendency to self-assemble, prompting the formation of amyloid aggregates from their soluble and functional states. Amyloids are linked to many devastating diseases, but self-assembling proteins can also represent formidable tools to produce new and sustainable biomaterials for biomedical and biotechnological applications. The mechanism of fibrillar aggregation, which influences the morphology and the properties of the protein aggregates, depend on factors such as pH, ionic strength, temperature, agitation, and protein concentration. We have here used intensive mechanical agitation, with or without beads, to prompt the aggregation of the single-chain derivative of the plant protein monellin, named MNEI, which is a well characterized sweet protein. Transmission electron microscopy confirmed the formation of fibrils several micrometers long, morphologically different from the previously characterized fibers of MNEI. Changes in the protein secondary structures during the aggregation process were monitored by Fourier transform infrared spectroscopy, which detected differences in the conformation of the final aggregates obtained under mechanical agitation. Moreover, soluble oligomers could be detected in the early phases of aggregation by polyacrylamide gel-electrophoresis. These findings emphasize the existence of multiple pathways of fibrillar aggregation for MNEI, which could be exploited for the design of innovative protein-based biomaterials.
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Affiliation(s)
- Masoud Delfi
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Serena Leone
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Alessandro Emendato
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Margherita Borriello
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milano, Italy
| | - Clara Iannuzzi
- Department of Precision Medicine, University of Campania "L. Vanvitelli", Via L. De Crecchio 7, 80138 Naples, Italy.
| | - Delia Picone
- Department of Chemical Sciences, University of Naples "Federico II", Complesso Universitario Monte S. Angelo, Via Cintia, 80126 Napoli, Italy.
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4
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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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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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6
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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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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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8
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Baliga C, Varadarajan R, Aghera N. Homodimeric Escherichia coli Toxin CcdB (Controller of Cell Division or Death B Protein) Folds via Parallel Pathways. Biochemistry 2016; 55:6019-6031. [PMID: 27696818 DOI: 10.1021/acs.biochem.6b00726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of parallel pathways in the folding of proteins seems intuitive, yet remains controversial. We explore the folding kinetics of the homodimeric Escherichia coli toxin CcdB (Controller of Cell Division or Death B protein) using multiple optical probes and approaches. Kinetic studies performed as a function of protein and denaturant concentrations demonstrate that the folding of CcdB is a four-state process. The two intermediates populated during folding are present on parallel pathways. Both form by rapid association of the monomers in a diffusion limited manner and appear to be largely unstructured, as they are silent to the optical probes employed in the current study. The existence of parallel pathways is supported by the insensitivity of the amplitudes of the refolding kinetic phases to the different probes used in the study. More importantly, interrupted refolding studies and ligand binding studies clearly demonstrate that the native state forms in a biexponential manner, implying the presence of at least two pathways. Our studies indicate that the CcdA antitoxin binds only to the folded CcdB dimer and not to any earlier folding intermediates. Thus, despite being part of the same operon, the antitoxin does not appear to modulate the folding pathway of the toxin encoded by the downstream cistron. This study highlights the utility of ligand binding in distinguishing between sequential and parallel pathways in protein folding studies, while also providing insights into molecular interactions during folding in Type II toxin-antitoxin systems.
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Affiliation(s)
- Chetana Baliga
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bangalore 560 004, India
| | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India
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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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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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11
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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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12
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Labastida-Polito A, Garza-Ramos G, Camarillo-Cadena M, Zubillaga RA, Hernández-Arana A. Complex kinetics and residual structure in the thermal unfolding of yeast triosephosphate isomerase. BMC BIOCHEMISTRY 2015; 16:20. [PMID: 26334568 PMCID: PMC4558838 DOI: 10.1186/s12858-015-0049-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 08/19/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Saccharomyces cerevisiae triosephosphate isomerase (yTIM) is a dimeric protein that shows noncoincident unfolding and refolding transitions (hysteresis) in temperature scans, a phenomenon indicative of the slow forward and backward reactions of the native-unfolded process. Thermal unfolding scans suggest that no stable intermediates appear in the unfolding of yTIM. However, reported evidence points to the presence of residual structure in the denatured monomer at high temperature. RESULTS Thermally denatured yTIM showed a clear trend towards the formation of aggregation-prone, β-strand-like residual structure when pH decreased from 8.0 to 6.0, even though thermal unfolding profiles retained a simple monophasic appearance regardless of pH. However, kinetic studies performed over a relatively wide temperature range revealed a complex unfolding mechanism comprising up to three observable phases, with largely different time constants, each accompanied by changes in secondary structure. Besides, a simple sequential mechanism is unlikely to explain the observed variation of amplitudes and rate constants with temperature. This kinetic complexity is, however, not linked to the appearance of residual structure. Furthermore, the rate constant for the main unfolding phase shows small, rather unvarying values in the pH region where denatured yTIM gradually acquires a β-strand-like conformation. It appears, therefore, that the residual structure has no influence on the kinetic stability of the native protein. However, the presence of residual structure is clearly associated with increased irreversibility. CONCLUSIONS The slow temperature-induced unfolding of yeast TIM shows three kinetic phases. Rather than a simple sequential pathway, a complex mechanism involving off-pathway intermediates or even parallel pathways may be operating. β-strand-type residual structure, which appears below pH 8.0, is likely to be associated with increased irreversible aggregation of the unfolded protein. However, this denatured form apparently accelerates the refolding process.
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Affiliation(s)
- Ariana Labastida-Polito
- Área de Biofisicoquímica, Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Iztapalapa, D.F. 09340, Mexico.
| | - Georgina Garza-Ramos
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Coyoacán, D.F. 04510, Mexico.
| | - Menandro Camarillo-Cadena
- Área de Biofisicoquímica, Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Iztapalapa, D.F. 09340, Mexico.
| | - Rafael A Zubillaga
- Área de Biofisicoquímica, Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Iztapalapa, D.F. 09340, Mexico.
| | - Andrés Hernández-Arana
- Área de Biofisicoquímica, Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Iztapalapa, D.F. 09340, Mexico.
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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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14
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Chen T, Chan HS. Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding. Phys Chem Chem Phys 2014; 16:6460-79. [DOI: 10.1039/c3cp54866j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained protein chain models with desolvation barriers or sidechains lead to stronger local–nonlocal coupling and more linear chevron plots.
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Affiliation(s)
- Tao Chen
- Departments of Biochemistry
- of Molecular Genetics
- of Physics
- University of Toronto
- Toronto, Canada
| | - Hue Sun Chan
- Departments of Biochemistry
- of Molecular Genetics
- of Physics
- University of Toronto
- Toronto, Canada
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