1
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Hashimoto S, Matsuo K. Dynamic Observation of the Membrane Interaction Processes of β-Lactoglobulin by Time-Resolved Vacuum-Ultraviolet Circular Dichroism. Anal Chem 2024. [PMID: 38907695 DOI: 10.1021/acs.analchem.4c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
The elucidation of protein-membrane interactions is pivotal for comprehending the mechanisms underlying diverse biological phenomena and membrane-related diseases. In this investigation, vacuum-ultraviolet circular dichroism (VUVCD) spectroscopy, utilizing synchrotron radiation (SR), was employed to dynamically observe membrane interaction processes involving water-soluble proteins at the secondary-structure level. The study utilized a time-resolved (TR) T-shaped microfluidic cell, facilitating the rapid and efficient mixing of protein and membrane solutions. This system was instrumental in acquiring measurements of the time-resolved circular dichroism (TRCD) spectra of β-lactoglobulin (bLG) during its interaction with lysoDMPG micelles. The results indicate that bLG undergoes a β-α conformation change, leading to the formation of the membrane-interacting state (M-state), with structural alterations occurring in more than two steps. Global fitting analysis, employing biexponential functions with all of the TRCD spectral data sets, yielded two distinct rate constants (0.18 ± 0.01 and 0.06 ± 0.003/s) and revealed a unique spectrum corresponding to an intermediate state (I-state). Secondary-structure analysis of bLG in its native (N-, I-, and M-states) highlighted that structural changes from the N- to I-states predominantly occurred in the N- and C-terminal regions, which were prominently exposed to the membrane. Meanwhile, transitions from the I- to M-states extended into the inner barrel regions of bLG. Further examination of the physical properties of α-helical segments, such as effective charge and hydrophobicity, revealed that the N- to I- and I- to M-state transitions, which are ascribed to first- and second-rate constants, respectively, are primarily driven by electrostatic and hydrophobic interactions, respectively. These findings underscore the capability of the TR-VUVCD system as a robust tool for characterizing protein-membrane interactions at the molecular level.
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Affiliation(s)
- Satoshi Hashimoto
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - Koichi Matsuo
- Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
- Research Institute for Synchrotron Radiation Science, Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
- International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM2), Hiroshima University, 2-313 Kagamiyama, Higashi-Hiroshima 739-0046, Japan
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2
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Jain A, Judy E, Kishore N. Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach. J Phys Chem B 2024; 128:5344-5362. [PMID: 38773936 DOI: 10.1021/acs.jpcb.4c01751] [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: 05/24/2024]
Abstract
Many studies have demonstrated the manner in which ANS interacts with bovine serum albumin (BSA), although they are limited by the extremely low solubility of dye. The present study demonstrates the binding of ANSA dye with BSA, and since this dye can easily replace ANS, it not only simplifies research but also improves sensor accuracy for serum albumin. A combination of calorimetry and spectroscopy has been employed to establish the thermodynamic signatures associated with the interaction of ANSA with the protein and the consequent conformational changes in the latter. The results of differential scanning calorimetry reveal that when the concentration of ANSA in solution is increased, the thermal stability of the protein increases substantially. The fluorescence data demonstrated a decrease in the binding affinity of ANSA with the protein when pH increased but was unable to identify a change in the mode of interaction of the ligand. ITC has demonstrated that the mode of interaction between ANSA and the protein varies from a single set of binding sites at pH 5 and 7.4 to a sequential binding site at pH 10, emphasizing the potential relevance of protein conformational changes. TCSPC experiments suggested a dynamic type in the presence of ANSA. Molecular docking studies suggest that ANSA molecules are able to find ionic centers in the hydrophobic pockets of BSA. The findings further imply that given its ease of use in experiments, ANSA may be a useful probe for tracking the presence of serum albumin and partially folded protein states.
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Affiliation(s)
- Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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3
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Tavili E, Aziziyan F, Dabirmanesh B. Pathways of amyloid fibril formation and protein aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:11-54. [PMID: 38811078 DOI: 10.1016/bs.pmbts.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The main cause of many neurodegenerative diseases and systemic amyloidoses is protein and peptide aggregation and the formation of amyloid fibrils. The study of aggregation mechanisms, the discovery and description of aggregate structures, and a comprehensive understanding of the molecular mechanisms of amyloid formation are of great importance for the diagnostic processes at the molecular level and for the development of therapeutic strategies to counter aggregation-associated disorders. Given that understanding protein misfolding phenomena is directly related to the protein folding process, we will briefly explain the protein folding mechanism and then discuss the important factors involved in protein aggregation. In the following, we review different mechanisms of amyloid formation and finally represent the current knowledge on how amyloid fibrils are formed based on kinetic and thermodynamic factors.
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Affiliation(s)
- Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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4
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Mahapatra A, Newberry RW. Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity. Protein Sci 2024; 33:e4951. [PMID: 38511533 PMCID: PMC10955625 DOI: 10.1002/pro.4951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 02/06/2024] [Accepted: 02/19/2024] [Indexed: 03/22/2024]
Abstract
The Parkinson's-associated protein α-synuclein (α-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of α-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to α-syn LLPS, independent of fibrillation. Herein, using a combination of subtle missense mutations, we show that LLPS of α-syn is highly sensitive to its sequence complexity. In fact, we find that even a highly conservative mutation (V16I) that increases sequence complexity without perturbing physicochemical and structural properties, is sufficient to reduce LLPS by 75%; this effect can be reversed by an adjacent V-to-I mutation (V15I) that restores the original sequence complexity. A18T, a complexity-enhancing PD-associated mutation, was likewise found to reduce LLPS, implicating sequence complexity in α-syn pathogenicity. Furthermore, leveraging the differences in LLPS propensities among different α-syn variants, we demonstrate that fibrillation of α-syn does not necessarily correlate with its LLPS. In fact, we identify mutations that selectively perturb LLPS or fibrillation of α-syn, unlike previously studied mutations. The variants and design principles reported herein should therefore empower future studies to disentangle these two phenomena and distinguish their (patho)biological roles.
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5
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Anderson B, Bryant DL, Gozem S, Brambley C, Handy ST, Farone A, Miller JM. Solvent-Dependent Emissions Properties of a Model Aurone Enable Use in Biological Applications. J Fluoresc 2024:10.1007/s10895-024-03607-x. [PMID: 38411859 DOI: 10.1007/s10895-024-03607-x] [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: 10/19/2023] [Accepted: 01/27/2024] [Indexed: 02/28/2024]
Abstract
Fluorophores are powerful visualization tools and the development of novel small organic fluorophores are in great demand. Small organic fluorophores have been derived from the aurone skeleton, 2-benzylidenebenzofuran-3(2H)-one. In this study, we have utilized a model aurone derivative with a methoxy group at the 3' position and a hydroxyl group at the 4' position, termed vanillin aurone, to develop a foundational understanding of structural factors impacting aurone fluorescence properties. The fluorescent behaviors of the model aurone were characterized in solvent environments differing in relative polarity and dielectric constant. These data suggested that hydrogen bonding or electrostatic interactions between excited state aurone and solvent directly impact emissions properties such as peak emission wavelength, emission intensity, and Stokes shift. Time-dependent Density Functional Theory (TD-DFT) model calculations suggest that quenched aurone emissions observed in water are a consequence of stabilization of a twisted excited state conformation that disrupts conjugation. In contrast, the calculations indicate that low polarity solvents such as toluene or acetone stabilize a brightly fluorescent planar state. Based on this, additional experiments were performed to demonstrate use as a turn-on probe in an aqueous environment in response to conditions leading to planar excited state stabilization. Vanillin aurone was observed to bind to a model ATP binding protein, YME1L, leading to enhanced emissions intensities with a dissociation equilibrium constant equal to ~ 30 µM. Separately, the aurone was observed to be cell permeable with significant toxicity at doses exceeding 6.25 µM. Taken together, these results suggest that aurones may be broadly useful as turn-on probes in aqueous environments that promote either a change in relative solvent polarity or through direct stabilization of a planar excited state through macromolecular binding.
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Affiliation(s)
- Beth Anderson
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Daniel L Bryant
- Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Samer Gozem
- Department of Chemistry, Georgia State University, 50 Decatur Street SE, Atlanta, GA, 30302, USA
| | - Chad Brambley
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Scott T Handy
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Anthony Farone
- Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA
| | - Justin M Miller
- Department of Chemistry, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, TN, 37132, USA.
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6
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Vaz DC, Rodrigues JR, Loureiro-Ferreira N, Müller TD, Sebald W, Redfield C, Brito RMM. Lessons on protein structure from interleukin-4: All disulfides are not created equal. Proteins 2024; 92:219-235. [PMID: 37814578 DOI: 10.1002/prot.26611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 09/09/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023]
Abstract
Interleukin-4 (IL-4) is a hematopoietic cytokine composed by a four-helix bundle stabilized by an antiparallel beta-sheet and three disulfide bonds: Cys3-Cys127, Cys24-Cys65, and Cys46-Cys99. IL-4 is involved in several immune responses associated to infection, allergy, autoimmunity, and cancer. Besides its physiological relevance, IL-4 is often used as a "model" for protein design and engineering. Hence, to understand the role of each disulfide in the structure and dynamics of IL-4, we carried out several spectroscopic analyses (circular dichroism [CD], fluorescence, nuclear magnetic resonance [NMR]), and molecular dynamics (MD) simulations on wild-type IL-4 and four IL-4 disulfide mutants. All disulfide mutants showed loss of structure, altered interhelical angles, and looser core packings, showing that all disulfides are relevant for maintaining the overall fold and stability of the four-helix bundle motif, even at very low pH. In the absence of the disulfide connecting both protein termini Cys3-Cys127, C3T-IL4 showed a less packed protein core, loss of secondary structure (~9%) and fast motions on the sub-nanosecond time scale (lower S2 order parameters and larger τc correlation time), especially at the two protein termini, loops, beginning of helix A and end of helix D. In the absence of Cys24-Cys65, C24T-IL4 presented shorter alpha-helices (14% loss in helical content), altered interhelical angles, less propensity to form the small anti-parallel beta-sheet and increased dynamics. Simultaneously deprived of two disulfides (Cys3-Cys127 and Cys24-Cys65), IL-4 formed a partially folded "molten globule" with high 8-anilino-1-naphtalenesulphonic acid-binding affinity and considerable loss of secondary structure (~50%decrease), as shown by the far UV-CD, NMR, and MD data.
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Affiliation(s)
- Daniela C Vaz
- School of Health Sciences, Polytechnic of Leiria, Leiria, Portugal
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, Coimbra Chemistry Centre, Institute of Molecular Sciences, Coimbra, Portugal
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Technology and Management, Polytechnic of Leiria, Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), University of Porto, Porto, Portugal
| | - J Rui Rodrigues
- Laboratory of Separation and Reaction Engineering-Laboratory of Catalysis and Materials (LSRE-LCM), School of Technology and Management, Polytechnic of Leiria, Leiria, Portugal
- Associate Laboratory in Chemical Engineering (ALiCE), University of Porto, Porto, Portugal
| | | | - Thomas D Müller
- Department of Molecular Plant Physiology and Biophysics, Julius-von-Sachs-Institute, University of Würzburg, Würzburg, Germany
| | - Walter Sebald
- Department of Physiological Chemistry II, Theodor-Boveri-Institute (Biocentre), University of Würzburg, Würzburg, Germany
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Rui M M Brito
- Chemistry Department, Faculty of Sciences and Technology, University of Coimbra, Coimbra Chemistry Centre, Institute of Molecular Sciences, Coimbra, Portugal
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7
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Rizzuti B, Abian O, Velazquez-Campoy A, Neira JL. Conformational Stability of the N-Terminal Region of MDM2. Molecules 2023; 28:7578. [PMID: 38005300 PMCID: PMC10673428 DOI: 10.3390/molecules28227578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
MDM2 is an E3 ubiquitin ligase which is crucial for the degradation and inhibition of the key tumor-suppressor protein p53. In this work, we explored the stability and the conformational features of the N-terminal region of MDM2 (N-MDM2), through which it binds to the p53 protein as well as other protein partners. The isolated domain possessed a native-like conformational stability in a narrow pH range (7.0 to 10.0), as shown by intrinsic and 8-anilinonapthalene-1-sulfonic acid (ANS) fluorescence, far-UV circular dichroism (CD), and size exclusion chromatography (SEC). Guanidinium chloride (GdmCl) denaturation followed by intrinsic and ANS fluorescence, far-UV CD and SEC at physiological pH, and differential scanning calorimetry (DSC) and thermo-fluorescence experiments showed that (i) the conformational stability of isolated N-MDM2 was very low; and (ii) unfolding occurred through the presence of several intermediates. The presence of a hierarchy in the unfolding intermediates was also evidenced through DSC and by simulating the unfolding process with the help of computational techniques based on constraint network analysis (CNA). We propose that the low stability of this protein is related to its inherent flexibility and its ability to interact with several molecular partners through different routes.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, 87036 Rende, Italy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
| | - Olga Abian
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Adrián Velazquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Madrid, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI)—Unidad mixta GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (O.A.); (A.V.-C.)
- Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDIBE), Universidad Miguel Hernández, 03202 Elche, Spain
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8
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Mahapatra A, Newberry RW. Liquid-liquid phase separation of α-synuclein is highly sensitive to sequence complexity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551831. [PMID: 37577712 PMCID: PMC10418173 DOI: 10.1101/2023.08.03.551831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
The Parkinson's-associated protein α-synuclein (α-syn) can undergo liquid-liquid phase separation (LLPS), which typically leads to the formation of amyloid fibrils. The coincidence of LLPS and amyloid formation has complicated the identification of the molecular determinants unique to LLPS of α-syn. Moreover, the lack of strategies to selectively perturb LLPS makes it difficult to dissect the biological roles specific to α-syn LLPS, independent of fibrillation. Herein, using a combination of subtle missense mutations, we show that LLPS of α-syn is highly sensitive to its sequence complexity. In fact, we find that even a highly conservative mutation (V16I) that increases sequence complexity without perturbing physicochemical and structural properties, is sufficient to reduce LLPS by 75%; this effect can be reversed by an adjacent V-to-I mutation (V15I) that restores the original sequence complexity. A18T, a complexity-enhancing PD-associated mutation, was likewise found to reduce LLPS, implicating sequence complexity in α-syn pathogenicity. Furthermore, leveraging the differences in LLPS propensities among different α-syn variants, we demonstrate that fibrillation of α-syn does not necessarily correlate with its LLPS. In fact, we identify mutations that selectively perturb LLPS or fibrillation of α-syn, unlike previously studied mutations. The variants and design principles reported herein should therefore empower future studies to disentangle these two phenomena and distinguish their (patho)biological roles.
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9
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Ooka K, Arai M. Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models. Nat Commun 2023; 14:6338. [PMID: 37857633 PMCID: PMC10587348 DOI: 10.1038/s41467-023-41664-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/10/2023] [Indexed: 10/21/2023] Open
Abstract
Recent breakthroughs in highly accurate protein structure prediction using deep neural networks have made considerable progress in solving the structure prediction component of the 'protein folding problem'. However, predicting detailed mechanisms of how proteins fold into specific native structures remains challenging, especially for multidomain proteins constituting most of the proteomes. Here, we develop a simple structure-based statistical mechanical model that introduces nonlocal interactions driving the folding of multidomain proteins. Our model successfully predicts protein folding processes consistent with experiments, without the limitations of protein size and shape. Furthermore, slight modifications of the model allow prediction of disulfide-oxidative and disulfide-intact protein folding. These predictions depict details of the folding processes beyond reproducing experimental results and provide a rationale for the folding mechanisms. Thus, our physics-based models enable accurate prediction of protein folding mechanisms with low computational complexity, paving the way for solving the folding process component of the 'protein folding problem'.
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Affiliation(s)
- Koji Ooka
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
- Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan
| | - Munehito Arai
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
- Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan.
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10
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Arakawa T, Akuta T. Mechanistic Insight into Poly-Reactivity of Immune Antibodies upon Acid Denaturation or Arginine Mutation in Antigen-Binding Regions. Antibodies (Basel) 2023; 12:64. [PMID: 37873861 PMCID: PMC10594486 DOI: 10.3390/antib12040064] [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: 08/08/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
The poly-reactivity of antibodies is defined as their binding to specific antigens as well as to related proteins and also to unrelated targets. Poly-reactivity can occur in individual molecules of natural serum antibodies, likely due to their conformation flexibility, and, for therapeutic antibodies, it plays a critical role in their clinical development. On the one hand, it can enhance their binding to target antigens and cognate receptors, but, on the other hand, it may lead to a loss of antibody function by binding to off-target proteins. Notably, poly-reactivity has been observed in antibodies subjected to treatments with dissociating, destabilizing or denaturing agents, in particular acidic pH, a common step in the therapeutic antibody production process involving the elution of Protein-A bound antibodies and viral clearance using low pH buffers. Additionally, poly-reactivity can emerge during the affinity maturation in the immune system, such as the germinal center. This review delves into the underlying potential causes of poly-reactivity, highlighting the importance of conformational flexibility, which can be further augmented by the acid denaturation of antibodies and the introduction of arginine mutations into the complementary regions of antibody-variable domains. The focus is placed on a particular antibody's acid conformation, meticulously characterized through circular dichroism, differential scanning calorimetry, and sedimentation velocity analyses. By gaining a deeper understanding of these mechanisms, we aim to shed light on the complexities of antibody poly-reactivity and its implications for therapeutic applications.
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Affiliation(s)
- Tsutomu Arakawa
- Alliance Protein Laboratories, 13380 Pantera Road, San Diego, CA 92130, USA
| | - Teruo Akuta
- Research and Development Division, Kyokuto Pharmaceutical Industrial Co., Ltd., 3333-26 Aza-Asayama, Kamitezuna, Takahagi-shi 318-0004, Ibaraki, Japan;
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11
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Sun Q, He X, Fu Y. The "Beacon" Structural Model of Protein Folding: Application for Trp-Cage in Water. Molecules 2023; 28:5164. [PMID: 37446826 DOI: 10.3390/molecules28135164] [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: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Protein folding is a process in which a polypeptide must undergo folding process to obtain its three-dimensional structure. Thermodynamically, it is a process of enthalpy to overcome the loss of conformational entropy in folding. Folding is primarily related to hydrophobic interactions and intramolecular hydrogen bondings. During folding, hydrophobic interactions are regarded to be the driving forces, especially in the initial structural collapse of a protein. Additionally, folding is guided by the strong interactions within proteins, such as intramolecular hydrogen bondings related to the α-helices and β-sheets of proteins. Therefore, a protein is divided into the folding key (FK) regions related to intramolecular hydrogen bondings and the non-folding key (non-FK) regions. Various conformations are expected for FK and non-FK regions. Different from non-FK regions, it is necessary for FK regions to form the specific conformations in folding, which are regarded as the necessary folding pathways (or "beacons"). Additionally, sequential folding is expected for the FK regions, and the intermediate state is found during folding. They are reflected on the local basins in the free energy landscape (FEL) of folding. To demonstrate the structural model, molecular dynamics (MD) simulations are conducted on the folding pathway of the TRP-cage in water.
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Affiliation(s)
- Qiang Sun
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Xian He
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
| | - Yanfang Fu
- Key Laboratory of Orogenic Belts and Crustal Evolution, Ministry of Education, The School of Earth and Space Sciences, Peking University, Beijing 100871, China
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12
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L P Hosszu L, Sangar D, Batchelor M, Risse E, Hounslow AM, Collinge J, Waltho JP, Bieschke J. Loss of residues 119 - 136, including the first β-strand of human prion protein, generates an aggregation-competent partially "open" form. J Mol Biol 2023:168158. [PMID: 37244570 DOI: 10.1016/j.jmb.2023.168158] [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: 11/18/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
In prion replication, the cellular form of prion protein (PrPC) must undergo a full conformational transition to its disease-associated fibrillar form. Transmembrane forms of PrP have been implicated in this structural conversion. The cooperative unfolding of a structural core in PrPC presents a substantial energy barrier to prion formation, with membrane insertion and detachment of parts of PrP presenting a plausible route to its reduction. Here, we examined the removal of residues 119 - 136 of PrP, a region which includes the first β-strand and a substantial portion of the conserved hydrophobic region of PrP, a region which associates with the ER membrane, on the structure, stability and self-association of the folded domain of PrPC. We see an "open" native-like conformer with increased solvent exposure which fibrilises more readily than the native state. These data suggest a stepwise folding transition, which is initiated by the conformational switch to this "open" form of PrPC.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Daljit Sangar
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Mark Batchelor
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Emmanuel Risse
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jan Bieschke
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK.
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13
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Evaluation of a Raman Chemometric Method for Detecting Protein Structural Conformational Changes in Solution. J Pharm Sci 2023; 112:573-586. [PMID: 36152698 DOI: 10.1016/j.xphs.2022.09.006] [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: 02/22/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
Raman scattering shows promise as a powerful routine tool, to determine both secondary and the smaller tertiary structural changes that precede aggregation in both solutions and solids. A method was developed utilizing principal component analysis (PCA) of Raman spectra for detection of small, but meaningful, pH induced changes in tertiary protein structure linked to aggregate formation using α-lactalbumin solutions as a model. The sample preparation and spectral parameters, were optimized for a bulk Raman probe. Analysis of large regions (600-1850 cm-1) yielded principal component (PC) scores useful for semi-quantitative comparison of protein conformation between formulations. PC loadings corresponded to specific structural peaks known to change with solution pH. PCA of circular dichroism (CD) spectra of dilute solutions yielded similar results. Sucrose is a common formulation excipient with a Raman spectrum that overlaps many protein peaks. With sucrose in the protein solution, the ability of PCA to discern protein structural changes from the Raman spectra was somewhat reduced. Analysis of a more limited spectral region (1530-1780 cm-1) with negligible sucrose spectral contribution improved the discrimination of protein conformational states. The new Raman method accurately distinguished differences in protein structure in concentrated solutions. The long-term goal is to explore Raman characterization as a routine monitoring tool of protein stability in both solution and solid states.
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14
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Golub M, Moldenhauer M, Schmitt FJ, Lohstroh W, Friedrich T, Pieper J. Light-Induced Conformational Flexibility of the Orange Carotenoid Protein Studied by Quasielastic Neutron Scattering with In Situ Illumination. J Phys Chem Lett 2023; 14:295-301. [PMID: 36599148 DOI: 10.1021/acs.jpclett.2c03198] [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: 06/17/2023]
Abstract
The orange carotenoid protein plays a vital role in the photoprotection of cyanobacteria and exhibits a significant structural change upon photoactivation. A rarely considered aspect is the importance of internal protein dynamics in facilitating the structural transition to the active state. In this study, we use quasielastic neutron scattering under (in situ) blue light illumination for the first time to directly probe the protein dynamics of the orange carotenoid protein in the dark-adapted and active states. This shows that the localized internal dynamics of amino acid residues is significantly enhanced upon photoactivation. This is attributed to the photoinduced structural changes exposing larger areas of the protein surface to the solvent, thus resulting in a higher degree of motional freedom. However, the flexibility of the W288A mutant assumed to mimic the active state structure is found to be different, thus highlighting the importance of in situ experiments.
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Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, W. Ostwald strasse 1, 50411 Tartu, Estonia
| | - Marcus Moldenhauer
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Franz-Josef Schmitt
- Martin-Luther-Universität Halle Wittenberg, Institute of Physics, Von-Danckelmann-Platz 3, 06120 Halle, Germany
| | - Wiebke Lohstroh
- Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstraße 1, 85748 Garching, Germany
| | - Thomas Friedrich
- Technische Universität Berlin, Institute of Chemistry PC 14, Straße des 17, Juni 135, 10623 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwald strasse 1, 50411 Tartu, Estonia
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15
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Waseem R, Singh Yadav N, Khan T, Ahmad F, Naqui Kazim S, Hassan I, Prakash A, Islam A. Molecular Basis of Structural Stability of Irisin: A Combined Molecular Dynamics Simulation and In vitro Studies for Urea-induced Denaturation. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2022.121120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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16
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Hossain M, Huda N, Bhuyan AK. A surprisingly simple three-state generic process for reversible protein denaturation by trifluoroethanol. Biophys Chem 2022; 291:106895. [PMID: 36182744 DOI: 10.1016/j.bpc.2022.106895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 12/30/2022]
Abstract
Despite the rich knowledge of the influence of 2,2,2-trifluoroethanol (TFE) on the structure and conformation of peptides and proteins, the mode(s) of TFE-protein interactions and the mechanism by which TFE reversibly denatures a globular protein remain elusive. This study systematically examines TFE-induced equilibrium transition curves for six paradigmatic globular proteins by using basic fluorescence and circular dichroism measurements under neutral pH conditions. The results are remarkably simple. Low TFE invariably unfolds the tertiary structure of all proteins to produce the obligate intermediate (I) which retains nearly all of native-state secondary structure, but enables the formation of extra α-helices as the level of TFE is raised higher. Inspection of the transitions at once reveals that the tertiary structure unfolding is always a distinct process, necessitating the inclusion of at least one obligate intermediate in the TFE-induced protein denaturation. It appears that the intermediate in the minimal unfolding mechanism N⇌I⇌D somehow acquires higher α-helical propensity to generate α-helices in excess of that in the native state to produce the denatured state (D), also called the TFE state. The low TFE-populated intermediate I may be called a universal intermediate by virtue of its α-helical propensity. Contrary to many earlier suggestions, this study dismisses molten globule (MG)-like attribute of I or D.
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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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17
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Liu W, Feng Y, Delaplace G, André C, Chen XD. Effect of calcium on the reversible and irreversible thermal denaturation pathway of β-lactoglobulin. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107943] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Finkelstein AV, Bogatyreva NS, Ivankov DN, Garbuzynskiy SO. Protein folding problem: enigma, paradox, solution. Biophys Rev 2022; 14:1255-1272. [PMID: 36659994 PMCID: PMC9842845 DOI: 10.1007/s12551-022-01000-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/19/2022] [Indexed: 01/22/2023] Open
Abstract
The ability of protein chains to spontaneously form their three-dimensional structures is a long-standing mystery in molecular biology. The most conceptual aspect of this mystery is how the protein chain can find its native, "working" spatial structure (which, for not too big protein chains, corresponds to the global free energy minimum) in a biologically reasonable time, without exhaustive enumeration of all possible conformations, which would take billions of years. This is the so-called "Levinthal's paradox." In this review, we discuss the key ideas and discoveries leading to the current understanding of protein folding kinetics, including folding landscapes and funnels, free energy barriers at the folding/unfolding pathways, and the solution of Levinthal's paradox. A special role here is played by the "all-or-none" phase transition occurring at protein folding and unfolding and by the point of thermodynamic (and kinetic) equilibrium between the "native" and the "unfolded" phases of the protein chain (where the theory obtains the simplest form). The modern theory provides an understanding of key features of protein folding and, in good agreement with experiments, it (i) outlines the chain length-dependent range of protein folding times, (ii) predicts the observed maximal size of "foldable" proteins and domains. Besides, it predicts the maximal size of proteins and domains that fold under solely thermodynamic (rather than kinetic) control. Complementarily, a theoretical analysis of the number of possible protein folding patterns, performed at the level of formation and assembly of secondary structures, correctly outlines the upper limit of protein folding times.
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Affiliation(s)
- Alexei V. Finkelstein
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
- Biotechnology Department of the Lomonosov Moscow State University, 4 Institutskaya Str, 142290 Pushchino, Moscow Region, Russia
- Biology Department of the Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Natalya S. Bogatyreva
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
| | - Dmitry N. Ivankov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia
| | - Sergiy O. Garbuzynskiy
- Institute of Protein Research of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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19
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Ahmad A, Mishra R. Polyol and sugar osmolytes stabilize the molten globule state of α-lactalbumin and inhibit amyloid fibril formation. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140853. [PMID: 36096464 DOI: 10.1016/j.bbapap.2022.140853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/29/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Protein misfolding and aggregation are associated with several human diseases such as Alzheimer's, Parkinson's, prion related disorders, type-II diabetes, etc. Different strategies using molecular chaperones, synthetic and naturally occurring small molecules, osmolytes, etc. have been used to prevent protein aggregation and amyloid fibril formation. In this study, we have used bovine α-lactalbumin at pH 1.6, 37 °C, and shaking conditions to promote amyloid fibril formation. Polyol and sugar osmolytes like glycerol, sorbitol, and trehalose have been used to inhibit the fibrillation of a number of proteins. In the present work, amyloid fibril formation of α-lactalbumin has been shown by ThT assay and AFM, while changes in the secondary structure during fibrillation has been followed by circular dichroism spectroscopy. Our results show that glycerol, sorbitol, and trehalose affect amyloid fibril formation of α-lactalbumin in a concentration-dependent manner. There is a delay in the lag phase of amyloid fibril formation in sorbitol and trehalose and complete inhibition in 6 M glycerol. Our results indicate that delay in the lag phase and inhibition of amyloid fibril formation are due to the stabilization of molten globule state by these osmolytes. At pH 1.6, the molten globule as well as the amyloid fibrils bind to ANS. However, when pH was shifted from 1.6 to 7, only the oligomeric and the fibrillar species bind to ANS due to refolding of molten globule state. The outcome of this study might be useful in designing small molecules which may stabilize the intermediate states, thus preventing amyloid fibril formation.
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Affiliation(s)
- Aziz Ahmad
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajesh Mishra
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
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20
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Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:molecules27206861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
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21
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FRTpred: A novel approach for accurate prediction of protein folding rate and type. Comput Biol Med 2022; 149:105911. [DOI: 10.1016/j.compbiomed.2022.105911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/08/2022] [Accepted: 07/23/2022] [Indexed: 11/20/2022]
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22
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Irukuvajjula SS, Reddy JG, Vadrevu R. Crowding by Poly(ethylene glycol) Destabilizes Chemotaxis Protein Y (CheY). Biochemistry 2022; 61:1431-1443. [PMID: 35796609 DOI: 10.1021/acs.biochem.2c00030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The prevailing understanding of various aspects of biochemical processes, including folding, stability, intermolecular interactions, and the binding of metals, substrates, and inhibitors, is derived from studies carried out under dilute and homogeneous conditions devoid of a crowding-related environment. The effect of crowding-induced modulation on the structure and stability of native and magnesium-dependent Chemotaxis Y (CheY), a bacterial signaling protein, was probed in the presence and absence of poly(ethylene glycol) (PEG). A combined analysis from circular dichroism, intrinsic and extrinsic fluorescence, and tryptophan fluorescence lifetime changes indicates that PEG perturbs the structure but leaves the thermal stability largely unchanged. Intriguingly, while the stability of the protein is enhanced in the presence of magnesium under dilute buffer conditions, PEG-induced crowding leads to reduced thermal stability in the presence of magnesium. Nuclear magnetic resonance (NMR) chemical shift perturbations and resonance broadening for a subset of residues indicate that PEG interacts specifically with a subset of hydrophilic and hydrophobic residues found predominantly in α helices, β strands, and in the vicinity of the metal-binding region. Thus, PEG prompted conformational perturbation, presumably provides a different situation for magnesium interaction, thereby perturbing the magnesium-prompted stability. In summary, our results highlight the dominance of enthalpic contributions between PEG and CheY via both hydrophilic and hydrophobic interactions, which can subtly affect the conformation, modulating the metal-protein interaction and stability, implying that in the context of cellular situation, structure, stability, and magnesium binding thermodynamics of CheY may be different from those measured in dilute solution.
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Affiliation(s)
- Shivkumar Sharma Irukuvajjula
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
| | - Jithender G Reddy
- NMR Division, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Ministry of Science and Technology, Uppal Road, Tarnaka, Hyderabad 500007, India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology & Science─Pilani, Hyderabad Campus, Jawahar Nagar, Shamirpet, Hyderabad 500078, India
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23
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Kuwajima K, Yagi-Utsumi M, Yanaka S, Kato K. DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123748. [PMID: 35744871 PMCID: PMC9230524 DOI: 10.3390/molecules27123748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
Hydrogen/deuterium (H/D) exchange combined with two-dimensional (2D) NMR spectroscopy has been widely used for studying the structure, stability, and dynamics of proteins. When we apply the H/D-exchange method to investigate non-native states of proteins such as equilibrium and kinetic folding intermediates, H/D-exchange quenching techniques are indispensable, because the exchange reaction is usually too fast to follow by 2D NMR. In this article, we will describe the dimethylsulfoxide (DMSO)-quenched H/D-exchange method and its applications in protein science. In this method, the H/D-exchange buffer is replaced by an aprotic DMSO solution, which quenches the exchange reaction. We have improved the DMSO-quenched method by using spin desalting columns, which are used for medium exchange from the H/D-exchange buffer to the DMSO solution. This improvement has allowed us to monitor the H/D exchange of proteins at a high concentration of salts or denaturants. We describe methodological details of the improved DMSO-quenched method and present a case study using the improved method on the H/D-exchange behavior of unfolded human ubiquitin in 6 M guanidinium chloride.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (K.K.); (K.K.)
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
| | - Saeko Yanaka
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems and Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan; (M.Y.-U.); (S.Y.)
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (the Graduate University for Advanced Studies), 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Aichi, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Aichi, Japan
- Correspondence: (K.K.); (K.K.)
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24
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Hovan A, Sedláková D, Berta M, Bánó G, Sedlák E. Singlet oxygen quenching as a probe for cytochrome c molten globule state formation. Phys Chem Chem Phys 2022; 24:13317-13324. [PMID: 35608043 DOI: 10.1039/d2cp01281b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Singlet oxygen refers to the nonradical metastable excited state of molecular oxygen that readily oxidizes various cellular components. Its behavior in different biological systems has been studied for many years. Recently, we analyzed the effect of singlet oxygen quenching by heme cofactor in cytochrome c (cyt c). Here, we have exploited this effect in the investigation of conformational differences in the molten globule states of cyt c induced by different sodium anions, namely sulfate, chloride and perchlorate. The high efficiency of heme toward quenching singlet oxygen enabled us to use this property for the analysis of the otherwise experimentally difficult-to-determine parameter of heme upon exposure to solvents as highly similar conformational states of cyt c in the molten globule states are induced by different salts at acidic pH. Our results from singlet oxygen quenching experiments correlate well with other spectroscopic methods, such as circular dichroism and fluorescence measurements, and suggest increasing availability of heme in the order: perchlorate < chloride < sulfate. Based on our findings we propose that singlet oxygen phosphorescence measurements are useful in determining the differences in the protein conformation of their heme regions, particularly regarding the relative heme exposure to the solvent.
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Affiliation(s)
- Andrej Hovan
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia
| | - Gregor Bánó
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia
| | - Erik Sedlák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University in Košice, Jesenná 5, 041 54 Košice, Slovakia
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25
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Fedorov AN. Biosynthetic Protein Folding and Molecular Chaperons. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:S128-S19. [PMID: 35501992 DOI: 10.1134/s0006297922140115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The problem of linear polypeptide chain folding into a unique tertiary structure is one of the fundamental scientific challenges. The process of folding cannot be fully understood without its biological context, especially for big multidomain and multisubunit proteins. The principal features of biosynthetic folding are co-translational folding of growing nascent polypeptide chains and involvement of molecular chaperones in the process. The review summarizes available data on the early events of nascent chain folding, as well as on later advanced steps, including formation of elements of native structure. The relationship between the non-uniformity of translation rate and folding of the growing polypeptide is discussed. The results of studies on the effect of biosynthetic folding features on the parameters of folding as a physical process, its kinetics and mechanisms, are presented. Current understanding and hypotheses on the relationship of biosynthetic folding with the fundamental physical parameters and current views on polypeptide folding in the context of energy landscapes are discussed.
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Affiliation(s)
- Alexey N Fedorov
- Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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26
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Tashiro D, Suetaka S, Sato N, Ooka K, Kunihara T, Kudo H, Inatomi J, Hayashi Y, Arai M. Intron-Encoded Domain of Herstatin, An Autoinhibitor of Human Epidermal Growth Factor Receptors, Is Intrinsically Disordered. Front Mol Biosci 2022; 9:862910. [PMID: 35573740 PMCID: PMC9100580 DOI: 10.3389/fmolb.2022.862910] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/31/2022] [Indexed: 11/17/2022] Open
Abstract
Human epidermal growth factor receptors (HER/ERBB) form dimers that promote cell proliferation, migration, and differentiation, but overexpression of HER proteins results in cancer. Consequently, inhibitors of HER dimerization may function as effective antitumor drugs. An alternatively spliced variant of HER2, called herstatin, is an autoinhibitor of HER proteins, and the intron 8-encoded 79-residue domain of herstatin, called Int8, binds HER family receptors even in isolation. However, the structure of Int8 remains poorly understood. Here, we revealed by circular dichroism, NMR, small-angle X-ray scattering, and structure prediction that isolated Int8 is largely disordered but has a residual helical structure. The radius of gyration of Int8 was almost the same as that of fully unfolded states, although the conformational ensemble of Int8 was less flexible than random coils. These results demonstrate that Int8 is intrinsically disordered. Thus, Int8 is an interesting example of an intrinsically disordered region with tumor-suppressive activity encoded by an intron. Furthermore, we show that the R371I mutant of Int8, which is defective in binding to HER2, is prone to aggregation, providing a rationale for the loss of function.
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Affiliation(s)
- Daisuke Tashiro
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Shunji Suetaka
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Nao Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Koji Ooka
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomoko Kunihara
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Hisashi Kudo
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Junichi Inatomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Yuuki Hayashi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Munehito Arai
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Physics, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- *Correspondence: Munehito Arai,
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27
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Robson B. De novo protein folding on computers. Benefits and challenges. Comput Biol Med 2022; 143:105292. [PMID: 35158120 DOI: 10.1016/j.compbiomed.2022.105292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/05/2023]
Abstract
There has been recent success in prediction of the three-dimensional folded native structures of proteins, most famously by the AlphaFold Algorithm running on Google's/Alphabet's DeepMind computer. However, this largely involves machine learning of protein structures and is not a de novo protein structure prediction method for predicting three-dimensional structures from amino acid residue sequences. A de novo approach would be based almost entirely on general principles of energy and entropy that govern protein folding energetics, and importantly do so without the use of the amino acid sequences and structural features of other proteins. Most consider that problem as still unsolved even though it has occupied leading scientists for decades. Many consider that it remains one of the major outstanding issues in modern science. There is crucial continuing help from experimental findings on protein unfolding and refolding in the laboratory, but only to a limited extent because many researchers consider that the speed by which real proteins folds themselves, often from milliseconds to minutes, is itself still not fully understood. This is unfortunate, because a practical solution to the problem would probably have a major effect on personalized medicine, the pharmaceutical industry, biotechnology, and nanotechnology, including for example "smaller" tasks such as better modeling of flexible "unfolded" regions of the SARS-COV-2 spike glycoprotein when interacting with its cell receptor, antibodies, and therapeutic agents. Some important ideas from earlier studies are given before moving on to lessons from periodic and aperiodic crystals, and a possible role for quantum phenomena. The conclusion is that better computation of entropy should be the priority, though that is presented guardedly.
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Affiliation(s)
- Barry Robson
- Ingine Inc.Cleveland Ohio and The Dirac Foundation, Oxfordshire, UK.
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28
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Khechinashvili NN, Kondratyev MS, Polozov RV. Thermodynamics of globular protein native structure. J Biomol Struct Dyn 2022; 41:3218-3221. [PMID: 35345984 DOI: 10.1080/07391102.2022.2046637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The temperature dependence of the partial heat capacity of the native protein structure in an aqueous solution has been analyzed. It is shown that the strictly linear temperature dependence is due to the contributions of the vibrational and conformational components, which indicates volume consistensy and the absence of conformational transitions up to the main two-state transition. The two-level structural and functional organization of the protein three-dimensional structure are considered in relation to the energy and conformational entropy properties in accordance with the principles of the organization of the protein macromolecule.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Maxim S Kondratyev
- Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Robert V Polozov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
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29
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Molten globule-like transition state of protein barnase measured with calorimetric force spectroscopy. Proc Natl Acad Sci U S A 2022; 119:e2112382119. [PMID: 35271392 PMCID: PMC8931224 DOI: 10.1073/pnas.2112382119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Understanding the molecular forces driving the unfolded polypeptide chain to self-assemble into a functional native structure remains an open question. However, identifying the states visited during protein folding (e.g., the transition state between the unfolded and native states) is tricky due to their transient nature. Here, we introduce calorimetric force spectroscopy in a temperature jump optical trap to determine the enthalpy, entropy, and heat capacity of the transition state of protein barnase. We find that the transition state has the properties of a dry molten globule, that is, high free energy and low configurational entropy, being structurally similar to the native state. This experimental single-molecule study characterizes the thermodynamic properties of the transition state in funneled energy landscapes. Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native conformation of globular proteins; however, its thermodynamic properties are poorly known. We perform single-molecule pulling experiments of protein barnase in the range of 7 ∘C to 37 ∘C using a temperature-jump optical trap. We derive the folding free energy, entropy and enthalpy, and heat capacity change (ΔCp = 1,050 ± 50 cal/mol·K) at low ionic strength conditions. From the measured unfolding and folding kinetic rates, we also determine the thermodynamic properties of the transition state, finding a significant change in ΔCp (∼90%) between the unfolded and the transition states. In contrast, the major change in enthalpy (∼80%) occurs between the transition and native states. These results highlight a transition state of high energy and low configurational entropy structurally similar to the native state, in agreement with the molten globule hypothesis.
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30
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Mohammad Zakariya S, Zaman M, Nabi F, Moasfar Ali S, Jahan I, Nayeem SM, Khan RH. The inhibitory effect of Sunset Yellow on thermally induced Human Serum Albumin aggregates: Possible role in naturopathy. Int J Biol Macromol 2022; 199:181-188. [PMID: 34973990 DOI: 10.1016/j.ijbiomac.2021.12.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/11/2021] [Accepted: 12/19/2021] [Indexed: 11/25/2022]
Abstract
Intensive research in the field of protein aggregation confirmed that the deposition of amyloid fibrils of proteins are the major cause for the development of various neurotoxic and neurodegenerative diseases, which could be controlled by ensuring the efficient inhibition of aggregation using anti aggregation strategies. Herein, we elaborated the anti amyloidogenic potential of Sunset Yellow (SY) dye against Human Serum Albumin (HSA) fibrillogenesis utilising different biophysical, computational and microscopic techniques. The inhibitory effect of sunset yellow was confirmed by Rayleigh Light Scattering (RLS) measurements along with different dye binding assays (ANS, ThT and CR) by showing concentration dependent reduction in scattering intensity and fluorescence intensity respectively. Further, destabilization and anti fibrillation activity of HSA aggregates were characterized through spectroscopic techniques like Circular Dichroism (CD) and other microscopic techniques like Transmission Electron Microscopy (TEM) for elucidating the structural properties. The SDS-PAGE was also carried out that render the disaggregation effect of the dye on the protein. Moreover, Molecular Docking studies revealed the binding parameters justifying the stable protein-dye complex. Simulation studies were also performed accordingly. Thus, this dye which is used as food additive can serve as a potential aggregation inhibiting agent that can aid in the prevention of amyloidogenic diseases.
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Affiliation(s)
| | - Masihuz Zaman
- Centre for Research in Basic Sciences, Jamia Millia Islamia, New Delhi.
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India.
| | - Syed Moasfar Ali
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India.
| | - Ishrat Jahan
- Department of Chemistry, Aligarh Muslim University Aligarh, UP, India.
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University Aligarh, UP, India.
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
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31
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Bondos SE, Dunker AK, Uversky VN. Intrinsically disordered proteins play diverse roles in cell signaling. Cell Commun Signal 2022; 20:20. [PMID: 35177069 PMCID: PMC8851865 DOI: 10.1186/s12964-022-00821-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/11/2021] [Indexed: 11/29/2022] Open
Abstract
Abstract Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple pathways, all while ensuring fidelity of the process. This sensitivity, adaptability, and tunability are possible, in part, due to the inclusion of intrinsically disordered regions in many proteins involved in cell signaling. The goal of this collection is to highlight the many roles of intrinsic disorder in cell signaling. Following an overview of resources that can be used to study intrinsically disordered proteins, this review highlights the critical role of intrinsically disordered proteins for signaling in widely diverse organisms (animals, plants, bacteria, fungi), in every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine) and at each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process. Thus, a cell signaling pathway cannot be fully described without understanding how intrinsically disordered protein regions contribute to its function. The ubiquitous presence of intrinsic disorder in different stages of diverse cell signaling pathways suggest that more mechanisms by which disorder modulates intra- and inter-cell signals remain to be discovered. Graphical abstract ![]()
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Affiliation(s)
- Sarah E Bondos
- Department of Molecular and Cellular Medicine, Texas A&M Health Science Center, College Station, TX, 77843, USA.
| | - A Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Pushchino, Moscow Region, Russia, 142290
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32
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Singh V, Singh R, Kumar D, Mahdi AA, Tripathi AK. A new variant of the human α-lactalbumin-oleic acid complex as an anticancer agent for chronic myeloid leukemia. J Med Life 2022; 14:620-635. [PMID: 35027964 PMCID: PMC8742887 DOI: 10.25122/jml-2021-0065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 06/09/2021] [Indexed: 11/21/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder of hematopoietic stem cells. Although there have been advancements in treatment, there is still a need to develop a biotherapeutic agent. A new variant of the human alpha-lactalbumin-oleic acid (HALOA) complex has been synthesized, which showed similarities with SNARE. The native α-LA was treated with EDTA to remove Ca2+ ions confirmed by ICP-OES and Arsenazo III to unfold and attain apo structure. The apo LA was mixed with OA in a specific ratio, leading to HALOA complex formation. The conformational state from native to complex was elucidated by circular dichroism (far; 190–260 nm and near; 260–340 nm UV-CD), which confirmed that the complex consists of a majority of turns and β-sheet structure. SDS-PAGE result showed the masking effect of OA on apo α-LA. In the lane of the complex, there was no band detected. However, 1-anilino-8-naphthalene sulfonate (ANS) dye has shown maximum fluorescence intensity with the complex because of the availability of hydrophobic patches, which was further validated by NMR spectroscopy indicating the masking effect of OA on the apo α-LA. The SNARE behavior of the complex (500 nm) has been confirmed by TEM. This new structural variant complex shows anti-tumor activity on chronic myeloid leukemia by targeting the IL-8, survivin, and induces apoptosis through DNA fragmentation, but not against normal cells. Overall, the formulated complex shows that SNARE-like behavior can be used as a promising anti-tumor agent with lower toxicity and maximum bioavailability.
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Affiliation(s)
- Vivek Singh
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Ranjana Singh
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Dinesh Kumar
- Centre of Biomedical Research, Sanjay Gandhi Post-Graduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Abbas Ali Mahdi
- Department of Biochemistry, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anil Kumar Tripathi
- Department of Clinical Hematology, King George's Medical University, Lucknow, Uttar Pradesh, India
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33
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Neira JL, Araujo-Abad S, Cámara-Artigas A, Rizzuti B, Abian O, Giudici AM, Velazquez-Campoy A, de Juan Romero C. Biochemical and biophysical characterization of PADI4 supports its involvement in cancer. Arch Biochem Biophys 2022; 717:109125. [DOI: 10.1016/j.abb.2022.109125] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/12/2022]
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34
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Parray ZA, Naqvi AAT, Ahmad F, Hassan MI, Islam A. Characterization of different intermediate states in myoglobin induced by polyethylene glycol: A process of spontaneous molecular self-organization foresees the energy landscape theory via in vitro and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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35
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Cai S, Kumar R, Singh BR. Clostridial Neurotoxins: Structure, Function and Implications to Other Bacterial Toxins. Microorganisms 2021; 9:2206. [PMID: 34835332 PMCID: PMC8618262 DOI: 10.3390/microorganisms9112206] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 01/20/2023] Open
Abstract
Gram-positive bacteria are ancient organisms. Many bacteria, including Gram-positive bacteria, produce toxins to manipulate the host, leading to various diseases. While the targets of Gram-positive bacterial toxins are diverse, many of those toxins use a similar mechanism to invade host cells and exert their functions. Clostridial neurotoxins produced by Clostridial tetani and Clostridial botulinum provide a classical example to illustrate the structure-function relationship of bacterial toxins. Here, we critically review the recent progress of the structure-function relationship of clostridial neurotoxins, including the diversity of the clostridial neurotoxins, the mode of actions, and the flexible structures required for the activation of toxins. The mechanism clostridial neurotoxins use for triggering their activity is shared with many other Gram-positive bacterial toxins, especially molten globule-type structures. This review also summarizes the implications of the molten globule-type flexible structures to other Gram-positive bacterial toxins. Understanding these highly dynamic flexible structures in solution and their role in the function of bacterial toxins not only fills in the missing link of the high-resolution structures from X-ray crystallography but also provides vital information for better designing antidotes against those toxins.
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Affiliation(s)
- Shuowei Cai
- Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA 02747, USA
| | - Raj Kumar
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA; (R.K.); (B.R.S.)
| | - Bal Ram Singh
- Botulinum Research Center, Institute of Advanced Sciences, Dartmouth, MA 02747, USA; (R.K.); (B.R.S.)
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36
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Dingfelder F, Macocco I, Benke S, Nettels D, Faccioli P, Schuler B. Slow Escape from a Helical Misfolded State of the Pore-Forming Toxin Cytolysin A. JACS AU 2021; 1:1217-1230. [PMID: 34467360 PMCID: PMC8397351 DOI: 10.1021/jacsau.1c00175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Indexed: 05/12/2023]
Abstract
The pore-forming toxin cytolysin A (ClyA) is expressed as a large α-helical monomer that, upon interaction with membranes, undergoes a major conformational rearrangement into the protomer conformation, which then assembles into a cytolytic pore. Here, we investigate the folding kinetics of the ClyA monomer with single-molecule Förster resonance energy transfer spectroscopy in combination with microfluidic mixing, stopped-flow circular dichroism experiments, and molecular simulations. The complex folding process occurs over a broad range of time scales, from hundreds of nanoseconds to minutes. The very slow formation of the native state occurs from a rapidly formed and highly collapsed intermediate with large helical content and nonnative topology. Molecular dynamics simulations suggest pronounced non-native interactions as the origin of the slow escape from this deep trap in the free-energy surface, and a variational enhanced path-sampling approach enables a glimpse of the folding process that is supported by the experimental data.
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Affiliation(s)
- Fabian Dingfelder
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Iuri Macocco
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- SISSA, Via Bonomea 265, 34136 Trieste, Italy
| | - Stephan Benke
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pietro Faccioli
- Department
of Physics, Trento University, Via Sommarive 14, 38123 Povo (Trento), Italy
- INFN-TIFPA, Via Sommarive 14, 38123 Povo (Trento), Italy
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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37
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Rose GD. Protein folding - seeing is deceiving. Protein Sci 2021; 30:1606-1616. [PMID: 33938055 PMCID: PMC8284583 DOI: 10.1002/pro.4096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/24/2021] [Accepted: 04/30/2021] [Indexed: 11/13/2022]
Abstract
This Perspective is intended to raise questions about the conventional interpretation of protein folding. According to the conventional interpretation, developed over many decades, a protein population can visit a vast number of conformations under unfolding conditions, but a single dominant native population emerges under folding conditions. Accordingly, folding comes with a substantial loss of conformational entropy. How is this price paid? The conventional answer is that favorable interactions between and among the side chains can compensate for entropy loss, and moreover, these interactions are responsible for the structural particulars of the native conformation. Challenging this interpretation, the Perspective introduces a proposal that high energy (i.e., unfavorable) excluding interactions winnow the accessible population substantially under physical-chemical conditions that favor folding. Both steric clash and unsatisfied hydrogen bond donors and acceptors are classified as excluding interactions, so called because conformers with such disfavored interactions will be largely excluded from the thermodynamic population. Both excluding interactions and solvent factors that induce compactness are somewhat nonspecific, yet together they promote substantial chain organization. Moreover, proteins are built on a backbone scaffold consisting of α-helices and strands of β-sheet, where the number of hydrogen bond donors and acceptors is exactly balanced. These repetitive secondary structural elements are the only two conformers that can be both completely hydrogen-bond satisfied and extended indefinitely without encountering a steric clash. Consequently, the number of fundamental folds is limited to no more than ~10,000 for a protein domain. Once excluding interactions are taken into account, the issue of "frustration" is largely eliminated and the Levinthal paradox is resolved. Putting the "bottom line" at the top: it is likely that hydrogen-bond satisfaction represents a largely under-appreciated parameter in protein folding models.
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Affiliation(s)
- George D. Rose
- T.C. Jenkins Department of BiophysicsJohns Hopkins UniversityBaltimoreMarylandUSA
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38
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The Right-Handed Parallel β-Helix Topology of Erwinia chrysanthemi Pectin Methylesterase Is Intimately Associated with Both Sequential Folding and Resistance to High Pressure. Biomolecules 2021; 11:biom11081083. [PMID: 34439750 PMCID: PMC8392785 DOI: 10.3390/biom11081083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/01/2021] [Accepted: 07/03/2021] [Indexed: 11/30/2022] Open
Abstract
The complex topologies of large multi-domain globular proteins make the study of their folding and assembly particularly demanding. It is often characterized by complex kinetics and undesired side reactions, such as aggregation. The structural simplicity of tandem-repeat proteins, which are characterized by the repetition of a basic structural motif and are stabilized exclusively by sequentially localized contacts, has provided opportunities for dissecting their folding landscapes. In this study, we focus on the Erwinia chrysanthemi pectin methylesterase (342 residues), an all-β pectinolytic enzyme with a right-handed parallel β-helix structure. Chemicals and pressure were chosen as denaturants and a variety of optical techniques were used in conjunction with stopped-flow equipment to investigate the folding mechanism of the enzyme at 25 °C. Under equilibrium conditions, both chemical- and pressure-induced unfolding show two-state transitions, with average conformational stability (ΔG° = 35 ± 5 kJ·mol−1) but exceptionally high resistance to pressure (Pm = 800 ± 7 MPa). Stopped-flow kinetic experiments revealed a very rapid (τ < 1 ms) hydrophobic collapse accompanied by the formation of an extended secondary structure but did not reveal stable tertiary contacts. This is followed by three distinct cooperative phases and the significant population of two intermediate species. The kinetics followed by intrinsic fluorescence shows a lag phase, strongly indicating that these intermediates are productive species on a sequential folding pathway, for which we propose a plausible model. These combined data demonstrate that even a large repeat protein can fold in a highly cooperative manner.
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Talha M, Mir AR, Habib S, Abidi M, Warsi MS, Islam S. Hydroxyl radical induced structural perturbations make insulin highly immunogenic and generate an auto-immune response in type 2 diabetes mellitus. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 255:119640. [PMID: 33744841 DOI: 10.1016/j.saa.2021.119640] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/18/2021] [Accepted: 02/21/2021] [Indexed: 06/12/2023]
Abstract
Reactive oxygen species (ROS) cause oxidative damage to proteins and generate deleterious by-products which induce a breakdown of immune tolerance and produce antibodies against host macromolecules with implication in human diseases. This study characterizes the hydroxyl radical (OH) modifications of insulin, evaluates its cytotoxicity and immunogenicity, and probes its role in type 2 diabetes (T2DM) autoimmunity. The results demonstrate susceptibility of insulin to modifications induced by OH, causing exposure of its chromophoric aromatic amino acid residues, quenching of tyrosine fluorescence intensity, loss of α-helix and gain in β content. Modification causes re-arrangement of native interactions of the aromatic residues in insulin. It enhanced the carbonyl content in insulin, exposed its hydrophobic patches and generated non-fibrillar, amorphous type of aggregates that are cytotoxic in nature. Native insulin induced low titre antibodies in immunized rabbits, whereas OH modified insulin generated a strong immune response. Competitive ELISA studies showed high specificity of antibodies generated against OH modified insulin towards the modified protein. Cross reaction studies showed the presence of common antigenic determinants on various oxidised proteins. Since T2DM patients show increased ROS production, oxidation of insulin is expected to occur, which might amplify autoimmune reactions against insulin. True to the assumption, direct binding ELISA showed the presence of anti-OH insulin circulating antibodies in T2DM patients which are specific for the oxidized insulin. In conclusion, insulin loses structural integrity to OH, forms cytotoxic amorphous aggregates, turns highly immunogenic and elicits humoral response in T2DM patients.
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Affiliation(s)
- Mohd Talha
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Safia Habib
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Minhal Abidi
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Sharib Warsi
- Department of Biochemistry, Jawaharlal Nehru Medical College, Faculty of Medicine, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Sidra Islam
- Department of Pathology, Case Western Reserve University, Cleveland, OH, USA
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40
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Hutchinson RB, Chen X, Zhou N, Cavagnero S. Fluorescence Anisotropy Decays and Microscale-Volume Viscometry Reveal the Compaction of Ribosome-Bound Nascent Proteins. J Phys Chem B 2021; 125:6543-6558. [PMID: 34110829 PMCID: PMC8741338 DOI: 10.1021/acs.jpcb.1c04473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This work introduces a technology that combines fluorescence anisotropy decay with microscale-volume viscometry to investigate the compaction and dynamics of ribosome-bound nascent proteins. Protein folding in the cell, especially when nascent chains emerge from the ribosomal tunnel, is poorly understood. Previous investigations based on fluorescence anisotropy decay determined that a portion of the ribosome-bound nascent protein apomyoglobin (apoMb) forms a compact structure. This work, however, could not assess the size of the compact region. The combination of fluorescence anisotropy with microscale-volume viscometry, presented here, enables identifying the size of compact nascent-chain subdomains using a single fluorophore label. Our results demonstrate that the compact region of nascent apoMb contains 57-83 amino acids and lacks residues corresponding to the two native C-terminal helices. These amino acids are necessary for fully burying the nonpolar residues in the native structure, yet they are not available for folding before ribosome release. Therefore, apoMb requires a significant degree of post-translational folding for the generation of its native structure. In summary, the combination of fluorescence anisotropy decay and microscale-volume viscometry is a powerful approach to determine the size of independently tumbling compact regions of biomolecules. This technology is of general applicability to compact macromolecules linked to larger frameworks.
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Affiliation(s)
| | - Xi Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ningkun Zhou
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Silvia Cavagnero
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
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41
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Di Rocco G, Bighi B, Borsari M, Bortolotti CA, Ranieri A, Sola M, Battistuzzi G. Electron Transfer and Electrocatalytic Properties of the Immobilized Met80Ala Cytochrome
c
Variant in Dimethylsulfoxide. ChemElectroChem 2021. [DOI: 10.1002/celc.202100499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Giulia Di Rocco
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Beatrice Bighi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Borsari
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Carlo Augusto Bortolotti
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Antonio Ranieri
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Marco Sola
- Department of Life Sciences University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry and Geology University of Modena and Reggio Emilia via Campi 103 41125 Modena Italy
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42
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Hydrophobicity, amphilicity, and flexibility: Relation between molecular protein properties and the macroscopic effects of surface activity. J Biotechnol 2021; 334:11-25. [PMID: 34015375 DOI: 10.1016/j.jbiotec.2021.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 04/16/2021] [Accepted: 05/05/2021] [Indexed: 11/24/2022]
Abstract
Their surface activity enables proteins to form and stabilize foam, which can be used for in situ product separation or foam fractionation. Thus, it would be highly desirable to predict the surface activity of proteins based on their molecular properties like hydrophobicity, amphilicity, or structure on primary, secondary, and tertiary level. Ionic strength and pH were adjusted to gain maximum surface activity. The surface activity decreased in the order α lactalbumin > β‑lactoglobulin > trypsinogen > papain. For the theoretical analysis, the database was extended by including 2 hydrophobins into the investigation, since they are known to exhibit an outstanding surface activity. No relation to the macroscopic behavior was found considering the hydrophobicity. I.e., the non-hydrophobins did not differ significantly from each other, and from the hydrophobins, one was significantly hydrophobic, and the other was significantly hydrophilic. Also, no relations were found considering the amphilicity of the secondary structure elements. However, taking into account the tertiary protein structure, it was found that for most of the proteins investigated, the presence of non-buried amphiphilic secondary structure elements in combination with a certain amount of flexibility correlates with the surface activity.
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43
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Chikunova A, Manley MP, Ud Din Ahmad M, Bilman T, Perrakis A, Ubbink M. Conserved residues Glu37 and Trp229 play an essential role in protein folding of β‐lactamase. FEBS J 2021; 288:5708-5722. [PMID: 33792206 PMCID: PMC8518976 DOI: 10.1111/febs.15854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 02/26/2021] [Accepted: 03/30/2021] [Indexed: 01/27/2023]
Abstract
Evolutionary robustness requires that the number of highly conserved amino acid residues in proteins is minimized. In enzymes, such conservation is observed for catalytic residues but also for some residues in the second shell or even further from the active site. β‐Lactamases evolve in response to changing antibiotic selection pressures and are thus expected to be evolutionarily robust, with a limited number of highly conserved amino acid residues. As part of the effort to understand the roles of conserved residues in class A β‐lactamases, we investigate the reasons leading to the conservation of two amino acid residues in the β‐lactamase BlaC, Glu37, and Trp229. Using site‐directed mutagenesis, we have generated point mutations of these residues and observed a drastic decrease in the levels of soluble protein produced in Escherichia coli, thus abolishing completely the resistance of bacteria against β‐lactam antibiotics. However, the purified proteins are structurally and kinetically very similar to the wild‐type enzyme, only differing by exhibiting a slightly lower melting temperature. We conclude that conservation of Glu37 and Trp229 is solely caused by an essential role in the folding process, and we propose that during folding Glu37 primes the formation of the central β‐sheet and Trp229 contributes to the hydrophobic collapse into a molten globule.
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Affiliation(s)
| | - Max P. Manley
- Leiden Institute of Chemistry Leiden University the Netherlands
| | - Misbha Ud Din Ahmad
- Oncode Institute and Division of Biochemistry the Netherlands Cancer Institute Amsterdam the Netherlands
| | - Tuğçe Bilman
- Leiden Institute of Chemistry Leiden University the Netherlands
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry the Netherlands Cancer Institute Amsterdam the Netherlands
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Uppal S, Khan MA, Kundu S. Stability and Folding of the Unusually Stable Hemoglobin from Synechocystis is Subtly Optimized and Dependent on the Key Heme Pocket Residues. Protein Pept Lett 2021; 28:164-182. [PMID: 32533815 DOI: 10.2174/0929866527666200613220245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/20/2020] [Accepted: 04/24/2020] [Indexed: 11/22/2022]
Abstract
AIMS The aim of our study is to understand the biophysical traits that govern the stability and folding of Synechocystis hemoglobin, a unique cyanobacterial globin that displays unusual traits not observed in any of the other globins discovered so far. BACKGROUND For the past few decades, classical hemoglobins such as vertebrate hemoglobin and myoglobin have been extensively studied to unravel the stability and folding mechanisms of hemoglobins. However, the expanding wealth of hemoglobins identified in all life forms with novel properties, like heme coordination chemistry and globin fold, have added complexity and challenges to the understanding of hemoglobin stability, which has not been adequately addressed. Here, we explored the unique truncated and hexacoordinate hemoglobin from the freshwater cyanobacterium Synechocystis sp. PCC 6803 known as "Synechocystis hemoglobin (SynHb)". The "three histidines" linkages to heme are novel to this cyanobacterial hemoglobin. OBJECTIVE Mutational studies were employed to decipher the residues within the heme pocket that dictate the stability and folding of SynHb. METHODS Site-directed mutants of SynHb were generated and analyzed using a repertoire of spectroscopic and calorimetric tools. RESULTS The results revealed that the heme was stably associated to the protein under all denaturing conditions with His117 playing the anchoring role. The studies also highlighted the possibility of existence of a "molten globule" like intermediate at acidic pH in this exceptionally thermostable globin. His117 and other key residues in the heme pocket play an indispensable role in imparting significant polypeptide stability. CONCLUSION Synechocystis hemoglobin presents an important model system for investigations of protein folding and stability in general. The heme pocket residues influenced the folding and stability of SynHb in a very subtle and specific manner and may have been optimized to make this Hb the most stable known as of date. Other: The knowledge gained hereby about the influence of heme pocket amino acid side chains on stability and expression is currently being utilized to improve the stability of recombinant human Hbs for efficient use as oxygen delivery vehicles.
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Affiliation(s)
- Sheetal Uppal
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
| | - Mohd Asim Khan
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi, 110021, India
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Neira JL, Cámara-Artigas A, Hernández-Cifre JG, Ortore MG. The Histidine Phosphocarrier Kinase/Phosphorylase from Bacillus Subtilis Is an Oligomer in Solution with a High Thermal Stability. Int J Mol Sci 2021; 22:3231. [PMID: 33810099 PMCID: PMC8004850 DOI: 10.3390/ijms22063231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/12/2021] [Accepted: 03/15/2021] [Indexed: 01/25/2023] Open
Abstract
The histidine phosphocarrier protein (HPr) kinase/phosphorylase (HPrK/P) modulates the phosphorylation state of the HPr protein, and it is involved in the use of carbon sources by Gram-positive bacteria. Its X-ray structure, as concluded from crystals of proteins from several species, is a hexamer; however, there are no studies about its conformational stability, and how its structure is modified by the pH. We have embarked on the conformational characterization of HPrK/P of Bacillus subtilis (bsHPrK/P) in solution by using several spectroscopic (namely, fluorescence and circular dichroism (CD)) and biophysical techniques (namely, small-angle X-ray-scattering (SAXS) and dynamic light-scattering (DLS)). bsHPrK/P was mainly a hexamer in solution at pH 7.0, in the presence of phosphate. The protein had a high conformational stability, with an apparent thermal denaturation midpoint of ~70 °C, at pH 7.0, as monitored by fluorescence and CD. The protein was very pH-sensitive, precipitated between pH 3.5 and 6.5; below pH 3.5, it had a molten-globule-like conformation; and it acquired a native-like structure in a narrow pH range (between pH 7.0 and 8.0). Guanidinium hydrochloride (GdmCl) denaturation occurred through an oligomeric intermediate. On the other hand, urea denaturation occurred as a single transition, in the range of concentrations between 1.8 and 18 µM, as detected by far-UV CD and fluorescence.
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Affiliation(s)
- José L. Neira
- IDIBE, Universidad Miguel Hernández, 03202 Alicante, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - Ana Cámara-Artigas
- Departamento de Química y Física, Research Center CIAIMBITAL, Universidad de Almería- ceiA3, 04120 Almería, Spain;
| | - José Ginés Hernández-Cifre
- Departamento de Química Física, Facultad de Química, Campus de Espinardo, Universidad de Murcia, 30100 Murcia, Spain;
| | - María Grazia Ortore
- Dipartimento DiSVA, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy;
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46
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The concept of protein folding/unfolding and its impacts on human health. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021. [PMID: 34090616 DOI: 10.1016/bs.apcsb.2021.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Proteins have evolved in specific 3D structures and play different functions in cells and determine various reactions and pathways. The newly synthesized amino acid chains once depart ribosome must crumple into three-dimensional structures so can be biologically active. This process of protein that makes a functional molecule is called protein folding. The protein folding is both a biological and a physicochemical process that depends on the sequence of it. In fact, this process occurs more complicated and in some cases and in exposure to some molecules like glucose (glycation), mistaken folding leads to amyloid structures and fatal disorders called conformational diseases. Such conditions are detected by the quality control system of the cell and these abnormal proteins undergo renovation or degradation. This scenario takes place by the chaperones, chaperonins, and Ubiquitin-proteasome complex. Understanding of protein folding mechanisms from different views including experimental and computational approaches has revealed some intermediate ensembles such as molten globule and has been subjected to biophysical and molecular biology attempts to know more about prevalent conformational diseases.
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47
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Mitra R, Gadkari VV, Meinen BA, van Mierlo CPM, Ruotolo BT, Bardwell JCA. Mechanism of the small ATP-independent chaperone Spy is substrate specific. Nat Commun 2021; 12:851. [PMID: 33558474 PMCID: PMC7870927 DOI: 10.1038/s41467-021-21120-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/08/2021] [Indexed: 11/17/2022] Open
Abstract
ATP-independent chaperones are usually considered to be holdases that rapidly bind to non-native states of substrate proteins and prevent their aggregation. These chaperones are thought to release their substrate proteins prior to their folding. Spy is an ATP-independent chaperone that acts as an aggregation inhibiting holdase but does so by allowing its substrate proteins to fold while they remain continuously chaperone bound, thus acting as a foldase as well. The attributes that allow such dual chaperoning behavior are unclear. Here, we used the topologically complex protein apoflavodoxin to show that the outcome of Spy's action is substrate specific and depends on its relative affinity for different folding states. Tighter binding of Spy to partially unfolded states of apoflavodoxin limits the possibility of folding while bound, converting Spy to a holdase chaperone. Our results highlight the central role of the substrate in determining the mechanism of chaperone action.
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Affiliation(s)
- Rishav Mitra
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Ben A Meinen
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - James C A Bardwell
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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Neira JL, Vega S, Martínez-Rodríguez S, Velázquez-Campoy A. The isolated GTPase-activating-protein-related domain of neurofibromin-1 has a low conformational stability in solution. Arch Biochem Biophys 2021; 700:108767. [PMID: 33476564 DOI: 10.1016/j.abb.2021.108767] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 11/28/2022]
Abstract
Neurofibromin-1 (NF1) is a large, multidomain tumour suppressor encoded by the NF1 gene. The gene is mutated in neurofibromatosis type I, a disease characterized by malignant tumours of the nervous system and benign neurofibromas. The best-known activity of NF1 is the down-regulation of the mitogen-activated protein kinase pathway via its three-hundred-residue-long GTPase-activating protein (GAP) domain (the so-called GAP-related domain (NF1-GRD)). The NF1-GRD stimulates Ras GTPase activity in turning off signalling. Despite this activity, NF1-GRD has been demonstrated to bind to other different proteins, such as SPRED1 or MC1R. We have embarked on the biophysical and conformational characterization of NF1-GRD in solution by using several spectroscopic (namely fluorescence and circular dichroism (CD)) and biophysical techniques (namely size exclusion chromatography (SEC) and differential scanning calorimetry (DSC)). This biophysical characterization is crucial in deciphering NF1-GRD interactome and in finding biochemical features, modulating possible protein interactions. The native-like structure of NF1-GRD (as monitored by intrinsic fluorescence and far-UV CD) was strongly pH-dependent showing a pH-titration causing a substantial increase in its helicity. NF1-GRD had a low conformational stability, as concluded from DSC experiments and thermal denaturations followed by intrinsic and ANS fluorescence, and CD. Chemical denaturations showed that NF1-GRD unfolded through an intermediate which has a substantial amount of solvent-exposed hydrophobic patches.
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Affiliation(s)
- José L Neira
- IDIBE, Universidad Miguel Hernández, 03202, Elche, Alicante, Spain; Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009, Zaragoza, Spain.
| | - Sonia Vega
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009, Zaragoza, Spain
| | - Sergio Martínez-Rodríguez
- Laboratorio de Estudios Cristalográficos, CSIC, 18100, Armilla, Granada, Spain; Dpto. Bioquímica y Biología Molecular III e Inmunología, Facultad de Medicina, Universidad de Granada, 18071, Granada, Spain.
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50009, Zaragoza, Spain; Instituto de Investigación Sanitaria Aragón (IIS Aragón), 50009, Zaragoza, Spain; Fundación ARAID, Government of Aragón, 50009, Zaragoza, Spain; Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009, Zaragoza, Spain; Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28006, Madrid, Spain
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Khan SH, Bijpuria S, Maurya A, Taneja B. Structural and thermodynamic characterization of a highly stable conformation of Rv2966c, a 16S rRNA methyltransferase, at low pH. Int J Biol Macromol 2020; 164:3909-3921. [PMID: 32888991 DOI: 10.1016/j.ijbiomac.2020.08.236] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/14/2020] [Accepted: 08/29/2020] [Indexed: 12/01/2022]
Abstract
Rv2966c is a highly specific methyltransferase that methylates G966 at the N2 position in 16S rRNA of mycobacterial ribosome and can be secreted inside the host cell to methylate host DNA. However, how the secreted protein retains its structure and function in the harsh environment of host cell, remains unclear. In this work, we investigate structural features of Rv2966c at pH 4.0 and pH 7.5 by far-UV- and near-UV-circular dichroism (CD) and fluorescence spectroscopy, to gain insights into its folding and stability at the acidic pH, that it is likely to encounter inside the macrophage. We show that Rv2966c exists in a compact, folded state at both pH 7.5 and pH 4.0, a result corroborated by molecular dynamics simulations as a function of pH. In fact, Rv2966c was found to be more stable at pH 4.0 than pH 7.5, as evidenced by thermal-induced CD and nanodifferential scanning fluorimetry, and urea-induced denaturation measurements. Interestingly, unlike pH 7.5 (two-state unfolding), denaturation of Rv2966c at pH 4.0 occurs in a biphasic (N ↔ X ↔ U) manner. Further spectroscopic characterization of 'X' state, identifies characteristics of a molten globule-like intermediate. We finally conclude that Rv2966c maintains a compact folded state at pH 4.0 akin to that at pH 7.5 but with higher stability.
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Affiliation(s)
- Sabab Hasan Khan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shipra Bijpuria
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India; Academy of Scientific and Innovative Research, Ghaziabad, India
| | - Anjali Maurya
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Bhupesh Taneja
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India; Academy of Scientific and Innovative Research, Ghaziabad, India.
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50
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Hilburg SL, Ruan Z, Xu T, Alexander-Katz A. Behavior of Protein-Inspired Synthetic Random Heteropolymers. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01886] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shayna L. Hilburg
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Zhiyuan Ruan
- Department of Materials Science & Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Ting Xu
- Department of Materials Science & Engineering, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Tsinghua−Berkeley Shenzhen Institute, University of California Berkeley, Berkeley, California 94720, United States
- Materials Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Alfredo Alexander-Katz
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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