1
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Gentili PL. The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence. Biomimetics (Basel) 2024; 9:121. [PMID: 38392167 PMCID: PMC10886813 DOI: 10.3390/biomimetics9020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
This work highlights the relevant contribution of conformational stereoisomers to the complexity and functions of any molecular compound. Conformers have the same molecular and structural formulas but different orientations of the atoms in the three-dimensional space. Moving from one conformer to another is possible without breaking covalent bonds. The interconversion is usually feasible through the thermal energy available in ordinary conditions. The behavior of most biopolymers, such as enzymes, antibodies, RNA, and DNA, is understandable if we consider that each exists as an ensemble of conformers. Each conformational collection confers multi-functionality and adaptability to the single biopolymers. The conformational distribution of any biopolymer has the features of a fuzzy set. Hence, every compound that exists as an ensemble of conformers allows the molecular implementation of a fuzzy set. Since proteins, DNA, and RNA work as fuzzy sets, it is fair to say that life's logic is fuzzy. The power of processing fuzzy logic makes living beings capable of swift decisions in environments dominated by uncertainty and vagueness. These performances can be implemented in chemical robots, which are confined molecular assemblies mimicking unicellular organisms: they are supposed to help humans "colonise" the molecular world to defeat diseases in living beings and fight pollution in the environment.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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2
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Lee KH, Kuczera K. Effect of alanine versus serine at position 88 of human transthyretin mutants on the protein stability. Protein Eng Des Sel 2023; 36:6972274. [PMID: 36611015 DOI: 10.1093/protein/gzad001] [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: 09/21/2022] [Revised: 10/22/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023] Open
Abstract
Human transthyretin (TTR) is a homo-tetrameric plasma protein associated with a high percentage of β-sheet forming amyloid fibrils. It accumulates in tissues or extracellular matrices to cause amyloid diseases. Free energy simulations with thermodynamic integration based on all-atom molecular dynamics simulations have been carried out to analyze the effects of the His88 → Ala and Ser mutations on the stability of human TTR. The calculated free energy change differences (ΔΔG) caused by the His88 → Ala and His88 → Ser mutations are -1.84 ± 0.86 and 7.56 ± 0.55 kcal/mol, respectively, which are in excellent agreement with prior reported experimental values. The simulation results show that the H88A mutant is more stable than the wild type, whereas the H88S mutant is less stable than the wild type. The free energy component analysis shows that the contribution to the free energy change difference (ΔΔG) for the His88 → Ala and His88 → Ser mutations mainly arise from electrostatic and van der Waals interactions, respectively. The electrostatic term stabilizes the H88A mutant more than the wild type, but the van der Waals interaction destabilizes the H88S mutant relative to the wild type. Individual residue contributions to the free energy change show neighboring residues exert stabilizing and destabilizing influence on the mutants. The implications of the simulation results for understanding the stabilizing and destabilizing effect and its contribution to protein stability are discussed.
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Affiliation(s)
- Kyung-Hoon Lee
- Department of Biology, Chowan University, One University Place, Murfreesboro, NC 27855, USA
| | - Krzysztof Kuczera
- Department of Chemistry and Department of Molecular Biosciences, University of Kansas, 1567 Irving Hill Road, Lawrence, KS 66045, USA
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3
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Pastore A, Temussi PA. The Protein Unfolded State: One, No One and One Hundred Thousand. J Am Chem Soc 2022; 144:22352-22357. [PMID: 36450361 PMCID: PMC9756289 DOI: 10.1021/jacs.2c07696] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 12/03/2022]
Abstract
Many in vitro studies, in which proteins have been unfolded by the action of a variety of physical or chemical agents, have led to the definition of a folded versus an unfolded state and to the question of what is the nature of the unfolded state. The unstructured nature of this state could suggest that "the" unfolded state is a unique entity which holds true for all kinds of unfolding processes. This assumption has to be questioned because the unfolding processes under different stress conditions are dictated by entirely different mechanisms. As a consequence, it can be easily understood that the final state, generically referred to as "the unfolded state", can be completely different for each of the unfolding processes. The present review examines recent data on the characteristics of the unfolded states emerging from experiments under different conditions, focusing specific attention to the level of compaction of the unfolded species.
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Affiliation(s)
| | - Piero Andrea Temussi
- UK Dementia Research Institute at
the Maurice Wohl Institute of King’s College London, London, SE5 9RT, United Kingdom
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4
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Bitonti A, Puglisi R, Meli M, Martin SR, Colombo G, Temussi PA, Pastore A. Recipes for Inducing Cold Denaturation in an Otherwise Stable Protein. J Am Chem Soc 2022; 144:7198-7207. [PMID: 35427450 PMCID: PMC9052743 DOI: 10.1021/jacs.1c13355] [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] [Indexed: 11/29/2022]
Abstract
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Although cold denaturation
is a fundamental phenomenon common to
all proteins, it can only be observed in a handful of cases where
it occurs at temperatures above the freezing point of water. Understanding
the mechanisms that determine cold denaturation and the rules that
permit its observation is an important challenge. A way to approach
them is to be able to induce cold denaturation in an otherwise stable
protein by means of mutations. Here, we studied CyaY, a relatively
stable bacterial protein with no detectable cold denaturation and
a high melting temperature of 54 °C. We have characterized for
years the yeast orthologue of CyaY, Yfh1, a protein that undergoes
cold and heat denaturation at 5 and 35 °C, respectively. We demonstrate
that, by transferring to CyaY the lessons learnt from Yfh1, we can
induce cold denaturation by introducing a restricted number of carefully
designed mutations aimed at destabilizing the overall fold and inducing
electrostatic frustration. We used molecular dynamics simulations
to rationalize our findings and demonstrate the individual effects
observed experimentally with the various mutants. Our results constitute
the first example of rationally designed cold denaturation and demonstrate
the importance of electrostatic frustration on the mechanism of cold
denaturation.
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Affiliation(s)
- Angela Bitonti
- Department of Molecular Medicine, University of Pavia, Via C Forlanini 6, 27100 Pavia, Italy
| | - Rita Puglisi
- UK Dementia Research Institute at the Maurice Wohl Institute of King’s College London, London SE5 9RT, United Kingdom
| | - Massimiliano Meli
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Stephen R. Martin
- Structural Biology Technology Platform, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, United Kingdom
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Torquato Taramelli, 12, Pavia 27100, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King’s College London, London SE5 9RT, United Kingdom
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King’s College London, London SE5 9RT, United Kingdom
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5
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Puglisi R. Protein Mutations and Stability, a Link with Disease: The Case Study of Frataxin. Biomedicines 2022; 10:biomedicines10020425. [PMID: 35203634 PMCID: PMC8962269 DOI: 10.3390/biomedicines10020425] [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: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/16/2022] Open
Abstract
Protein mutations may lead to pathologies by causing protein misfunction or propensity to degradation. For this reason, several studies have been performed over the years to determine the capability of proteins to retain their native conformation under stress condition as well as factors to explain protein stabilization and the mechanisms behind unfolding. In this review, we explore the paradigmatic example of frataxin, an iron binding protein involved in Fe–S cluster biogenesis, and whose impairment causes a neurodegenerative disease called Friedreich’s Ataxia (FRDA). We summarize what is known about most common point mutations identified so far in heterozygous FRDA patients, their effects on frataxin structure and function and the consequences of its binding with partners.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King's College London, London SE59RT, UK
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6
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Guo Z, Parakra RD, Xiong Y, Johnston WA, Walden P, Edwardraja S, Moradi SV, Ungerer JPJ, Ai HW, Phillips JJ, Alexandrov K. Engineering and exploiting synthetic allostery of NanoLuc luciferase. Nat Commun 2022; 13:789. [PMID: 35145068 PMCID: PMC8831504 DOI: 10.1038/s41467-022-28425-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 01/25/2022] [Indexed: 02/08/2023] Open
Abstract
Allostery enables proteins to interconvert different biochemical signals and form complex metabolic and signaling networks. We hypothesize that circular permutation of proteins increases the probability of functional coupling of new N- and C- termini with the protein's active center through increased local structural disorder. To test this we construct a synthetically allosteric version of circular permutated NanoLuc luciferase that can be activated through ligand-induced intramolecular non-covalent cyclisation. This switch module is tolerant of the structure of binding domains and their ligands, and can be used to create biosensors of proteins and small molecules. The developed biosensors covers a range of emission wavelengths and displays sensitivity as low as 50pM and dynamic range as high as 16-fold and could quantify their cognate ligand in human fluids. We apply hydrogen exchange kinetic mass spectroscopy to analyze time resolved structural changes in the developed biosensors and observe ligand-mediated folding of newly created termini.
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Affiliation(s)
- Zhong Guo
- ARC Centre of Excellence in Synthetic Biology, Sydney, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Rinky D Parakra
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Ying Xiong
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Wayne A Johnston
- ARC Centre of Excellence in Synthetic Biology, Sydney, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Patricia Walden
- ARC Centre of Excellence in Synthetic Biology, Sydney, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shayli Varasteh Moradi
- ARC Centre of Excellence in Synthetic Biology, Sydney, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia
| | - Jacobus P J Ungerer
- Department of Chemical Pathology, Pathology Queensland, Brisbane, QLD, 4001, Australia
- Faculty of Health and Behavioural Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, Department of Molecular Physiology and Biological Physics, Department of Chemistry, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Jonathan J Phillips
- Living Systems Institute, Department of Biosciences, University of Exeter, Exeter, EX4 4QD, UK.
- Alan Turing Institute, British Library 96, Euston road, London, NW1 2DB, UK.
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic Biology, Sydney, Australia.
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, 4001, Australia.
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7
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Abstract
The natural function of many proteins depends on their ability to switch their conformation driven by environmental changes. In this work, we present a small, monomeric β-sheet peptide that switches between a molten globule and a folded state through Zn(II) binding. The solvent-exposed hydrophobic core on the β-sheet surface was substituted by a His3-site, whereas the internal hydrophobic core was left intact. Zn(II) is specifically recognized by the peptide relative to other divalent metal ions, binds in the lower micromolar range, and can be removed and re-added without denaturation of the peptide. In addition, the peptide is fully pH-switchable, has a pKa of about 6, and survives several cycles of acidification and neutralization. In-depth structural characterization of the switch was achieved by concerted application of circular dichroism (CD) and multinuclear NMR spectroscopy. Thus, this study represents a viable approach toward a globular β-sheet Zn(II) mini-receptor prototype.
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Affiliation(s)
- Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Michael Kovermann
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
- Centre for Advanced Materials, Heidelberg University, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
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8
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Brylski O, Shrestha P, Gnutt P, Gnutt D, Mueller JW, Ebbinghaus S. Cellular ATP Levels Determine the Stability of a Nucleotide Kinase. Front Mol Biosci 2021; 8:790304. [PMID: 34966785 PMCID: PMC8710738 DOI: 10.3389/fmolb.2021.790304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/26/2021] [Indexed: 11/13/2022] Open
Abstract
The energy currency of the cell ATP, is used by kinases to drive key cellular processes. However, the connection of cellular ATP abundance and protein stability is still under investigation. Using Fast Relaxation Imaging paired with alanine scanning and ATP depletion experiments, we study the nucleotide kinase (APSK) domain of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) synthase, a marginally stable protein. Here, we show that the in-cell stability of the APSK is determined by ligand binding and directly connected to cellular ATP levels. The observed protein stability change for different ligand-bound states or under ATP-depleted conditions ranges from ΔGf 0 = -10.7 to +13.8 kJ/mol, which is remarkable since it exceeds changes measured previously, for example upon osmotic pressure, cellular stress or differentiation. The results have implications for protein stability during the catalytic cycle of APS kinase and suggest that the cellular ATP level functions as a global regulator of kinase activity.
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Affiliation(s)
- Oliver Brylski
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
| | - Puja Shrestha
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Patricia Gnutt
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
| | - David Gnutt
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
| | - Jonathan Wolf Mueller
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, Birmingham, United Kingdom
| | - Simon Ebbinghaus
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
- Institute of Physical Chemistry II, Ruhr University, Bochum, Germany
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9
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Sarimov RM, Binhi VN, Matveeva TA, Penkov NV, Gudkov SV. Unfolding and Aggregation of Lysozyme under the Combined Action of Dithiothreitol and Guanidine Hydrochloride: Optical Studies. Int J Mol Sci 2021; 22:2710. [PMID: 33800175 PMCID: PMC7962454 DOI: 10.3390/ijms22052710] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/16/2022] Open
Abstract
Using a number of optical techniques (interferometry, dynamic light scattering, and spectroscopy), denaturation of hen egg white lysozyme (HEWL) by treatment with a combination of dithiothreitol (DTT) and guanidine hydrochloride (GdnHCl) has been investigated. The denaturing solutions were selected so that protein denaturation occurred with aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM) or without aggregation (Tris-HCl pH = 8.0, 50 mM, DTT 30 mM, GdnHCl 6 M) and can be evaluated after 60 min of treatment. It has been found that denatured by solution with 6 M GdnHCl lysozyme completely loses its enzymatic activity after 30 min and the size of the protein molecule increases by 1.5 times, from 3.8 nm to 5.7 nm. Denaturation without of GdnHCl led to aggregation with preserving about 50% of its enzymatic activity. Denaturation of HEWL was examined using interferometry. Previously, it has been shown that protein denaturation that occurs without subsequent aggregation leads to an increase in the refractive index (Δn ~ 4.5 × 10-5). This is most likely due to variations in the HEWL-solvent interface area. By applying modern optical techniques conjointly, it has been possible to obtain information on the nature of time-dependent changes that occur inside a protein and its hydration shell as it undergoes denaturation.
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Affiliation(s)
- Ruslan M. Sarimov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
| | - Vladimir N. Binhi
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
| | - Tatiana A. Matveeva
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
| | - Nikita V. Penkov
- Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS, Institutskaya St., 3, Pushchino, 142290 Moscow, Russia;
| | - Sergey V. Gudkov
- Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilov St., 38, 119991 Moscow, Russia; (R.M.S.); (V.N.B.); (T.A.M.)
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10
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Puglisi R, Brylski O, Alfano C, Martin SR, Pastore A, Temussi PA. Quantifying the thermodynamics of protein unfolding using 2D NMR spectroscopy. Commun Chem 2020; 3:100. [PMID: 33718626 PMCID: PMC7116895 DOI: 10.1038/s42004-020-00358-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/17/2020] [Indexed: 01/13/2023] Open
Abstract
A topic that has attracted considerable interest in recent years is the possibility to perform thermodynamic studies of proteins directly in-cell or in complex environments which mimic the cellular interior. Nuclear magnetic resonance (NMR) could be an attractive technique for these studies but its applicability has so far been limited by technical issues. Here, we demonstrate that 2D NMR methods can be successfully applied to measure thermodynamic parameters provided that a suitable choice of the residues used for the calculation is made. We propose a new parameter, named RAD, which reflects the level of protection of a specific amide proton in the protein core and can guide through the selection of the resonances. We also suggest a way to calibrate the volumes to become independent of technical limitations. The methodology we propose leads to stability curves comparable to that calculated from CD data and provides a new tool for thermodynamic measurements in complex environments.
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Affiliation(s)
- Rita Puglisi
- UK-DRI at the Wohl Institute of King’s College London, 5 Cutcombe Road, SE59RT London, UK
| | - Oliver Brylski
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | - Annalisa Pastore
- UK-DRI at the Wohl Institute of King’s College London, 5 Cutcombe Road, SE59RT London, UK
| | - Piero A. Temussi
- UK-DRI at the Wohl Institute of King’s College London, 5 Cutcombe Road, SE59RT London, UK
- Dipartimento di Scienze Chimiche, Universita’ di Napoli Federico II, Napoli, Italy
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11
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Puglisi R, Boeri Erba E, Pastore A. A Guide to Native Mass Spectrometry to determine complex interactomes of molecular machines. FEBS J 2020; 287:2428-2439. [PMID: 32142206 PMCID: PMC8647915 DOI: 10.1111/febs.15281] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/01/2020] [Accepted: 03/04/2020] [Indexed: 01/17/2023]
Abstract
Native mass spectrometry is an emerging technique in biology that gives the possibility to study noncovalently bound complexes with high sensitivity and accuracy. It thus allows the characterization of macromolecular assemblies, assessing their mass and stoichiometries and mapping the interacting surfaces. In this review, we discuss the application of native mass spectrometry to dynamic molecular machines based on multiple weak interactions. In the study of these machines, it is crucial to understand which and under which conditions various complexes form at any time point. We focus on the specific example of the iron-sulfur cluster biogenesis machine because this is an archetype of a dynamic machine that requires very specific and demanding experimental conditions, such as anaerobicity and the need of retaining the fold of marginally folded proteins. We describe the advantages, challenges and current limitations of the technique by providing examples from our own experience and suggesting possible future solutions.
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Affiliation(s)
- Rita Puglisi
- UK Dementia Research Institute at the Wohl Institute of King’s College LondonUK
| | | | - Annalisa Pastore
- UK Dementia Research Institute at the Wohl Institute of King’s College LondonUK
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12
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Lee HS, Lim YB. Slow-Motion Self-Assembly: Access to Intermediates with Heterochiral Peptides to Gain Control over Alignment Media Development. ACS NANO 2020; 14:3344-3352. [PMID: 32058708 DOI: 10.1021/acsnano.9b09070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Understanding the intermediates or transition states in organic reactions has made it possible to develop theories and to synthesize important compounds. In contrast to organic reaction intermediates and even protein folding intermediates, the intermediates of peptide/protein self-assembly are not very well understood. Here we report that the self-assembly kinetics of linear heterochiral peptides are significantly slower than those of the corresponding homochiral peptides, which enables direct microscopic observation of assembly intermediates. By designing racemic or asymmetric heterochiral peptides, we were able to discover unusual mixed helical (MP-helix) and overtwisted intermediates. The convergence of equilibrium morphology between the homochiral and heterochiral peptides enables us to reasonably deduce the unobservable intermediates of rapidly assembling homochiral peptides. By utilizing the discovered information about the assembly intermediates, we were able to develop a functional NMR alignment medium that enables the measurement of residual dipolar couplings (RDCs) in a time-dependent manner. Although much less studied than their cyclic counterparts, the linear form of heterochiral peptides provides a means of obtaining a more in-depth understanding of the self-assembly pathway and of developing sophisticated bottom-up materials.
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Affiliation(s)
- Hye-Soo Lee
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science and Engineering, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
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13
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Timr S, Madern D, Sterpone F. Protein thermal stability. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:239-272. [PMID: 32145947 DOI: 10.1016/bs.pmbts.2019.12.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Proteins, in general, fold to a well-organized three-dimensional structure in order to function. The stability of this functional shape can be perturbed by external environmental conditions, such as temperature. Understanding the molecular factors underlying the resistance of proteins to the thermal stress has important consequences. First of all, it can aid the design of thermostable enzymes able to perform efficient catalysis in the high-temperature regime. Second, it is an essential brick of knowledge required to decipher the evolutionary pathways of life adaptation on Earth. Thanks to the development of atomistic simulations and ad hoc enhanced sampling techniques, it is now possible to investigate this problem in silico, and therefore provide support to experiments. After having described the methodological aspects, the chapter proposes an extended discussion on two problems. First, we focus on thermophilic proteins, a perfect model to address the issue of thermal stability and molecular evolution. Second, we discuss the issue of how protein thermal stability is affected by crowded in vivo-like conditions.
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Affiliation(s)
- Stepan Timr
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | | | - Fabio Sterpone
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, Paris, France; Institut de Biologie Physico-Chimique-Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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14
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Sekhon G, Singh R. Human aldose reductase unfolds through an intermediate. F1000Res 2019; 8:564. [PMID: 31723418 PMCID: PMC6844136 DOI: 10.12688/f1000research.18963.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Human aldose reductase (hAR) is the first and rate-limiting enzyme of the polyol pathway. For the development of secondary complications of diabetes in chronic hyperglycemic conditions, one of the critical factors is the increased flux of glucose through the polyol pathway. Due to this clinical implication, hAR attracted considerable attention from the drug discovery perspective. In spite of extensive characterization in the context of biochemical and structural aspects, we know very little about the unfolding behavior of hAR. This study reports equilibrium unfolding studies of hAR. Methods: We carried out thermal denaturation and chemical-induced equilibrium unfolding studies of hAR monitored by circular dichroism and fluorescence spectroscopy. Results: Thermal denaturation studies presented a classical picture of two-state unfolding from native to the denatured state. The data was used to derive thermodynamic parameters and study the thermostability of hAR. Chemical induced equilibrium unfolding studies led us to discover an intermediate state, which gets populated at 3.5-4.0 M and 0.7-2.0 M of urea and GuHCl, respectively. Thermodynamic parameters derived from chemical-induced unfolding are in agreement with those obtained from thermal denaturation of hAR. Conclusion: This study revealed that aldose reductase unfolds from native to the unfolded state via an intermediate. Assessment of the thermodynamic stability of native, intermediate, and unfolded states shows that significant energy barriers separate these states, which ensures the cooperativity of unfolding. As hAR functions in cells that are under osmotic and oxidative stress, these
in vitro findings may have implications for its native conformation under the physiological state.
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Affiliation(s)
- Gurprit Sekhon
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
| | - Ranvir Singh
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
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