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Gallo P, Bachler J, Bove LE, Böhmer R, Camisasca G, Coronas LE, Corti HR, de Almeida Ribeiro I, de Koning M, Franzese G, Fuentes-Landete V, Gainaru C, Loerting T, de Oca JMM, Poole PH, Rovere M, Sciortino F, Tonauer CM, Appignanesi GA. Advances in the study of supercooled water. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:143. [PMID: 34825973 DOI: 10.1140/epje/s10189-021-00139-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/17/2021] [Indexed: 06/13/2023]
Abstract
In this review, we report recent progress in the field of supercooled water. Due to its uniqueness, water presents numerous anomalies with respect to most simple liquids, showing polyamorphism both in the liquid and in the glassy state. We first describe the thermodynamic scenarios hypothesized for the supercooled region and in particular among them the liquid-liquid critical point scenario that has so far received more experimental evidence. We then review the most recent structural indicators, the two-state model picture of water, and the importance of cooperative effects related to the fact that water is a hydrogen-bonded network liquid. We show throughout the review that water's peculiar properties come into play also when water is in solution, confined, and close to biological molecules. Concerning dynamics, upon mild supercooling water behaves as a fragile glass former following the mode coupling theory, and it turns into a strong glass former upon further cooling. Connections between the slow dynamics and the thermodynamics are discussed. The translational relaxation times of density fluctuations show in fact the fragile-to-strong crossover connected to the thermodynamics arising from the existence of two liquids. When considering also rotations, additional crossovers come to play. Mobility-viscosity decoupling is also discussed in supercooled water and aqueous solutions. Finally, the polyamorphism of glassy water is considered through experimental and simulation results both in bulk and in salty aqueous solutions. Grains and grain boundaries are also discussed.
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Affiliation(s)
- Paola Gallo
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy.
| | - Johannes Bachler
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Livia E Bove
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
- Sorbonne Université, CNRS UMR 7590, IMPMC, 75005, Paris, France
| | - Roland Böhmer
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Gaia Camisasca
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Luis E Coronas
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Horacio R Corti
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, Comisión Nacional de Energía Atómica, B1650LWP, Buenos Aires, Argentina
| | - Ingrid de Almeida Ribeiro
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
| | - Maurice de Koning
- Instituto de Física "Gleb Wataghin", Universidade Estadual de Campinas, UNICAMP, 13083-859, Campinas, São Paulo, Brazil
- Center for Computing in Engineering & Sciences, Universidade Estadual de Campinas, UNICAMP, 13083-861, Campinas, São Paulo, Brazil
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Universitat de Barcelona, & Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, C. Martí i Franquès 1, 08028, Barcelona, Spain
| | - Violeta Fuentes-Landete
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Catalin Gainaru
- Fakultät Physik, Technische Universität Dortmund, 44221, Dortmund, Germany
| | - Thomas Loerting
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | | | - Peter H Poole
- Department of Physics, St. Francis Xavier University, Antigonish, NS, B2G 2W5, Canada
| | - Mauro Rovere
- Dipartimento di Matematica e Fisica, Università degli Studi Roma Tre, Via della Vasca Navale 84, 00146, Roma, Italy
| | - Francesco Sciortino
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185, Roma, Italy
| | - Christina M Tonauer
- Institute of Physical Chemistry, University of Innsbruck, Innrain 52c, A-6020, Innsbruck, Austria
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
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2
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Evaluation of FRET X for single-molecule protein fingerprinting. iScience 2021; 24:103239. [PMID: 34729466 PMCID: PMC8546410 DOI: 10.1016/j.isci.2021.103239] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 11/20/2022] Open
Abstract
Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and accumulated FRET efficiencies constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines, and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics. We propose a FRET-based single-molecule protein identification method Peptides are experimentally distinguishable by their fingerprints Our approach can classify the constituents of complex samples with 95% accuracy
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Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins. Commun Chem 2021; 4:57. [PMID: 36697562 PMCID: PMC9814862 DOI: 10.1038/s42004-021-00499-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 03/16/2021] [Indexed: 02/02/2023] Open
Abstract
Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.
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Kihara S, Köper I, Mata JP, McGillivray DJ. Reviewing nanoplastic toxicology: It's an interface problem. Adv Colloid Interface Sci 2021; 288:102337. [PMID: 33385776 DOI: 10.1016/j.cis.2020.102337] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/06/2020] [Accepted: 12/07/2020] [Indexed: 01/19/2023]
Abstract
Multiple international agencies have recently raised environmental and health concerns regarding plastics in nanoforms (nanoplastics), but there is insufficient knowledge of their properties to allow for an accurate risk assessment to be conducted and any risks managed. For this reason, research into the toxicity of nanoplastics has focused strongly on documenting their impacts on biological organisms. One scope of this review is to summarise the recent findings on the adverse effects on biological organisms and strategies which can be adopted to advance our understanding of nanoplastic properties and their toxicity. Specifically, a mechanistic approach has already been employed in nanotoxicology, which focuses on the cause-and-effect relationships to establish a tool that predicts the biological impacts based on nanoparticle characteristics. Identifying the chemical and biological bases behind the observed biological effects (such as in vitro cellular response) is a major challenge, due to the intricate nature of nanoparticle-biological molecule complexes and an unawareness of their interaction with other biological targets, particularly at interfacial level. An exemplary case includes protein corona formation and ecological molecule corona (eco-corona) for nanoplastics. Therefore, the second scope of this review is to discuss recent findings and importance of (for both non-plastic and plastic nanoparticles) coronae formation and structure. Finally, we discuss the opportunities provided by model system approaches (model protein corona and lipid bilayer) to deepen the understanding of the above-mentioned perspectives, and corroborate the findings from in vitro experiments.
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Affiliation(s)
- Shinji Kihara
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
| | - Ingo Köper
- Institute for Nanoscale Science and Technology, College for Science and Engineering, Flinders University, Adelaide, SA 5042, Australia
| | - Jitendra P Mata
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, New Illawarra Rd, Lucas Heights, NSW 2234, Australia.
| | - Duncan J McGillivray
- School of Chemical Sciences, The University of Auckland, Auckland 1010, New Zealand; The MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6140, New Zealand
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5
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March D, Bianco V, Franzese G. Protein Unfolding and Aggregation near a Hydrophobic Interface. Polymers (Basel) 2021; 13:polym13010156. [PMID: 33401542 PMCID: PMC7795562 DOI: 10.3390/polym13010156] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/22/2020] [Accepted: 12/24/2020] [Indexed: 01/29/2023] Open
Abstract
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we study how the presence of a hydrophobic surface affects this course of events. To this goal, we use a coarse-grained model of proteins and study by simulations their folding and aggregation near an ideal hydrophobic surface in an aqueous environment by changing parameters such as temperature and hydrophobic strength, related, e.g., to ions concentration. We show that the hydrophobic surface, as well as the other parameters, affect both the protein unfolding and aggregation. We discuss the interpretation of these results and define future lines for further analysis, with their possible implications in neurodegenerative diseases.
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Affiliation(s)
- David March
- Secció de Física Estadística i Interdisciplinària—Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
| | - Valentino Bianco
- Chemical Physics Department, Faculty of Chemistry, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, 28040 Madrid, Spain
- Correspondence: (V.B.); (G.F.)
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària—Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain;
- Correspondence: (V.B.); (G.F.)
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6
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Nwamba OC. Membranes as the third genetic code. Mol Biol Rep 2020; 47:4093-4097. [PMID: 32279211 DOI: 10.1007/s11033-020-05437-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
Biological membranes and their compositions influence cellular function, age and disease states of organisms. They achieve this by effecting the outcome of bound enzymes/proteins and carbohydrate moieties. While the membrane-bound carbohydrates give rise to antigenicity, membranes impact the eventual outcome of protein structures that would function even outside their enclosure. This is achieved by membrane modulation of translational and post-translational protein folding. Thus, the eventual 3D structures and functions of proteins might not be solely dependent on their primary amino acid sequences and surrounding environments. The 3D protein structures would also depend on enclosing membrane properties such as fluidity, other intrinsic and extrinsic proteins and carbohydrate functionalities. Also, membranes moderate DNA activities with consequences on gene activation-inactivation mechanisms. Consequently, membranes are almost indispensable to the functioning of other cell compositions and serve to modulate these other components. Besides, membrane lipid compositions are also moderated by nutrition and diets and the converse is true. Thus, it could be argued that membranes are the third genetic codes. Suggestively, membranes are at the center of the interplay between nature and nurture in health and disease states.
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7
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Nerattini F, Figliuzzi M, Cardelli C, Tubiana L, Bianco V, Dellago C, Coluzza I. Identification of Protein Functional Regions. Chemphyschem 2020; 21:335-347. [PMID: 31944517 DOI: 10.1002/cphc.201900898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/01/2019] [Indexed: 11/12/2022]
Abstract
Protein sequence stores the information relative to both functionality and stability, thus making it difficult to disentangle the two contributions. However, the identification of critical residues for function and stability has important implications for the mapping of the proteome interactions, as well as for many pharmaceutical applications, e. g. the identification of ligand binding regions for targeted pharmaceutical protein design. In this work, we propose a computational method to identify critical residues for protein functionality and stability and to further categorise them in strictly functional, structural and intermediate. We evaluate single site conservation and use Direct Coupling Analysis (DCA) to identify co-evolved residues both in natural and artificial evolution processes. We reproduce artificial evolution using protein design and base our approach on the hypothesis that artificial evolution in the absence of any functional constraint would exclusively lead to site conservation and co-evolution events of the structural type. Conversely, natural evolution intrinsically embeds both functional and structural information. By comparing the lists of conserved and co-evolved residues, outcomes of the analysis on natural and artificial evolution, we identify the functional residues without the need of any a priori knowledge of the biological role of the analysed protein.
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Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Matteo Figliuzzi
- Sorbonne Universites, UPMC, Institut de Biologie Paris-Seine, CNRS, Laboratoire de Biologie Computationnelle et Quantitative UMR, 7238, Paris, France
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Luca Tubiana
- Physics Department, Universitá degli studi di Trento, via Sommarive 14, 38123, Trento, IT
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria.,Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid, 28040, Spain
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Ivan Coluzza
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain, and IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain
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8
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Nerattini F, Tubiana L, Cardelli C, Bianco V, Dellago C, Coluzza I. Protein design under competing conditions for the availability of amino acids. Sci Rep 2020; 10:2684. [PMID: 32060385 PMCID: PMC7021711 DOI: 10.1038/s41598-020-59401-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/08/2019] [Indexed: 11/09/2022] Open
Abstract
Isolating the properties of proteins that allow them to convert sequence into the structure is a long-lasting biophysical problem. In particular, studies focused extensively on the effect of a reduced alphabet size on the folding properties. However, the natural alphabet is a compromise between versatility and optimisation of the available resources. Here, for the first time, we include the impact of the relative availability of the amino acids to extract from the 20 letters the core necessary for protein stability. We present a computational protein design scheme that involves the competition for resources between a protein and a potential interaction partner that, additionally, gives us the chance to investigate the effect of the reduced alphabet on protein-protein interactions. We devise a scheme that automatically identifies the optimal reduced set of letters for the design of the protein, and we observe that even alphabets reduced down to 4 letters allow for single protein folding. However, it is only with 6 letters that we achieve optimal folding, thus recovering experimental observations. Additionally, we notice that the binding between the protein and a potential interaction partner could not be avoided with the investigated reduced alphabets. Therefore, we suggest that aggregation could have been a driving force in the evolution of the large protein alphabet.
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Affiliation(s)
- Francesca Nerattini
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Luca Tubiana
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Chiara Cardelli
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Valentino Bianco
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Christoph Dellago
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090, Vienna, Austria
| | - Ivan Coluzza
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 182, 20014, San Sebastian, Spain. .,IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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9
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Bianco V, Franzese G, Coluzza I. In Silico Evidence That Protein Unfolding is a Precursor of Protein Aggregation. Chemphyschem 2020; 21:377-384. [DOI: 10.1002/cphc.201900904] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/01/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Valentino Bianco
- Faculty of Chemistry, Chemical Physics Department, Universidad Complutense de Madrid, Plaza de las Ciencias Ciudad Universitaria Madrid 28040 Spain
| | - Giancarlo Franzese
- Secció de Física Estadística i Interdisciplinària-Departament de Física de la Matèria Condensada, Facultat de Física & Institute of Nanoscience and Nanotechnology (IN2UB) Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
| | - Ivan Coluzza
- CIC biomaGUNE Paseo Miramon 182 20014 San Sebastian Spain
- IKERBASQUE, Basque Foundation for Science 48013 Bilbao Spain
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10
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Erfani A, Flynn NH, Ramsey JD, Aichele CP. Increasing protein stability by association with zwitterionic amphiphile cocamidopropyl betaine. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111631] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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11
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Kozuch DJ, Stillinger FH, Debenedetti PG. Low temperature protein refolding suggested by molecular simulation. J Chem Phys 2019; 151:185101. [DOI: 10.1063/1.5128211] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Daniel J. Kozuch
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Frank H. Stillinger
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Pablo G. Debenedetti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA
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12
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Bianco V, Alonso-Navarro M, Di Silvio D, Moya S, Cortajarena AL, Coluzza I. Proteins are Solitary! Pathways of Protein Folding and Aggregation in Protein Mixtures. J Phys Chem Lett 2019; 10:4800-4804. [PMID: 31373499 DOI: 10.1021/acs.jpclett.9b01753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a computational and experimental study on the folding and aggregation in solutions of multiple protein mixtures at different concentrations. We show how in protein mixtures each component is capable of maintaining its folded state at densities greater than the one at which they would precipitate in single-species solutions. We demonstrate the generality of our observation over many different proteins using computer simulations capable of fully characterizing the cross-aggregation phase diagram of all the mixtures. Dynamic light scattering experiments were performed to evaluate the aggregation of two proteins, bovine serum albumin (BSA) and consensus tetratricopeptide repeat (CTPR), in solutions of one or both proteins. The experiments confirm our hypothesis and the simulations. These findings elucidate critical aspects of the cross-regulation of expression and aggregation of proteins exerted by the cell and on the evolutionary selection of folding and non-aggregating protein sequences, paving the way for new experimental tests.
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Affiliation(s)
- Valentino Bianco
- Faculty of Chemistry, Chemical Physics Deprtment, Universidad Complutense de Madrid, Plaza de las Ciencias, Ciudad Universitaria, Madrid 28040, Spain
| | | | | | - Sergio Moya
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
| | - Aitziber L Cortajarena
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Ivan Coluzza
- CIC biomaGUNE, Paseo Miramon 182, 20014 San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
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13
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Bianco V, Franzese G. Hydrogen bond correlated percolation in a supercooled water monolayer as a hallmark of the critical region. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Abstract
Hydration-shell vibrational spectroscopy provides an experimental window into solute-induced water structure changes that mediate aqueous folding, binding, and self-assembly. Decomposition of measured Raman and infrared (IR) spectra of aqueous solutions using multivariate curve resolution (MCR) and related methods may be used to obtain solute-correlated spectra revealing solute-induced perturbations of water structure, such as changes in water hydrogen-bond strength, tetrahedral order, and the presence of dangling (non-hydrogen-bonded) OH groups. More generally, vibrational-MCR may be applied to both aqueous and nonaqueous solutions, including multicomponent mixtures, to quantify solvent-mediated interactions between oily, polar, and ionic solutes, in both dilute and crowded fluids. Combining vibrational-MCR with emerging theoretical modeling strategies promises synergetic advances in the predictive understanding of multiscale self-assembly processes of both biological and technological interest.
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry , Purdue University , West Lafayette , Indiana 47907 , United States
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15
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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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16
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Tuccitto N, Messina GML, Li-Destri G, Wietecka A, Marletta G. Chelating Surfaces for Oriented Human Serum Albumin Molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:3354-3362. [PMID: 30741553 DOI: 10.1021/acs.langmuir.9b00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Protein immobilization in a specific conformation or orientation at an interface is influenced by specific interactions with the outer layer of the surface. A strategy to build-up a complex construct which is able to orient protein molecules, based on metal-cation chelation processes, is reported. The proposed methodology implies the formation of a mercaptoundecanoic acid monolayer on a gold surface that is activated to attach covalently the tripeptide glycyl-l-histidyl-l-lysine (GHK) on the surface, whose sites are then employed to chelate copper ions, providing a selective platform for the orientation of human serum albumin (HSA) molecules. The protein adsorption process on GHK and GHK-Cu(II)-complex surfaces was monitored by the in situ quartz crystal microbalance with dissipation monitoring (QCM-D) and force spectroscopy technique. The changes in frequency and dissipation factor as well as the D- f plots from QCM-D measurements help to characterize the changes in the protein conformation and are confirmed by force curve spectroscopy results. An improved kinetic model, based on random sequential adsorption with variable protein footprints, has been developed to predict and simulate the experimentally found HSA average surface coverage onto the GHK and GHK-Cu(II)-complex surfaces.
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Affiliation(s)
- N Tuccitto
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Department of Chemical Sciences , University of Catania and CSGI , Viale Andrea Doria 6 , 95125 Catania , Italy
| | - G M L Messina
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Department of Chemical Sciences , University of Catania and CSGI , Viale Andrea Doria 6 , 95125 Catania , Italy
| | - G Li-Destri
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Department of Chemical Sciences , University of Catania and CSGI , Viale Andrea Doria 6 , 95125 Catania , Italy
| | - A Wietecka
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Department of Chemical Sciences , University of Catania and CSGI , Viale Andrea Doria 6 , 95125 Catania , Italy
- Faculty of Chemistry , Adam Mickiewicz University in Poznan , Umultowska 89b , PL-61-614 Poznan , Poland
| | - G Marletta
- Laboratory for Molecular Surfaces and Nanotechnology (LAMSUN), Department of Chemical Sciences , University of Catania and CSGI , Viale Andrea Doria 6 , 95125 Catania , Italy
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17
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Jong K, Ansari N, Grisanti L, Hassanali A. Understanding the quantum mechanical properties of hydrogen bonds in solvated biomolecules from cluster calculations. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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