1
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Chialvo AA. Preferential Solvation Phenomena as Solute-Induced Structure-Making/Breaking Processes: Linking Thermodynamic Preferential Interaction Parameters to Fundamental Structure Making/Breaking Functions. J Phys Chem B 2024; 128:5228-5245. [PMID: 38754065 DOI: 10.1021/acs.jpcb.4c00385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
In this work, we identify the explicit macroscopic-to-microscopic rigorous links between existing thermodynamic preferential interaction parameters Γ Q α Q β ( χ i ) and microstructural descriptors based on total correlation function integrals, leading to their unambiguous characterization in terms of fundamental structure making/breaking functions S α β . First, we provide the statistics mechanical framework to identify a universal molecular-based signature for the preferential solvation P S phenomenon involving solutes at infinite dilution in mixed-solvent environments and discuss its fundamental properties. Then, we characterize the S α β functions relevant to the P S process, identify the microscopic markers for the existing preferential interaction parameters Γ Q α Q β ( χ i ) in terms of the S α β functions, and test their compliance with a pair of essential microstructural constraints linked to the properties of the universal P S signature. Moreover, we illustrate the analysis by probing the behavior of a representative ternary system comprising the solubility of methane in aqueous 1,4-dioxane mixed-solvent environments under ambient conditions. Finally, we discuss some relevant issues surrounding the statistical mechanical (microstructural) interpretation of the thermodynamic (macroscopic) preferential interaction parameters, review some pitfalls in their evaluation from molecular simulation, and provide an outlook.
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Affiliation(s)
- Ariel A Chialvo
- Retired Scientist, Knoxville, Tennessee 37922-3108, United States
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2
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Seo J, Singh R, Ryu J, Choi JH. Molecular Aggregation Behavior and Microscopic Heterogeneity in Binary Osmolyte-Water Solutions. J Chem Inf Model 2024; 64:138-149. [PMID: 37983534 DOI: 10.1021/acs.jcim.3c01382] [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: 11/22/2023]
Abstract
Osmolytes, small organic compounds, play a key role in modulating the protein stability in aqueous solutions, but the operating mechanism of the osmolyte remains inconclusive. Here, we attempt to clarify the mode of osmolyte action by quantitatively estimating the microheterogeneity of osmolyte-water mixtures with the aid of molecular dynamics simulation, graph theoretical analysis, and spatial distribution measurement in the four osmolyte solutions of trimethylamine-N-oxide (TMAO), tetramethylurea (TMU), dimethyl sulfoxide, and urea. TMAO, acting as a protecting osmolyte, tends to remain isolated with no formation of osmolyte aggregates while preferentially interacting with water, but there is a strong aggregation propensity in the denaturant TMU solution, characterized by favored hydrophobic interactions between TMU molecules. Taken together, the mechanism of osmolyte action on protein stability is proposed as a comprehensive one that encompasses the direct interactions between osmolytes and proteins and indirect interactions through the regulation of water properties in the osmolyte-water mixtures.
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Affiliation(s)
- Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Ravi Singh
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jonghyuk Ryu
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology (GIST), 123 Cheomdangwagi-ro, Buk-gu, Gwangju 61005, Republic of Korea
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3
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Garfagnini T, Bemporad F, Harries D, Chiti F, Friedler A. Amyloid Aggregation Is Potently Slowed Down by Osmolytes Due to Compaction of Partially Folded State. J Mol Biol 2023; 435:168281. [PMID: 37734431 DOI: 10.1016/j.jmb.2023.168281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/30/2023] [Accepted: 09/11/2023] [Indexed: 09/23/2023]
Abstract
Amyloid aggregation is a key process in amyloidoses and neurodegenerative diseases. Hydrophobicity is one of the major driving forces for this type of aggregation, as an increase in hydrophobicity generally correlates with aggregation susceptibility and rate. However, most experimental systems in vitro and prediction tools in silico neglect the contribution of protective osmolytes present in the cellular environment. Here, we assessed the role of hydrophobic mutations in amyloid aggregation in the presence of osmolytes. To achieve this goal, we used the model protein human muscle acylphosphatase (mAcP) and mutations to leucine that increased its hydrophobicity without affecting its thermodynamic stability. Osmolytes significantly slowed down the aggregation kinetics of the hydrophobic mutants, with an effect larger than that observed on the wild-type protein. The effect increased as the mutation site was closer to the middle of the protein sequence. We propose that the preferential exclusion of osmolytes from mutation-introduced hydrophobic side-chains quenches the aggregation potential of the ensemble of partially unfolded states of the protein by inducing its compaction and inhibiting its self-assembly with other proteins. Our results suggest that including the effect of the cellular environment in experimental setups and predictive softwares, for both mechanistic studies and drug design, is essential in order to obtain a more complete combination of the driving forces of amyloid aggregation.
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Affiliation(s)
- Tommaso Garfagnini
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Daniel Harries
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel; The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel.
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4
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Arsiccio A, Sarter T, Polidori I, Winter G, Pisano R, Shea JE. Thermodynamic Modeling and Experimental Data Reveal That Sugars Stabilize Proteins According to an Excluded Volume Mechanism. J Am Chem Soc 2023. [PMID: 37466340 DOI: 10.1021/jacs.3c04293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We present a new thermodynamic model to investigate the relative effects of excluded volume and soft interaction contributions in determining whether a cosolute will either destabilize or stabilize a protein in solution. This model is unique in considering an atomistically detailed model of the protein and accounting for the preferential accumulation/exclusion of the osmolyte molecules from the protein surface. Importantly, we use molecular dynamics simulations and experiments to validate the model. The experimental approach presents a unique means of decoupling excluded volume and soft interaction contributions using a linear polymeric series of cosolutes with different numbers of glucose subunits, from 1 (glucose) to 8 (maltooctaose), as well as an 8-mer of glucose units in the closed form (γ-CD). By studying the stabilizing effect of cosolutes along this polymeric series using lysozyme as a model protein, we validate the thermodynamic model and show that sugars stabilize proteins according to an excluded volume mechanism.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tim Sarter
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Ilaria Polidori
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Gerhard Winter
- Department of Pharmacy, Ludwig-Maximilians-University, 81377 Munich, Germany
| | - Roberto Pisano
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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5
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Arsiccio A, Liu X, Ganguly P, Buratto SK, Bowers MT, Shea JE. Effect of Cosolutes on the Aggregation of a Tau Fragment: A Combined Experimental and Simulation Approach. J Phys Chem B 2023; 127:4022-4031. [PMID: 37129599 DOI: 10.1021/acs.jpcb.3c00433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The intrinsically disordered protein Tau represents the main component of neurofibrillary tangles that are a hallmark of Alzheimer's disease. A small fragment of Tau, known as paired helical filament 6 (PHF6), is considered to be important for the formation of the β-structure core of the fibrils. Here we study the aggregation of this fragment in the presence of different cosolutes, including urea, TMAO, sucrose and 2-hydroxypropyl-β-cyclodextrin (2-HPβCD), using both experiments and molecular dynamics simulations. A novel implicit solvation approach (MIST - Model with Implicit Solvation Thermodynamics) is used, where an energetic contribution based on the concept of transfer free energies describes the effect of the cosolutes. The simulation predictions are compared to thioflavin-T and atomic force microscopy results, and the good agreement observed confirms the predictive ability of the computational approach herein proposed. Both simulations and experiments indicate that PHF6 aggregation is inhibited in the presence of urea and 2-HPβCD, while TMAO and sucrose stabilize associated conformations. The remarkable ability of HPβCD to inhibit aggregation represents an extremely promising result for future applications, especially considering the widespread use of this molecule as a drug carrier to the brain and as a solubilizer/excipient in pharmaceutical formulations.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Xikun Liu
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Steven K Buratto
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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6
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Workman RJ, Gorle S, Pettitt BM. Effects of Conformational Constraint on Peptide Solubility Limits. J Phys Chem B 2022; 126:10510-10518. [PMID: 36450134 DOI: 10.1021/acs.jpcb.2c06458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Liquid-liquid phase separation of proteins preferentially involves intrinsically disordered proteins or disordered regions. Understanding the solution chemistry of these phase separations is key to learning how to quantify and manipulate systems that involve such processes. Here, we investigate the effect of cyclization on the liquid-liquid phase separation of short polyglycine peptides. We simulated separate aqueous systems of supersaturated cyclic and linear GGGGG and observed spontaneous liquid-liquid phase separation in each of the solutions. The cyclic GGGGG phase separates less robustly than linear GGGGG and has a higher aqueous solubility, even though linear GGGGG has a more favorable single molecule solvation free energy. The versatile and abundant interpeptide contacts formed by the linear GGGGG stabilize the condensed droplet phase, driving the phase separation in this system. In particular, we find that van der Waals close contact interactions are enriched in the droplet phase as opposed to electrostatic interactions. An analysis of the change in backbone conformational entropy that accompanies the phase transition revealed that cyclic peptides lose significantly less entropy in this process as expected. However, we find that the enhanced interaction enthalpy of linear GGGGG in the droplet phase is enough to compensate for a larger decrease in conformational entropy.
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Affiliation(s)
- Riley J Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
| | - Suresh Gorle
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555-0304, United States
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7
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Folberth A, van der Vegt NFA. Influence of TMAO and Pressure on the Folding Equilibrium of TrpCage. J Phys Chem B 2022; 126:8374-8380. [PMID: 36251479 DOI: 10.1021/acs.jpcb.2c04034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Trimethylamine-N-oxide (TMAO) is an osmolyte known for its ability to counteract the pressure denaturation of proteins. Computational studies addressing the molecular mechanisms of TMAO's osmolyte action have however focused exclusively on its protein-stabilizing properties at ambient pressure, neglecting the changes that may occur under high-pressure conditions where TMAO's hydration structure changes to that of increased water binding. Here, we present the first study on the combined effect of pressure and TMAO on a mini-protein, TrpCage. The results showed that at high pressures, nonpolar residues packed less tightly and the salt bridge of TrpCage was destabilized. This effect was mitigated by TMAO which was found to be strongly depleted from the protein/water interface at 1 kbar than at 1 bar ambient pressure, thus counterbalancing the thermodynamically unfavorable effect of elevated pressure in the free energy of folding. TMAO was depleted from charged groups, like the salt bridge-forming ones, and accumulated around hydrophobic groups. Still, it stabilized both kinds of interactions. Furthermore, enthalpically favorable TrpCage-water hydrogen bonds were reduced in the presence of TMAO, causing a stronger destabilization of the unfolded state than the folded state. This shifted the protein-folding equilibrium toward the folded state. Therefore, TMAO showed stabilizing effects on different kinds of groups, which were partially enhanced at high pressures.
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Affiliation(s)
- Angelina Folberth
- Eduard-Zintl-Institut Fuer Anorganische und Physikalische Chemie, Technical University of Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut Fuer Anorganische und Physikalische Chemie, Technical University of Darmstadt, Alarich-Weiss-Strasse 10, 64287 Darmstadt, Germany
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8
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Ganguly P, Bubák D, Polák J, Fagan P, Dračínský M, van der Vegt NFA, Heyda J, Shea JE. Cosolvent Exclusion Drives Protein Stability in Trimethylamine N-Oxide and Betaine Solutions. J Phys Chem Lett 2022; 13:7980-7986. [PMID: 35984361 DOI: 10.1021/acs.jpclett.2c01692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Using a combination of molecular dynamics simulation, dialysis experiments, and electronic circular dichroism measurements, we studied the solvation thermodynamics of proteins in two osmolyte solutions, trimethylamine N-oxide (TMAO) and betaine. We showed that existing force fields are unable to capture the solvation properties of the proteins lysozyme and ribonuclease T1 and that the inaccurate parametrization of protein-osmolyte interactions in these force fields promoted an unphysical strong thermal denaturation of the trpcage protein. We developed a novel force field for betaine (the KBB force field) which reproduces the experimental solution Kirkwood-Buff integrals and density. We further introduced appropriate scaling to protein-osmolyte interactions in both the betaine and TMAO force fields which led to successful reproduction of experimental protein-osmolyte preferential binding coefficients for lysozyme and ribonuclease T1 and prevention of the unphysical denaturation of trpcage in osmolyte solutions. Correct parametrization of protein-TMAO interactions also led to the stabilization of the collapsed conformations of a disordered elastin-like peptide, while the uncorrected parameters destabilized the collapsed structures. Our results establish that the thermodynamic stability of proteins in both betaine and TMAO solutions is governed by osmolyte exclusion from proteins.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California93106, United States
| | - Dominik Bubák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Jakub Polák
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Patrik Fagan
- Department of Analytical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 160 00Prague, Czech Republic
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, Alarich-Weiss-Straße 10, Darmstadt64287, Germany
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, 166 28Prague 6, Czech Republic
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, Santa Barbara, California93106, United States
- Department of Physics, University of California at Santa Barbara, Santa Barbara, California93106, United States
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9
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Arsiccio A, Ganguly P, Shea JE. A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study. J Phys Chem B 2022; 126:4472-4482. [PMID: 35679169 DOI: 10.1021/acs.jpcb.2c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We developed a method for implicit solvent molecular dynamics simulations of proteins in solvent mixtures (model with implicit solvation thermodynamics, MIST). The MIST method introduces experimental group transfer free energies to the generalized Born formulation for generating molecular trajectories without the need for developing rigorous explicit-solvent force fields for multicomponent solutions. As a test case, we studied the urea-induced denaturation of the Trp-cage miniprotein in water. We demonstrate that our method allows efficient exploration of the conformational space of the protein in only a few hundreds of nanoseconds of all-atom unbiased simulations. Furthermore, selective implementation of the transfer free energies of specific peptide groups, backbone, and side chains enables us to decouple their specific energetic contributions to the conformational changes of the protein. The approach herein developed can readily be extended to the investigation of complex matrices as well as to the characterization of protein aggregation. The MIST method is implemented in Plumed (ver. 2.8) as a separate module called SASA.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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10
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Contessoto VG, Ferreira PHB, Chahine J, Leite VBP, Oliveira RJ. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. J Phys Chem B 2021; 125:11673-11686. [PMID: 34644091 DOI: 10.1021/acs.jpcb.1c07663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular crowding is a ubiquitous phenomenon in biological systems, with significant consequences on protein folding and stability. Small compounds, such as the osmolyte trimethylamine N-oxide (TMAO), can also present similar effects. To analyze the effects arising from these solute-like molecules, we performed a series of crowded coarse-grained folding simulations. Two well-known proteins were chosen, CI2 and SH3, modeled by the alpha-carbon-structure-based model. In the simulations, the crowding molecules were represented by low-sized neutral atom beads in different concentrations. The results show that a low level of the volume fraction occupied by neutral agents can change protein stability and folding kinetics for the two systems. However, the kinetics were shown to be unaffected in their respective folding temperatures. The faster kinetics correlates with changes in the folding route for systems at the same temperature, where non-native contacts were shown to be relevant. The transition states of the two systems with and without crowders are similar. In the case of SH3, there are differences in the structuring of two strands, which may be associated with the increase in its folding rate, in addition to the destabilization of the denatured ensemble. The present study also detected a crossover in the thermodynamic stability behavior, previously observed experimentally and theoretically. As the temperature increases, crowders change from destabilizing to stabilizing agents.
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Affiliation(s)
- Vinícius G Contessoto
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Paulo H B Ferreira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
| | - Jorge Chahine
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Vitor B P Leite
- Department of Physics, Institute of Biosciences, Letters and Exact Sciences, São Paulo State University, São José do Rio Preto 15054-000, Brazil
| | - Ronaldo J Oliveira
- Laboratório de Biofísica Teórica, Departamento de Física, Instituto de Ciências Exatas, Naturais e Educação, Universidade Federal do Triângulo Mineiro, Uberaba 38064-200, Brazil
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11
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Avagyan S, Makhatadze GI. Effects of Hydrostatic Pressure on the Thermodynamics of CspB-Bs Interactions with the ssDNA Template. Biochemistry 2021; 60:3086-3097. [PMID: 34613715 DOI: 10.1021/acs.biochem.1c00561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the thermodynamic mechanisms of adaptation of biomacromolecules to high hydrostatic pressure can help shed light on how piezophilic organisms can survive at pressures reaching over 1000 atmospheres. Interaction of proteins with nucleic acids is one of the central processes that allow information flow encoded in the sequence of DNA. Here, we report the results of a study on the interaction of cold shock protein B from Bacillus subtilis (CspB-Bs) with heptadeoxythymine template (pDT7) as a function of temperature and hydrostatic pressure. Experimental data collected at different CspB-Bs:pDT7 ratios were analyzed using a thermodynamic linkage model that accounts for both protein unfolding and CspB-Bs:pDT7 binding. The global fit to the model provided estimates of the stability of CspB-Bs, ΔGProto, the volume change upon CspB-Bs unfolding, ΔVProt, the association constant for CspB-Bs:pDT7 complex, Kao, and the volume changes upon pDT7 single-stranded DNA (ssDNA) template binding, ΔVBind. The protein, CspB-Bs, unfolds with an increase in hydrostatic pressure (ΔVProt < 0). Surprisingly, our study showed that ΔVBind < 0, which means that the binding of CspB-Bs to ssDNA is stabilized by an increase in hydrostatic pressure. Thus, CspB-Bs binding to pDT7 represents a case of linked equilibrium in which folding and binding react differently upon an increase in hydrostatic pressure: protein folding/unfolding equilibrium favors the unfolded state, while protein-ligand binding equilibrium favors the bound state. These opposing effects set a "maximum attainable" pressure tolerance to the protein-ssDNA complex under given conditions.
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Affiliation(s)
- Samvel Avagyan
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Department on Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York 12180, United States.,Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
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12
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Gelb MB, Maynard HD. Effect of Poly(trehalose methacrylate) Molecular Weight and Concentration on the Stability and Viscosity of Insulin. MACROMOLECULAR MATERIALS AND ENGINEERING 2021; 306:2100197. [PMID: 35591895 PMCID: PMC9113406 DOI: 10.1002/mame.202100197] [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: 03/24/2021] [Indexed: 05/23/2023]
Abstract
Instability to storage and shipping conditions and injection administration remain major challenges in treating chronic conditions with biopharmaceuticals. Herein, formulations of poly(trehalose methacrylate) (pTrMA) were successfully optimized to stabilize insulin without appreciably increasing viscosity. Polymers were synthesized (2,400 - 29,200 Da), and added to insulin at different concentrations. pTrMA maintained >95% intact insulin against 250 rpm at 37 °C for 3 hours with at least 10 mol. eq. of 5.0 kDa, 7.5 mol. eq. of 9.4 kDa, 5 mol. eq. of 12.8 kDa, 1 mol. eq. of 19.8 kDa, and 0.5 mol. eq. of 29.2 kDa polymers, compared to 13.1% of insulin alone. The lowest pTrMA concentration formulations were more viscous than insulin alone, but the highest viscosity, U-600 with 10 mol. eq. of 5 kDa pTrMA, was only 1.43 cP at 25 °C. This data demonstrates that pTrMA is a promising low viscosity additive to stabilize the diabetes therapeutic insulin.
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Affiliation(s)
- Madeline B Gelb
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA
| | - Heather D Maynard
- Department of Chemistry and Biochemistry and California NanoSystems Institute, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, USA
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13
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Arsiccio A, Rospiccio M, Shea JE, Pisano R. Force Field Parameterization for the Description of the Interactions between Hydroxypropyl-β-Cyclodextrin and Proteins. J Phys Chem B 2021; 125:7397-7405. [PMID: 34210121 PMCID: PMC8287564 DOI: 10.1021/acs.jpcb.1c04033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclodextrins are cyclic oligosaccharides, widely used as drug carriers, solubilizers, and excipients. Among cyclodextrins, the functionalized derivative known as hydroxypropyl-β-cyclodextrin (HPβCD) offers several advantages due to its unique structural features. Its optimal use in pharmaceutical and medical applications would benefit from a molecular-level understanding of its behavior, as can be offered by molecular dynamics simulations. Here, we propose a set of parameters for all-atom simulations of HPβCD, based on the ADD force field for sugars developed in our group, and compare it to the original CHARMM36 description. Using Kirkwood-Buff integrals of binary HPβCD-water mixtures as target experimental data, we show that the ADD-based description results in a considerably improved prediction of HPβCD self-association and interaction with water. We then use the new set of parameters to characterize the behavior of HPβCD toward the different amino acids. We observe pronounced interactions of HPβCD with both polar and nonpolar moieties, with a special preference for the aromatic rings of tyrosine, phenylalanine, and tryptophan. Interestingly, our simulations further highlight a preferential orientation of HPβCD's hydrophobic cavity toward the backbone atoms of amino acids, which, coupled with a favorable interaction of HPβCD with the peptide backbone, suggest a propensity for HPβCD to denature proteins.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Marcello Rospiccio
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, California 93106, United States
| | - Roberto Pisano
- Molecular Engineering Laboratory, Department of Applied Science and Technology, Politecnico di Torino, 24 corso Duca degli Abruzzi, Torino 10129, Italy
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14
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Workman RJ, Pettitt BM. Thermodynamic Compensation in Peptides Following Liquid-Liquid Phase Separation. J Phys Chem B 2021; 125:6431-6439. [PMID: 34110175 DOI: 10.1021/acs.jpcb.1c02093] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid-liquid phase separation of proteins often incorporates intrinsically disordered proteins or those with disordered regions. Examining these processes via the entropy change is desirable for establishing a quantitative foundation with which to probe and understand these phase transitions. Of interest is the effect of residue sequence on the entropy of the peptide backbone. In this work we model these systems via all atom simulations of liquid-liquid phase separation of peptides. Systems of supersaturated pentapeptides separate into a peptide-dense liquid droplet phase as well as a dilute (saturated) aqueous phase. An analysis of the change in backbone conformational entropy associated with the phase transition was performed. We examined systems of four different pentapeptides (GGGGG, GGQGG, GGNGG, and GGVGG) in order to explore the effect of sequence variation on the conformational entropy, as well as the effect of side chain variation on the physical characteristics of the droplet phases. We find that the loss of conformational entropy that accompanies aqueous → droplet transitions is more than compensated by a decrease in interaction enthalpy as contributions to the free energy change for the process.
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Affiliation(s)
- Riley J Workman
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - B Montgomery Pettitt
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States
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15
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Arsiccio A, Shea JE. Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach. J Phys Chem B 2021; 125:5222-5232. [DOI: 10.1021/acs.jpcb.1c01694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Department of Physics, University of California, Santa Barbara, California 93106, United States
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16
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Trimethylamine N-oxide alters structure-function integrity of β-casein: Structural disorder co-regulates the aggregation propensity and chaperone activity. Int J Biol Macromol 2021; 182:921-930. [PMID: 33872615 DOI: 10.1016/j.ijbiomac.2021.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs), involved in the regulation and function of various cellular processes like transcription, translation, cell cycle etc., exist as ensembles of rapidly interconverting structures with functional plasticity. Among numerous cellular regulatory mechanisms involved in structural and functional regulation of IDPs, osmolytes are emerging as promising regulatory agents due to their ability to affect the structure-function integrity of IDPs. The present study investigated the effect of methylamine osmolytes on β-casein, an IDP essential for maintaining the overall stability of casein complex in milk. It was observed that trimethylamine N-oxide induces a compact structural state in β-casein with slightly decreased chaperone activity and insignificant aggregation propensity. However, the other two osmolytes from this group, i.e., sarcosine and betaine, had no significant effect on the overall structure and chaperone activity of the IDP. The present study hints towards the possible evolutionary selection of higher structural disorder in β-casein, compared to α-casein, for stability of the casein complex and prevention of amyloidosis in the mammary gland.
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17
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Tiwari MK, Murarka RK. Interaction strength of osmolytes with the anion of a salt-bridge determines its stability. Phys Chem Chem Phys 2021; 23:5527-5539. [PMID: 33651069 DOI: 10.1039/d0cp05378c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to understand the role of osmolytes in regulating physicochemical behavior of proteins, we investigated the influence of protein destabilizing (urea and guanidinium chloride) and stabilizing osmolytes (TMAO, glycerol, and betaine) on a model salt-bridge (SB) formed between structural analogues of arginine and glutamate/aspartate sidechains in a solvent continuum using first-principles quantum chemical calculations based on DFT and MP2 methods. The binding strength of the osmolyte with the SB is found to be in the order of betaine > TMAO > Gdm+ > glycerol > urea. The osmolytes (TMAO and betaine) that preferentially bind to the SB cation have a marginal influence on SB stability. Also, pure π-π stacking interaction between Gdm+ and the SB cation plays an insignificant role in destabilizing the SB. In fact, the interaction strength of osmolytes with the SB anion mainly determines the stability of SB. For instance, a competition between Gdm+ and the SB cation to bind with the SB anion is responsible for instability and subsequent dissociation of the SB. The competition provided by other osmolytes is too weak to break the SB. Exploiting this information, we designed three structural derivatives of Gdm+, all having a stronger interaction with SB anion, and thereby show a stronger SB dissociation potential. Furthermore, we find an excellent linear anti-correlation between SB interaction energy and the energy of interaction between osmolyte and the SB anion, which suggests that by knowing only the strength of osmolyteacetate interaction, one can predict the influence of osmolytes on the salt-bridge instability. This information is useful in fine-tuning the SB dissociation power of Gdm+, which has a practical significance in obtaining the mechanistic insight into the influence of GdmCl on protein stability. Our results also provide a basis for understanding the chemistry of other ion-pairs formed between a cationic hydrogen donor and an anionic acceptor.
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Affiliation(s)
- Mrityunjay K Tiwari
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
| | - Rajesh K Murarka
- A Department of Chemistry Indian Institute of Science Education and Research Bhopal Bhopal Bypass Road, Bhauri, Bhopal, MP 462066, India.
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18
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Banks DD, Cordia JF. Suppression of Electrostatic Mediated Antibody Liquid-Liquid Phase Separation by Charged and Noncharged Preferentially Excluded Excipients. Mol Pharm 2021; 18:1285-1292. [PMID: 33555888 DOI: 10.1021/acs.molpharmaceut.0c01138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isotonic concentrations of inert cosolutes or excipients are routinely used in protein therapeutic formulations to minimize physical instabilities including aggregation, particulation, and precipitation that are often manifested during drug substance/product manufacture and long-term storage. Despite their prevalent use within the biopharmaceutical industry, a more detailed understanding for how excipients modulate the specific protein-protein interactions responsible for these instabilities is still needed so that informed formulation decisions can be made at the earliest stages of development when protein supply and time are limited. In the present report, subisotonic concentrations of the five common formulation excipients, sucrose, proline, sorbitol, glycerol, arginine hydrochloride, and the denaturant urea, were studied for their effect on the room temperature liquid-liquid phase separation of a model monoclonal antibody (mAb-B). Although each excipient lowered the onset temperatures of mAb-B liquid-liquid phase separation to different extents, all six were found to be preferentially excluded from the native state monomer by vapor pressure osmometry, and no apparent correlations to the excipient dependence of mAb-B melting temperatures were observed. These results and those of the effects of solution pH, addition of salt, and impact of a small number of charge mutations were most consistent with a mechanism of local excipient accumulation, to an extent dependent on their type, with the specific residues that mediate mAb-B electrostatic protein-protein interactions. These findings suggest that selection of excipients on the basis of their interaction with the solvent exposed residues of the native state may at times be a more effective strategy for limiting protein-protein interactions at pharmaceutically relevant storage conditions than choosing those that are excluded from the residues of the native state interior.
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Affiliation(s)
- Douglas D Banks
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb, 4242 Campus Point Court, Suite 700, San Diego, California 92121, United States
| | - Jon F Cordia
- Department of Pharmaceutical Candidate Optimization, Bristol Myers Squibb, 4242 Campus Point Court, Suite 700, San Diego, California 92121, United States
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19
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Tsuruta M, Sugitani Y, Sugimoto N, Miyoshi D. Combined Effects of Methylated Cytosine and Molecular Crowding on the Thermodynamic Stability of DNA Duplexes. Int J Mol Sci 2021; 22:ijms22020947. [PMID: 33477917 PMCID: PMC7833394 DOI: 10.3390/ijms22020947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/31/2022] Open
Abstract
Methylated cytosine within CpG dinucleotides is a key factor for epigenetic gene regulation. It has been revealed that methylated cytosine decreases DNA backbone flexibility and increases the thermal stability of DNA. Although the molecular environment is an important factor for the structure, thermodynamics, and function of biomolecules, there are few reports on the effects of methylated cytosine under a cell-mimicking molecular environment. Here, we systematically investigated the effects of methylated cytosine on the thermodynamics of DNA duplexes under molecular crowding conditions, which is a critical difference between the molecular environment in cells and test tubes. Thermodynamic parameters quantitatively demonstrated that the methylation effect and molecular crowding effect on DNA duplexes are independent and additive, in which the degree of the stabilization is the sum of the methylation effect and molecular crowding effect. Furthermore, the effects of methylation and molecular crowding correlate with the hydration states of DNA duplexes. The stabilization effect of methylation was due to the favorable enthalpic contribution, suggesting that direct interactions of the methyl group with adjacent bases and adjacent methyl groups play a role in determining the flexibility and thermodynamics of DNA duplexes. These results are useful to predict the properties of DNA duplexes with methylation in cell-mimicking conditions.
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Affiliation(s)
- Mitsuki Tsuruta
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
| | - Yui Sugitani
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe 650-0047, Japan
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe 650-0047, Japan; (M.T.); (Y.S.); (N.S.)
- Correspondence: ; Tel.: +81-(07)-8303-1426
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20
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Iwaya N, Goda N, Matsuzaki M, Narita A, Shigemitsu Y, Tenno T, Abe Y, Hoshi M, Hiroaki H. Principal component analysis of data from NMR titration experiment of uniformly 15N labeled amyloid beta (1-42) peptide with osmolytes and phenolic compounds. Arch Biochem Biophys 2020; 690:108446. [PMID: 32593678 DOI: 10.1016/j.abb.2020.108446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/11/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
A simple NMR method to analyze the data obtained by NMR titration experiment of amyloid formation inhibitors against uniformly 15N-labeled amyloid-β 1-42 peptide (Aβ(1-42)) was described. By using solution nuclear magnetic resonance (NMR) measurement, the simplest method for monitoring the effects of Aβ fibrilization inhibitors is the NMR chemical shift perturbation (CSP) experiment using 15N-labeled Aβ(1-42). However, the flexible and dynamic nature of Aβ(1-42) monomer may hamper the interpretation of CSP data. Here we introduced principal component analysis (PCA) for visualizing and analyzing NMR data of Aβ(1-42) in the presence of amyloid inhibitors including high concentration osmolytes. We measured 1H-15N 2D spectra of Aβ(1-42) at various temperatures as well as of Aβ(1-42) with several inhibitors, and subjected all the data to PCA (PCA-HSQC). The PCA diagram succeeded in differentiating the various amyloid inhibitors, including epigallocatechin gallate (EGCg), rosmarinic acid (RA) and curcumin (CUR) from high concentration osmolytes. We hypothesized that the CSPs reflected the conformational equilibrium of intrinsically disordered Aβ(1-42) induced by weak inhibitor binding rather than the specific molecular interactions.
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Affiliation(s)
- Naoko Iwaya
- Research Fellowship for Young Scientists, Japan Society for the Promotion of Science, Japan; Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Mizuki Matsuzaki
- Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Akihiro Narita
- Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Yoshiki Shigemitsu
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuda, 4259, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan; Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
| | - Yoshito Abe
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.
| | - Minako Hoshi
- Institute of Biomedical Research and Innovation, Kobe, 650-0047, Japan.
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan; Structural Biology Research Center and Division of Biological Sciences, Graduate School of Science, Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8601, Japan.
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21
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Arsiccio A, Ganguly P, La Cortiglia L, Shea JE, Pisano R. ADD Force Field for Sugars and Polyols: Predicting the Additivity of Protein-Osmolyte Interaction. J Phys Chem B 2020; 124:7779-7790. [PMID: 32790371 PMCID: PMC7901642 DOI: 10.1021/acs.jpcb.0c05345] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
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The protein–osmolyte interaction has been shown experimentally to follow an
additive construct, where the individual osmolyte–backbone and
osmolyte–side-chain interactions contribute to the overall conformational
stability of proteins. Here, we computationally reconstruct this additive relation using
molecular dynamics simulations, focusing on sugars and polyols, including sucrose and
sorbitol, as model osmolytes. A new set of parameters (ADD) is developed for this
purpose, using the individual Kirkwood–Buff integrals for sugar–backbone
and sugar–side-chain interactions as target experimental data. We show that the
ADD parameters can reproduce the additivity of protein–sugar interactions and
correctly predict sucrose and sorbitol self-association and their interaction with
water. The accurate description of the separate osmolyte–backbone and
osmolyte–side-chain contributions also automatically translates into a good
prediction of preferential exclusion from the surface of ribonuclease A and
α-chymotrypsinogen A. The description of sugar polarity is improved compared to
previous force fields, resulting in closer agreement with the experimental data and
better compatibility with charged groups, such as the guanidinium moiety. The ADD
parameters are developed in combination with the CHARMM36m force field for proteins, but
good compatibility is also observed with the AMBER 99SB-ILDN and the OPLS-AA force
fields. Overall, exploiting the additivity of protein–osmolyte interactions is a
promising approach for the development of new force fields.
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Affiliation(s)
- Andrea Arsiccio
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Pritam Ganguly
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Lorenzo La Cortiglia
- Department of Applied Science and Technology, Politecnico di Torino, 24 Corso Duca Degli Abruzzi, Torino 10129, Italy
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, California 93106, United States.,Department of Physics, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Roberto Pisano
- Department of Applied Science and Technology, Politecnico di Torino, 24 Corso Duca Degli Abruzzi, Torino 10129, Italy
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23
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Disorder under stress: Role of polyol osmolytes in modulating fibrillation and aggregation of intrinsically disordered proteins. Biophys Chem 2020; 264:106422. [PMID: 32707418 DOI: 10.1016/j.bpc.2020.106422] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/18/2022]
Abstract
Intrinsically disordered proteins (IDPs) comprise ~30-40% of the proteome, have key roles in cellular processes, and have been reported to be involved in stress regulation working in synergy with osmolytes. Osmolytes are known to accumulate against various stresses in living systems and are known to stabilize the native conformation of globular proteins. However, little is known of their effect on IDPs and their mechanism of action is unclear. We have investigated the effect of a series of polyol osmolytes on the conformation, aggregation and fibrillation properties of the IDPs α and β-synuclein, involved in Parkinson's disease, using fluorescence, CD, light scattering and TEM. We observe inhibition of fibril and aggregate formation with increasing concentration as well as the number of hydroxyl groups in polyols as observed by light scattering measurements which correlates well with the increase in viscosity of solution with increasing number of OH groups in them. However, ThT assay, while indicating suppression of fibril formation at various concentrations of polyols, shows enhanced fibrillation at some other concentrations which could be due to the heterogeneity of the species formed that are ThT insensitive. Fibril formation was, thus, probed by using Nile red fluorescence which showed sensitivity towards the species formed. ANS binding fluorescence also indicates a decrease in the hydrophobicity of the fibrils with increasing number of OH groups in polyols. Polyols do not have any effect on the fibrillation of β-syn but lead to enhanced amorphous aggregate formation in presence of Ethylene Glycol and Glycerol and a reduction in the presence of Sorbitol. The net free energy of transfer of the proteins from water to Sorbitol is large and positive while it is relatively negligible in the case of Glycerol suggestive of greater preferential exclusion effect of Sorbitol in comparison with Glycerol in the case of IDPs as well. The results overall show differential and complex effect of osmolytes towards the fibrillation/aggregation properties of the two IDPs and suggest that an appropriate balance between the concentration and type of polyol or osmolyte would be required for the survival of organisms rich in IDPs under various stress conditions.
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Bhat MY, Singh LR, Dar TA. Taurine Induces an Ordered but Functionally Inactive Conformation in Intrinsically Disordered Casein Proteins. Sci Rep 2020; 10:3503. [PMID: 32103094 PMCID: PMC7044306 DOI: 10.1038/s41598-020-60430-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 01/31/2020] [Indexed: 11/30/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are involved in various important biological processes, such as cell signalling, transcription, translation, cell division regulation etc. Many IDPs need to maintain their disordered conformation for proper function. Osmolytes, natural organic compounds responsible for maintaining osmoregulation, have been believed to regulate the functional activity of macromolecules including globular proteins and IDPs due to their ability of modulating the macromolecular structure, conformational stability, and functional integrity. In the present study, we have investigated the effect of all classes of osmolytes on two model IDPs, α- and β-casein. It was observed that osmolytes can serve either as folding inducers or folding evaders. Folding evaders, in general, do not induce IDP folding and therefore had no significant effect on structural and functional integrity of IDPs. On the other hand, osmolytes taurine and TMAO serve as folding inducers by promoting structural collapse of IDPs that eventually leads to altered structural and functional integrity of IDPs. This study sheds light on the osmolyte-induced regulation of IDPs and their possible role in various disease pathologies.
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Affiliation(s)
- Mohd Younus Bhat
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, J&K, 190006, India
| | | | - Tanveer Ali Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, J&K, 190006, India.
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25
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Dilip.H.N., Chakraborty D. Effect of cosolvents in the preferential binding affinity of water in aqueous solutions of amino acids and amides. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2019.112375] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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26
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Raghunathan S, Jaganade T, Priyakumar UD. Urea-aromatic interactions in biology. Biophys Rev 2020; 12:65-84. [PMID: 32067192 PMCID: PMC7040157 DOI: 10.1007/s12551-020-00620-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.
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Affiliation(s)
- Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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27
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Tischer A, Machha VR, Moon-Tasson L, Benson LM, Auton M. Glycosylation sterically inhibits platelet adhesion to von Willebrand factor without altering intrinsic conformational dynamics. J Thromb Haemost 2020; 18:79-90. [PMID: 31479573 PMCID: PMC6940534 DOI: 10.1111/jth.14628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/26/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND A molecular basis for von Willebrand factor (VWF) self-inhibition has been proposed by which the N-terminal and C-terminal flanking sequences of the globular A1 domain disulfide loop bind to and suppress the conformational dynamics of A1. These flanking sequences are rich in O-linked glycosylation (OLG), which is known to suppress platelet adhesion to VWF, presumably by steric hindrance. The inhibitory mechanism remains unresolved as to whether inhibition is due to steric exclusion by OLGs or a direct self-association interaction that stabilizes the domain. OBJECTIVES The platelet adhesive function, thermodynamic stability, and conformational dynamics of the wild-type and type 2M G1324S A1 domain lacking glycosylation (Escherichia coli) are compared with the wild-type glycosylated A1 domain (HEK293 cell culture) to decipher the self-inhibitory mechanism. METHODS Surface plasmon resonance and analytical rheology are utilized to assess Glycoprotein Ibα (GPIbα) binding at equilibrium and platelet adhesion under shear flow. The conformational stability is assessed through a combination of protein unfolding thermodynamics and hydrogen-deuterium exchange mass spectrometry (HXMS). RESULTS A1 glycosylation inhibits both GPIbα binding and platelet adhesion. Glycosylation increases the hydrodynamic size of A1 and stabilizes the thermal unfolding of A1 without changing its equilibrium stability. Glycosylation does not alter the intrinsic conformational dynamics of the A1 domain. CONCLUSIONS These studies invalidate the proposed inhibition through conformational suppression since glycosylation within these flanking sequences does not alter the native state stability or the conformational dynamics of A1. Rather, they confirm a mechanism by which glycosylation sterically hinders platelet adhesion to the A1 domain at equilibrium and under rheological shear stress.
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Affiliation(s)
- Alexander Tischer
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Venkata R. Machha
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Laurie Moon-Tasson
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Linda M. Benson
- Proteomics Core, Department of Biochemistry and Molecular Biology, College of Medicine, Mayo Clinic, Rochester, Minnesota, 55905, USA
| | - Matthew Auton
- Division of Hematology, Departments of Internal Medicine and Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, 55905, USA
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28
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Yan C, Huang X, Chen J, Guo H, Shao H. Study on Preferential Solvation of Water by Electrochemical Method. ELECTROANAL 2019. [DOI: 10.1002/elan.201900243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Chunxia Yan
- Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, Key Laboratory of Cluster Science (Ministry of Education), School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing 102488 P.R. China
| | - Ximing Huang
- Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, Key Laboratory of Cluster Science (Ministry of Education), School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing 102488 P.R. China
| | - Jingchao Chen
- Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, Key Laboratory of Cluster Science (Ministry of Education), School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing 102488 P.R. China
| | - Haixia Guo
- Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, Key Laboratory of Cluster Science (Ministry of Education), School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing 102488 P.R. China
| | - Huibo Shao
- Beijing Key Laboratory of Photoelectronic and Electrophotonic Conversion Materials, Key Laboratory of Cluster Science (Ministry of Education), School of Chemistry and Chemical EngineeringBeijing Institute of Technology Beijing 102488 P.R. China
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Shukla N, Goeks J, Taylor EA, Othon CM. Hydration Dynamics in Solutions of Cyclic Polyhydroxyl Osmolytes. J Phys Chem B 2019; 123:8472-8479. [PMID: 31508961 DOI: 10.1021/acs.jpcb.9b06861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Simple sugars are remarkably effective at preserving protein and enzymatic structures against thermal and hydrostatic stress. Here, we investigate the hydrodynamic and biopreservative properties of three small cyclic molecules: glucose, myo-inositol, and methyl-α-d-glucopyranoside using circular dichroism spectroscopy and isothermal calorimetry. Using ultrafast fluorescence frequency upconversion spectroscopy, we measure the dynamical retardation of hydration dynamics in cosolute solutions. We find that all three molecules are effective modifiers of hydration dynamics in solution and all are also effective at protecting model protein systems against thermal denaturation. Methyl-α-d-glucopyranoside is found to be the most effective dynamic reducer displaying an approximately 30% increase in solvation relaxation time as compared to water in a cosolute free solution. myo-Inositol and glucose both exhibit a smaller reduction in dynamics with similar magnitudes of concentration dependence. Using these cosolute models, we demonstrate that the thermal enhancement of protein structure does not correlate strongly with either the dynamical reduction of the bulk solution nor with the number of hydrogen bonds a cosolute makes with the solvent. Furthermore, solutions of glucose at twice the concentration of trehalose are shown to have similar magnitudes of dynamical impact. This implies that regulation of hydration dynamics is not a distinguishing characteristic of successful osmolytes. This work highlights the need for further studies and computational analysis to understand the phenomena of preferential exclusion and the contribution of hydration dynamics to protein structural stability.
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Affiliation(s)
| | - Julia Goeks
- Department of Physics , Ripon College , Ripon , Wisconsin 54971 , United States
| | | | - Christina M Othon
- Department of Physics , Ripon College , Ripon , Wisconsin 54971 , United States
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30
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Hirai M, Ajito S, Sugiyama M, Iwase H, Takata SI, Shimizu N, Igarashi N, Martel A, Porcar L. Direct Evidence for the Effect of Glycerol on Protein Hydration and Thermal Structural Transition. Biophys J 2019; 115:313-327. [PMID: 30021107 DOI: 10.1016/j.bpj.2018.06.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 01/07/2023] Open
Abstract
The mechanisms of protein stabilization by uncharged solutes, such as polyols and sugars, have been intensively studied with respect to the chemical thermodynamics of molecular crowding. In particular, many experimental and theoretical studies have been conducted to explain the mechanism of the protective action on protein structures by glycerol through the relationship between hydration and glycerol solvation on protein surfaces. We used wide-angle x-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation to quantitatively characterize the hydration and/or solvation shell of myoglobin in aqueous solutions of up to 75% v/v glycerol. At glycerol concentrations below ∼40% v/v, the preservation of the hydration shell was dominant, which was reasonably explained by the preferential exclusion of glycerol from the protein surface (preferential hydration). In contrast, at concentrations above 50% v/v, the partial penetration or replacement of glycerol into or with hydration-shell water (neutral solvation by glycerol) was gradually promoted. WAXS results quantitatively demonstrated the neutral solvation, in which the replacement of hydrated water by glycerol was proportional to the volume fraction of glycerol in the solvent multiplied by an exchange rate (β ≤ 1). These phenomena were confirmed by small-angle neutron scattering measurements. The observed WAXS data covered the entire hierarchical structure of myoglobin, ranging from tertiary to secondary structures. We separately analyzed the effect of glycerol on the thermal stability of myoglobin at each hierarchical structural level. The thermal transition midpoint temperature at each hierarchical structural level was raised depending on the glycerol concentration, with enhanced transition cooperativeness between different hierarchical structural levels. The onset temperature of the helix-to-cross β-sheet transition (the initial process of amyloid formation) was evidently elevated. However, oligomerization connected to fibril formation was suppressed, even at a low glycerol concentration.
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Affiliation(s)
- Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, Maebashi, Gunma, Japan.
| | - Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, Maebashi, Gunma, Japan
| | - Masaaki Sugiyama
- Kyoto University Research Reactor Institute, Kumatori, Osaka, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, Tokai, Japan
| | | | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
| | - Noriyuki Igarashi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, Tsukuba, Ibaraki, Japan
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31
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Banks DD, Cordia JF, Spasojevic V, Sun J, Franc S, Cho Y. Isotonic concentrations of excipients control the dimerization rate of a therapeutic immunoglobulin G1 antibody during refrigerated storage based on their rank order of native-state interaction. Protein Sci 2019; 27:2073-2083. [PMID: 30267438 DOI: 10.1002/pro.3518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 09/06/2018] [Accepted: 09/25/2018] [Indexed: 01/12/2023]
Abstract
Inert co-solutes, or excipients, are often included in protein biologic formulations to adjust the tonicity of liquid dosage forms intended for subcutaneous delivery. Despite the low concentration of their use, many of these excipients alter protein-protein interactions such as dimerization and aggregation rates of high concentration monoclonal antibody (mAb) therapeutics to varying extents during long-term refrigerated clinical storage, challenging the formulation scientist to make informed excipient selections at the earliest stages of development when protein supply and time are often limited. The objectives of this study were to better understand how isotonic concentrations of excipients influence the dimerization rates of a model mAb stored at refrigerated and room temperatures and explore protein sparing biophysical methods capable of predicting this dependence. Despite their prevalence of use in the biopharmaceutical industry, methods for assessing conformational stability such differential scanning calorimetry and isothermal equilibrium unfolding showed little predictive power and we highlight some of the assumptions and technical challenges of their use with mAbs. Conversely, measures of colloidal stability of the native-state such as preferential interaction coefficients measured by vapor pressure osmometry and solubility assessed by polyethylene-glycol induced precipitation correlated reasonably well with the mAb dimerization data and are most consistent with the excipients tested minimizing dimerization by interacting favorably with the residues comprising the protein-protein association interface.
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Affiliation(s)
- Douglas D Banks
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Jon F Cordia
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Vladimir Spasojevic
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Jeonghoon Sun
- Department of Biotherapeutics, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Sarah Franc
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
| | - Younhee Cho
- Department of Biologics Drug Product Development, Celgene Corp, 10300 Campus Point Drive Suite 100, San Diego, California, 92121
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32
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Roy S, Bhat R. Effect of polyols on the structure and aggregation of recombinant human γ-Synuclein, an intrinsically disordered protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1866:1029-1042. [DOI: 10.1016/j.bbapap.2018.07.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/06/2018] [Accepted: 07/05/2018] [Indexed: 10/28/2022]
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33
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Ajito S, Iwase H, Takata SI, Hirai M. Sugar-Mediated Stabilization of Protein against Chemical or Thermal Denaturation. J Phys Chem B 2018; 122:8685-8697. [DOI: 10.1021/acs.jpcb.8b06572] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Satoshi Ajito
- Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
| | - Hiroki Iwase
- Comprehensive Research Organization for Science and Society, Tokai 319-1106, Japan
| | - Shin-ichi Takata
- J-PARC Center, Japan Atomic Energy Agency, Tokai 319-1106, Japan
| | - Mitsuhiro Hirai
- Graduate School of Science and Technology, Gunma University, 4-2 Aramaki, Maebashi, Gunma 371-8510, Japan
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34
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Ghosh R, Kishore N. Physicochemical Insights into the Stabilization of Stressed Lysozyme and Glycine Homopeptides by Sorbitol. J Phys Chem B 2018; 122:7839-7854. [DOI: 10.1021/acs.jpcb.8b04394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ritutama Ghosh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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35
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Improving Viscosity and Stability of a Highly Concentrated Monoclonal Antibody Solution with Concentrated Proline. Pharm Res 2018; 35:133. [DOI: 10.1007/s11095-018-2398-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/28/2018] [Indexed: 12/22/2022]
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36
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Choi JH, Lee H, Choi HR, Cho M. Graph Theory and Ion and Molecular Aggregation in Aqueous Solutions. Annu Rev Phys Chem 2018; 69:125-149. [DOI: 10.1146/annurev-physchem-050317-020915] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jun-Ho Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
- Current affiliation: Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hochan Lee
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Hyung Ran Choi
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
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37
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Alvarado YJ, Ferrebuz A, Paz JL, Rodríguez-Lugo P, Restrepo J, Romero F, Fernández-Acuña J, Williams YO, Toro-Mendoza J. Surface Behavior of BSA/Water/Carbohydrate Systems from Molecular Polarizability Measurements. J Phys Chem B 2018; 122:4231-4238. [PMID: 29582658 DOI: 10.1021/acs.jpcb.7b11998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of the presence of glucose and sucrose on the nonintrinsic contribution to partial molar volume ⟨Θ⟩ni of bovine serum albumin (BSA) is determined by means of static and dynamic electronic polarizability measurements. For that aim, a combined strategy based on high-resolution refractometry, high exactitude densitometry, and synchronous fluorescence spectroscopy is applied. Both static and dynamic mean electronic molecular polarizability values are found to be sensitive to the presence of glucose. In the case of sucrose, the polarizability of BSA is not appreciably affected. In fact, our results revealed that the electronic changes observed occurred without a modification of the native conformation of BSA. On the contrary, a nonmonotonous behavior with the concentration is observed in presence of glucose. These results advocate the influence of the electronic polarization on the repulsive and attractive protein-carbohydrate interactions. An analysis using the scaled particle theory indicates that the accumulation of glucose on the protein surface promotes dehydration. Inversely, hydration and preferential exclusion occur in the vicinity of the protein surface for sucrose-enriched systems.
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Affiliation(s)
| | | | - Jose Luis Paz
- Departamento de Física , Escuela Politécnica Nacional , Ladron de Guevara , Quito 170517 , Ecuador
| | - Patricia Rodríguez-Lugo
- Laboratorio de Electrónica Molecular, Facultad Experimental de Ciencias, Departamento de Química , Universidad del Zulia , Maracaibo 4001 , Venezuela
| | | | - Freddy Romero
- Center for Translational Medicine and Korman Lung Center , Thomas Jefferson University , Philadelphia , Pennsylvania 19107 , United States
| | - Jaqueline Fernández-Acuña
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
| | - Yhan O'Neil Williams
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
| | - Jhoan Toro-Mendoza
- Centro de Estudios Interdisciplinarios de la Física , Instituto Venezolano de Investigaciones Científicas (IVIC) , Caracas 1020A , Venezuela
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38
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Abstract
Cytochrome c (Cyt c) was rapidly oxidized by molecular oxygen in the presence, but not absence of PEG. The redox potential of heme c was determined by the potentiometric titration to be +236 ± 3 mV in the absence of PEG, which was negatively shifted to +200 ± 4 mV in the presence of PEG. The underlying the rapid oxidation was explored by examining the structural changes in Cyt c in the presence of PEG using UV-visible absorption, circular dichroism, resonance Raman, and fluorescence spectroscopies. These spectroscopic analyses suggested that heme oxidation was induced by a modest tertiary structural change accompanied by a slight shift in the heme position (<1.0 Å) rather than by partial denaturation, as is observed in the presence of cardiolipin. The near-infrared spectra showed that PEG induced dehydration from Cyt c, which triggered heme displacement. The primary dehydration site was estimated to be around surface-exposed hydrophobic residues near the heme center: Ile81 and Val83. These findings and our previous studies, which showed that hydrated water molecules around Ile81 and Val83 are expelled when Cyt c forms a complex with CcO, proposed that dehydration of these residues is functionally significant to electron transfer from Cyt c to CcO.
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39
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Su Z, Ravindhran G, Dias CL. Effects of Trimethylamine-N-oxide (TMAO) on Hydrophobic and Charged Interactions. J Phys Chem B 2018; 122:5557-5566. [DOI: 10.1021/acs.jpcb.7b11847] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Zhaoqian Su
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Gopal Ravindhran
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
| | - Cristiano L. Dias
- Department of Physics, New Jersey Institute of Technology, University Heights Newark, New Jersey 07102-1982, United States
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40
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Hall D, Kinjo AR, Goto Y. A new look at an old view of denaturant induced protein unfolding. Anal Biochem 2018; 542:40-57. [DOI: 10.1016/j.ab.2017.11.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 11/11/2017] [Accepted: 11/16/2017] [Indexed: 12/15/2022]
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41
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Imoto S, Forbert H, Marx D. Aqueous TMAO solutions as seen by theoretical THz spectroscopy: hydrophilic versus hydrophobic water. Phys Chem Chem Phys 2018; 20:6146-6158. [DOI: 10.1039/c7cp07003a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
All THz resonances of aqueous TMAO solutions are computed and assigned based on ab initio molecular dynamics simulations.
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Affiliation(s)
- Sho Imoto
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Harald Forbert
- Center for Solvation Science ZEMOS
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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42
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Nicol TWJ, Matubayasi N, Shimizu S. Origin of non-linearity in phase solubility: solubilisation by cyclodextrin beyond stoichiometric complexation. Phys Chem Chem Phys 2017; 18:15205-17. [PMID: 27206059 DOI: 10.1039/c6cp01582d] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The low solubility of drugs, which poses a serious problem in drug development, can in part be overcome by the use of cyclodextrins (CDs) and their derivatives. Here, the key to solubilisation is identified as the formation of inclusion complexes with the drug molecule. If inclusion complexation were the only contribution to drug solubility, it would increase linearly with CD concentration (as per the Higuchi-Connors model); this is because inclusion complexation is a 1 : 1 stoichiometric process. However, solubility curves often deviate from this linearity, whose mechanism is yet to be understood. Here we aim to clarify the origin of such non-linearity, based on the Kirkwood-Buff and the McMillan-Mayer theories of solutions. The rigorous statistical thermodynamic theory shows that non-linearity of solubilisation can be rationalised by two contributions: CD-drug interaction and the drug-induced change of CD-CD interaction.
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Affiliation(s)
- Thomas W J Nicol
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan and Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan
| | - Seishi Shimizu
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.
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43
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44
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Su Z, Mahmoudinobar F, Dias CL. Effects of Trimethylamine-N-oxide on the Conformation of Peptides and its Implications for Proteins. PHYSICAL REVIEW LETTERS 2017; 119:108102. [PMID: 28949191 DOI: 10.1103/physrevlett.119.108102] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Indexed: 05/16/2023]
Abstract
To provide insights into the stabilizing mechanisms of trimethylamine-N-oxide (TMAO) on protein structures, we perform all-atom molecular dynamics simulations of peptides and the Trp-cage miniprotein. The effects of TMAO on the backbone and charged residues of peptides are found to stabilize compact conformations, whereas effects of TMAO on nonpolar residues lead to peptide swelling. This suggests competing mechanisms of TMAO on proteins, which accounts for hydrophobic swelling, backbone collapse, and stabilization of charge-charge interactions. These mechanisms are observed in Trp cage.
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Affiliation(s)
- Zhaoqian Su
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Farbod Mahmoudinobar
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
| | - Cristiano L Dias
- Physics Department, New Jersey Institute of Technology, Newark, 07102-1982 New Jersey, USA
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45
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Papini CM, Pandharipande PP, Royer CA, Makhatadze GI. Putting the Piezolyte Hypothesis under Pressure. Biophys J 2017; 113:974-977. [PMID: 28803626 DOI: 10.1016/j.bpj.2017.07.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/15/2017] [Accepted: 07/25/2017] [Indexed: 12/01/2022] Open
Abstract
A group of small molecules that stabilize proteins against high hydrostatic pressure has been classified as piezolytes, a subset of stabilizing cosolutes. This distinction would imply that piezolytes counteract the effects of high hydrostatic pressure through effects on the volumetric properties of the protein. The purpose of this study was to determine if cosolutes proposed to be piezolytes have an effect on the volumetric properties of proteins through direct experimental measurements of volume changes upon unfolding of model proteins lysozyme and ribonuclease A, in solutions containing varying cosolute concentrations. Solutions containing the proposed piezolytes glutamate, sarcosine, and betaine were used, as well as solutions containing the denaturants guanidinium hydrochloride and urea. Changes in thermostability were monitored using differential scanning calorimetry whereas changes in volume were monitored using pressure perturbation calorimetry. Our findings indicate that increasing stabilizing cosolute concentration increases the stability and transition temperature of the protein, but does not change the temperature dependence of volume changes upon unfolding. The results suggest that the pressure stability of a protein in solution is not directly affected by the presence of these proposed piezolytes, and so they cannot be granted this distinction.
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Affiliation(s)
- Christina M Papini
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Pranav P Pandharipande
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
| | - Catherine A Royer
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - George I Makhatadze
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.
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46
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Feig M, Yu I, Wang PH, Nawrocki G, Sugita Y. Crowding in Cellular Environments at an Atomistic Level from Computer Simulations. J Phys Chem B 2017; 121:8009-8025. [PMID: 28666087 PMCID: PMC5582368 DOI: 10.1021/acs.jpcb.7b03570] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
The
effects of crowding in biological environments on biomolecular
structure, dynamics, and function remain not well understood. Computer
simulations of atomistic models of concentrated peptide and protein
systems at different levels of complexity are beginning to provide
new insights. Crowding, weak interactions with other macromolecules
and metabolites, and altered solvent properties within cellular environments
appear to remodel the energy landscape of peptides and proteins in
significant ways including the possibility of native state destabilization.
Crowding is also seen to affect dynamic properties, both conformational
dynamics and diffusional properties of macromolecules. Recent simulations
that address these questions are reviewed here and discussed in the
context of relevant experiments.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States.,Quantitative Biology Center, RIKEN , Kobe, Japan
| | - Isseki Yu
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan
| | - Po-Hung Wang
- Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan
| | - Grzegorz Nawrocki
- Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan, United States
| | - Yuji Sugita
- Quantitative Biology Center, RIKEN , Kobe, Japan.,Theoretical Molecular Science Laboratory, RIKEN , Wako, Japan.,iTHES Research Group, RIKEN , Wako, Japan.,Advanced Institute for Computational Science, RIKEN , Kobe, Japan
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47
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Sirotkin VA, Kuchierskaya AA. α-chymotrypsin in water-acetone and water-dimethyl sulfoxide mixtures: Effect of preferential solvation and hydration. Proteins 2017; 85:1808-1819. [PMID: 28612358 DOI: 10.1002/prot.25334] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 11/10/2022]
Abstract
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin. α-Chymotrypsin is preferentially hydrated at high water content. The residual enzyme activity values are close to 100%. At intermediate water content, the dehydrated α-chymotrypsin has a higher affinity for acetone/DMSO than for water. Residual enzyme activity is minimal in this concentration range. The acetone/DMSO molecules are preferentially excluded from the protein surface at the lowest water content, resulting in preferential hydration. The residual catalytic activity in the water-poor acetone is ∼80%, compared with that observed after incubation in pure water. This effect is very small for the water-poor DMSO. Two different schemes are operative for the hydrated enzyme. At high and intermediate water content, α-chymotrypsin exhibits preferential hydration. However, at intermediate water content, in contrast to the dried enzyme, the initially hydrated α-chymotrypsin possesses increased preferential hydration parameters. At low water content, no residual enzyme activity was observed. Preferential binding of DMSO/acetone to α-chymotrypsin was detected. Our data clearly demonstrate that the hydrogen bond accepting ability of organic solvents and the protein hydration level constitute key factors in determining the stability of protein-water-organic solvent systems.
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Affiliation(s)
- Vladimir A Sirotkin
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
| | - Alexandra A Kuchierskaya
- Department of Physical Chemistry, Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kazan, 420008, Russia
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48
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Sirotkin VA, Kuchierskaya AA. Lysozyme in water-acetonitrile mixtures: Preferential solvation at the inner edge of excess hydration. J Chem Phys 2017; 146:215101. [PMID: 28576085 DOI: 10.1063/1.4984116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Preferential solvation/hydration is an effective way for regulating the mechanism of the protein destabilization/stabilization. Organic solvent/water sorption and residual enzyme activity measurements were performed to monitor the preferential solvation/hydration of hen egg-white lysozyme at high and low water content in acetonitrile at 25 °C. The obtained results show that the protein destabilization/stabilization depends essentially on the initial hydration level of lysozyme and the water content in acetonitrile. There are three composition regimes for the dried lysozyme. At high water content, the lysozyme has a higher affinity for water than for acetonitrile. The residual enzyme activity values are close to 100%. At the intermediate water content, the dehydrated lysozyme has a higher affinity for acetonitrile than for water. A minimum on the residual enzyme activity curve was observed in this concentration range. At the lowest water content, the organic solvent molecules are preferentially excluded from the dried lysozyme, resulting in the preferential hydration. The residual catalytic activity is ∼80%, compared with that observed after incubation in pure water. Two distinct schemes are operative for the hydrated lysozyme. At high and intermediate water content, lysozyme is preferentially hydrated. However, in contrast to the dried protein, at the intermediate water content, the initially hydrated lysozyme has the increased preferential hydration parameters. At low water content, the preferential binding of the acetonitrile molecules to the initially hydrated lysozyme was detected. No residual enzyme activity was observed in the water-poor acetonitrile. Our data clearly show that the initial hydration level of the protein macromolecules is one of the key factors that govern the stability of the protein-water-organic solvent systems.
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Affiliation(s)
- Vladimir A Sirotkin
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
| | - Alexandra A Kuchierskaya
- A.M. Butlerov Institute of Chemistry, Kazan Federal University, Kremlevskaya Str., 18, Kazan 420008, Russia
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Sirotkin VA, Kuchierskaya AA. Preferential Solvation/Hydration of α-Chymotrypsin in Water–Acetonitrile Mixtures. J Phys Chem B 2017; 121:4422-4430. [PMID: 28414445 DOI: 10.1021/acs.jpcb.7b01632] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vladimir A. Sirotkin
- Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kremlevskaya str., 18, Kazan 420008, Russia
| | - Alexandra A. Kuchierskaya
- Kazan Federal University, A.M. Butlerov Institute of Chemistry, Kremlevskaya str., 18, Kazan 420008, Russia
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Fedotova MV, Kruchinin SE, Chuev GN. Hydration structure of osmolyte TMAO: concentration/pressure-induced response. NEW J CHEM 2017. [DOI: 10.1039/c6nj03296f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The effect of solute concentration/pressure on the TMAO hydration structure was studied to understand its protective action under abiotic stressors.
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Affiliation(s)
- Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Sergey E. Kruchinin
- G.A. Krestov Institute of Solution Chemistry
- The Russian Academy of Sciences
- Ivanovo
- Russia
| | - Gennady N. Chuev
- Institute of Theoretical and Experimental Biophysics
- The Russian Academy of Sciences
- Pushchino
- Russia
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