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Lang X, Shi L, Zhao Z, Min W. Probing the structure of water in individual living cells. Nat Commun 2024; 15:5271. [PMID: 38902250 PMCID: PMC11190263 DOI: 10.1038/s41467-024-49404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/04/2024] [Indexed: 06/22/2024] Open
Abstract
Water regulates or even governs a wide range of biological processes. Despite its fundamental importance, surprisingly little is known about the structure of intracellular water. Herein we employ a Raman micro-spectroscopy technique to uncover the composition, abundance and vibrational spectra of intracellular water in individual living cells. In three different cell types, we show a small but consistent population (~3%) of non-bulk-like water. It exhibits a weakened hydrogen-bonded network and a more disordered tetrahedral structure. We attribute this population to biointerfacial water located in the vicinity of biomolecules. Moreover, our whole-cell modeling suggests that all soluble (globular) proteins inside cells are surrounded by, on average, one full molecular layer (about 2.6 Angstrom) of biointerfacial water. Furthermore, relative invariance of biointerfacial water is observed among different single cells. Overall, our study not only opens up experimental possibilities of interrogating water structure in vivo but also provides insights into water in life.
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Affiliation(s)
- Xiaoqi Lang
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Lixue Shi
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, 10027, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, 10027, USA.
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2
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König B, Pezzotti S, Ramos S, Schwaab G, Havenith M. Real-time measure of solvation free energy changes upon liquid-liquid phase separation of α-elastin. Biophys J 2024; 123:1367-1375. [PMID: 37515326 PMCID: PMC11163292 DOI: 10.1016/j.bpj.2023.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
Biological condensates are known to retain a large fraction of water to remain in a liquid and reversible state. Local solvation contributions from water hydrating hydrophilic and hydrophobic protein surfaces were proposed to play a prominent role for the formation of condensates through liquid-liquid phase separation (LLPS). However, although the total free energy is accessible by calorimetry, the partial solvent contributions to the free energy changes upon LLPS remained experimentally inaccessible so far. Here, we show that the recently developed THz calorimetry approach allows to quantify local hydration enthalpy and entropy changes upon LLPS of α-elastin in real time, directly from experimental THz spectroscopy data. We find that hydrophobic solvation dominates the entropic solvation term, whereas hydrophilic solvation mainly contributes to the enthalpy. Both terms are in the order of hundreds of kJ/mol, which is more than one order of magnitude larger than the total free energy changes at play during LLPS. However, since we show that entropy/enthalpy mostly compensates, a small entropy/enthalpy imbalance is sufficient to tune LLPS. Theoretically, a balance was proposed before. Here we present experimental evidence based on our spectroscopic approach. We finally show that LLPS can be steered by inducing small changes of solvation entropy/enthalpy compensation via concentration or temperature in α-elastin.
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Affiliation(s)
- Benedikt König
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Simone Pezzotti
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Sashary Ramos
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Gerhard Schwaab
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany
| | - Martina Havenith
- Lehrstuhl für Physikalische Chemie II, Ruhr-Universität Bochum, Bochum, Germany.
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3
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Ramos S, Kamps J, Pezzotti S, Winklhofer KF, Tatzelt J, Havenith M. Hydration makes a difference! How to tune protein complexes between liquid-liquid and liquid-solid phase separation. Phys Chem Chem Phys 2023; 25:28063-28069. [PMID: 37840355 DOI: 10.1039/d3cp03299j] [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: 10/17/2023]
Abstract
Understanding how protein rich condensates formed upon liquid-liquid phase separation (LLPS) evolve into solid aggregates is of fundamental importance for several medical applications, since these are suspected to be hot-spots for many neurotoxic diseases. This requires developing experimental approaches to observe in real-time both LLPS and liquid-solid phase separation (LSPS), and to unravel the delicate balance of protein and water interactions dictating the free energy differences between the two. We present a vibrational THz spectroscopy approach that allows doing so from the point of view of hydration water. We focus on a cellular prion protein of high medical relevance, which we can drive to undergo either LLPS or LSPS with few mutations. We find that it is a subtle balance of hydrophobic and hydrophilic solvation contributions that allows tuning between LLPS and LSPS. Hydrophobic hydration provides an entropic driving force to phase separation, through the release of hydration water into the bulk. Water hydrating hydrophilic groups provides an enthalpic driving force to keep the condensates in a liquid state. As a result, when we modify the protein by a few mutations to be less hydrophilic, we shift from LLPS to LSPS. This molecular understanding paves the way for a rational design of proteins.
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Affiliation(s)
- Sashary Ramos
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
| | - Janine Kamps
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr Unviersity Bochum, Bochum, Germany
| | - Jörg Tatzelt
- Department of Biochemistry of Neurodegenerative Diseases, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.
- Department of Physics, TU Dortmund, Dortmund, Germany
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4
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Roterman I, Konieczny L. Protein Is an Intelligent Micelle. ENTROPY (BASEL, SWITZERLAND) 2023; 25:850. [PMID: 37372194 DOI: 10.3390/e25060850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/22/2023] [Accepted: 04/28/2023] [Indexed: 06/29/2023]
Abstract
Interpreting biological phenomena at the molecular and cellular levels reveals the ways in which information that is specific to living organisms is processed: from the genetic record contained in a strand of DNA, to the translation process, and then to the construction of proteins that carry the flow and processing of information as well as reveal evolutionary mechanisms. The processing of a surprisingly small amount of information, i.e., in the range of 1 GB, contains the record of human DNA that is used in the construction of the highly complex system that is the human body. This shows that what is important is not the quantity of information but rather its skillful use-in other words, this facilitates proper processing. This paper describes the quantitative relations that characterize information during the successive steps of the "biological dogma", illustrating a transition from the recording of information in a DNA strand to the production of proteins exhibiting a defined specificity. It is this that is encoded in the form of information and that determines the unique activity, i.e., the measure of a protein's "intelligence". In a situation of information deficit at the transformation stage of a primary protein structure to a tertiary or quaternary structure, a particular role is served by the environment as a supplier of complementary information, thus leading to the achievement of a structure that guarantees the fulfillment of a specified function. Its quantitative evaluation is possible via using a "fuzzy oil drop" (FOD), particularly with respect to its modified version. This can be achieved when taking into account the participation of an environment other than water in the construction of a specific 3D structure (FOD-M). The next step of information processing on the higher organizational level is the construction of the proteome, where the interrelationship between different functional tasks and organism requirements can be generally characterized by homeostasis. An open system that maintains the stability of all components can be achieved exclusively in a condition of automatic control that is realized by negative feedback loops. This suggests a hypothesis of proteome construction that is based on the system of negative feedback loops. The purpose of this paper is the analysis of information flow in organisms with a particular emphasis on the role of proteins in this process. This paper also presents a model introducing the component of changed conditions and its influence on the protein folding process-since the specificity of proteins is coded in their structure.
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Affiliation(s)
- Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University-Medical College, Medyczna 7, 30-688 Kraków, Poland
| | - Leszek Konieczny
- Chair of Medical Biochemistry, Jagiellonian University-Medical College, Kopernika 7, 31-034 Kraków, Poland
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Pezzotti S, König B, Ramos S, Schwaab G, Havenith M. Liquid-Liquid Phase Separation? Ask the Water! J Phys Chem Lett 2023; 14:1556-1563. [PMID: 36745512 DOI: 10.1021/acs.jpclett.2c02697] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Water is more than an inert spectator during liquid-liquid phase separation (LLPS), the reversible compartmentalization of protein solutions into a protein-rich and a dilute phase. We show that LLPS is driven by changes in hydration entropy and enthalpy. Tuning LLPS by adjusting experimental parameters, e.g., addition of co-solutes, is a major goal for biological and medical applications. This requires a general model to quantify thermodynamic driving forces. Here, we develop such a model based on the measured amplitudes of characteristic THz-features of two hydration populations: "Cavity-wrap" water hydrating hydrophobic patches is released during LLPS leading to an increase in entropy. "Bound" water hydrating hydrophilic patches is retained since it is enthalpically favorable. We introduce a THz-phase diagram mapping these spectroscopic/thermodynamic changes. This provides not only a precise understanding of hydrophobic and hydrophilic hydration driving forces as a function of temperature and concentration but also a rational means to tune LLPS.
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Affiliation(s)
- Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Benedikt König
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Sashary Ramos
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44801Bochum, Germany
- Department of Physics, Technische Universität Dortmund, 44227Dortmund, Germany
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6
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Pezzotti S, Sebastiani F, van Dam EP, Ramos S, Conti Nibali V, Schwaab G, Havenith M. Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain. Angew Chem Int Ed Engl 2022; 61:e202203893. [PMID: 35500074 PMCID: PMC9401576 DOI: 10.1002/anie.202203893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Indexed: 11/09/2022]
Abstract
Hydration free energies are dictated by a subtle balance of hydrophobic and hydrophilic interactions. We present here a spectroscopic approach, which gives direct access to the two main contributions: Using THz-spectroscopy to probe the frequency range of the intermolecular stretch (150-200 cm-1 ) and the hindered rotations (450-600 cm-1 ), the local contributions due to cavity formation and hydrophilic interactions can be traced back. We show that via THz calorimetry these fingerprints can be correlated 1 : 1 with the group specific solvation entropy and enthalpy. This allows to deduce separately the hydrophobic (i.e. cavity formation) and hydrophilic contributions to thermodynamics, as shown for hydrated alcohols as a case study. Accompanying molecular dynamics simulations quantitatively support our experimental results. In the future our approach will allow to dissect hydration contributions in inhomogeneous mixtures and under non-equilibrium conditions.
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Affiliation(s)
- Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Federico Sebastiani
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.,Current affiliation: Department of Chemistry "U. Schiff", University of Florence, I-50019, Sesto Fiorentino, FI, Italy
| | - Eliane P van Dam
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Sashary Ramos
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Valeria Conti Nibali
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.,Current affiliation: Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166, Messina, Italy
| | - Gerhard Schwaab
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, Bochum, Germany.,Department of Physics, Technische Universität Dortmund, 44227, Dortmund, Germany
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7
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Pezzotti S, Sebastiani F, Dam EP, Ramos S, Conti Nibali V, Schwaab G, Havenith M. Spectroscopic Fingerprints of Cavity Formation and Solute Insertion as a Measure of Hydration Entropic Loss and Enthalpic Gain. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Simone Pezzotti
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
| | - Federico Sebastiani
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
- Current affiliation: Department of Chemistry “U. Schiff” University of Florence I-50019 Sesto Fiorentino FI Italy
| | - Eliane P. Dam
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
| | - Sashary Ramos
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
| | - Valeria Conti Nibali
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
- Current affiliation: Dipartimento di Scienze Matematiche e Informatiche Scienze Fisiche e Scienze della Terra (MIFT) Università di Messina 98166 Messina Italy
| | - Gerhard Schwaab
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
| | - Martina Havenith
- Department of Physical Chemistry II Ruhr University Bochum Bochum Germany
- Department of Physics Technische Universität Dortmund 44227 Dortmund Germany
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8
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Abstract
Hydrogen bond charge transfer in water may have far-reaching chemical implications.
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Affiliation(s)
- Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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9
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Shen Y, Liu L, Zheng Q, Zhao X, Han Y, Guo Q, Wang Y. Quantitative insights into tightly and loosely bound water in hydration shells of amino acids. SOFT MATTER 2021; 17:10080-10089. [PMID: 34714904 DOI: 10.1039/d1sm01234g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The hydration of amino acids closely correlates the hydration of peptides and proteins and is critical to their biological functions. However, complete and quantitative understanding about the hydration of amino acids is lacking. Here, tightly and loosely bound water of 20 zwitterionic amino acids are quantitatively distinguished and determined by Raman spectroscopy with multivariate curve resolution (Raman-MCR) and differential scanning calorimetry (DSC). The total hydration water obtained from Raman-MCR and the tightly bound water determined by DSC have certain relevance, but they do not exactly correspond. In particular, Pro, Arg and Lys exhibit larger number of tightly bound water molecules (4.02-6.59), showing a significant influence on the onset transition temperature and the melting enthalpy values of water molecules, which provides direct evidence for their unique functions associated with biological water. Asn, Ser, Thr, Met, His and Glu have a smaller number of tightly bound water molecules (0.30-1.31), whilst the other remaining 11 amino acids only contain loosely bound water molecules. Four exceptional amino acids Ile, Leu, Phe and Val show fewer tightly bound water molecules but a higher number of loosely bound water molecules. As for the hydration shell structure, most amino acids except Pro and Trp enhance tetrahedral water structure and H-bonds relative to pure water and at least 1.9% of the hydration water molecules associated with the amino acids show non-hydrogen-bonded OH defects. This work combines two effective experimental techniques to reveal the hydration water structure and quantitatively analyze two kinds of bound water molecules of 20 amino acids.
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Affiliation(s)
- Yutan Shen
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Lu Liu
- Institute of Theoretical Chemistry, Jilin University, 130012, P. R. China
| | - Qiancheng Zheng
- Institute of Theoretical Chemistry, Jilin University, 130012, P. R. China
| | - Xi Zhao
- Institute of Theoretical Chemistry, Jilin University, 130012, P. R. China
| | - Yuchun Han
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
| | - Qianjin Guo
- Key Laboratory of Molecular Reaction Dynamics and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
| | - Yilin Wang
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, CAS Research/Education Center for Excellence in Molecular Sciences, Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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10
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Zupančič B, Grdadolnik J. Solute-induced changes in the water H-bond network of different alcohol-aqueous systems. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Effects of hydrophobic solute on water normal modes. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Sahu R, Nayar D. Crowding effects on water-mediated hydrophobic interactions. J Chem Phys 2021; 155:024903. [PMID: 34266250 DOI: 10.1063/5.0054410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the fundamental forces such as hydrophobic interactions in a crowded intracellular environment is necessary to comprehensively decipher the mechanisms of protein folding and biomolecular self-assemblies. The widely accepted entropic depletion view of crowding effects primarily attributes biomolecular compaction to the solvent excluded volume effects exerted by the "inert" crowders, neglecting their soft interactions with the biomolecule. In this study, we examine the effects of chemical nature and soft attractive energy of crowders on the water-mediated hydrophobic interaction between two non-polar neopentane solutes using molecular dynamics simulations. The crowded environment is modeled using dipeptides composed of polar and non-polar amino acids of varying sizes. The results show that amongst the non-polar crowders, Leu2 strengthens the hydrophobic interactions significantly, whereas the polar and small-sized non-polar crowders do not show significant strengthening. Distinct underlying thermodynamic driving forces are illustrated where the small-sized crowders drive hydrophobic interaction via a classic entropic depletion effect and the bulky crowders strengthen it by preferential interaction with the solute. A crossover from energy-stabilized solvent-separated pair to entropy-stabilized contact pair state is observed in the case of bulky non-polar (Leu2) and polar (Lys2) crowders. The influence of solute-crowder energy in affecting the dehydration energy penalty is found to be crucial for determining the neopentane association. The findings demonstrate that along with the entropic (size) effects, the energetic effects also play a crucial role in determining hydrophobic association. The results can be extended and have implications in understanding the impact of protein crowding with varying chemistry in modulating the protein free energy landscapes.
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Affiliation(s)
- Rahul Sahu
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Divya Nayar
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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13
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Mendes de Oliveira D, Ben-Amotz D. Spectroscopically Quantifying the Influence of Salts on Nonionic Surfactant Chemical Potentials and Micelle Formation. J Phys Chem Lett 2021; 12:355-360. [PMID: 33355467 DOI: 10.1021/acs.jpclett.0c03349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The influence of two salts (NaSCN and Na2SO4) on the micellization of a nonionic surfactant (1,2-hexanediol) is quantified using Raman multivariate curve resolution spectroscopy, combined with a generalized theoretical analysis of the corresponding chemical potential changes. Although the SCN- and SO42- anions are on opposite ends of the Hofmeister series, they are both found to lower the critical micelle concentration. Our combined spectroscopic and theoretical analysis traces these observations to the fact that in both salt solutions the ions have a greater affinity for (or are less strongly expelled from) the hydration shell of the micelle than the free surfactant monomer, as quantified using the corresponding chemical potentials and Wyman-Tanford coefficients. This probe-free experimental and theoretical analysis strategy may readily be extended to micelle formation processes involving other surfactants, salts, and cosolvents, as well as to other sorts of aggregation and binding processes.
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Affiliation(s)
| | - Dor Ben-Amotz
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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