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Saha D, Jana B. Decoupling of Interactions between Model-Charged Peptides Reveals Key Factors Responsible for Liquid-Liquid Phase Separation. J Phys Chem B 2023; 127:6656-6667. [PMID: 37480340 DOI: 10.1021/acs.jpcb.3c03087] [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: 07/24/2023]
Abstract
Liquid-liquid phase separation (LLPS) by disordered proteins has been shown to govern biological processes and cause numerous diseases. Therefore, a deeper understanding of the interactions and their variation with external factors is key to modulating the LLPS behavior of different systems and protecting proteins from pathological aggregation. In this context, we have looked at interactions between similarly charged peptides to understand the molecular features that may drive or prevent condensate formation under various conditions. We have studied dimer formation for model peptides where charged and noncharged amino acids have been placed alternatively. Using arginine and glutamic acid as the charged residues and varying the other residues with glycine, alanine, and proline to alter hydrophobicity, we have obtained the free-energy surface (FES) for the dimer formation for these systems under high salt concentration at two different temperatures using all-atom molecular dynamics simulations and the well-tempered metadynamics method. Our results indicate that a combination of effects such as hydrophobicity, arginine-arginine interactions, or water release from the solvation shell makes dimerization free energy more favorable for the positively charged peptides with lower flexibility. For the negatively charged peptides, the crucial role of water has been found in governing the FES. Systems having charged residues and phenylalanine in the peptide sequence also have been studied at high salt concentrations using unbiased simulations. In this case, only the positively charged peptides were found to aggregate through temperature-dependent hydrophobic and cation-π interactions. Overall, our study indicates that the negatively charged peptides are more likely to remain in the dilute phase under various conditions compared to the positively charged systems. The findings from our study would be helpful in designing and controlling systems to obtain LLPS behavior for therapeutic usage.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
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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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Chopra G, Chopra N, Kaur D. Elucidating the intermolecular hydrogen bonding interaction of proline with amides—quantum chemical calculations. Struct Chem 2018. [DOI: 10.1007/s11224-018-1235-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ulman K, Busch S, Hassanali AA. Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water. J Chem Phys 2018; 148:222826. [DOI: 10.1063/1.5008665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kanchan Ulman
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ), Helmholtz-Zentrum Geesthacht GmbH, Lichtenbergstr. 1, 85747 Garching bei München, Germany
| | - Ali A. Hassanali
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
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Malo de Molina P, Alvarez F, Frick B, Wildes A, Arbe A, Colmenero J. Investigation of the dynamics of aqueous proline solutions using neutron scattering and molecular dynamics simulations. Phys Chem Chem Phys 2017; 19:27739-27754. [PMID: 28984889 DOI: 10.1039/c7cp05474b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We applied quasielastic neutron scattering (QENS) techniques to samples with two different contrasts (deuterated solute/hydrogenated solvent and the opposite label) to selectively study the component dynamics of proline/water solutions. Results on diluted and concentrated solutions (31 and 6 water molecules/proline molecule, respectively) were analyzed in terms of the susceptibility and considering a recently proposed model for water dynamics [Arbe et al., Phys. Rev. Lett., 2016, 117, 185501] which includes vibrations and the convolution of localized motions and diffusion. We found that proline molecules not only reduce the average diffusion coefficient of water but also extend the time/frequency range of the crossover region ('cage') between the vibrations and purely diffusive behavior. For the high proline concentration we also found experimental evidence of water heterogeneous dynamics and a distribution of diffusion coefficients. Complementary molecular dynamics simulations show that water molecules start to perform rotational diffusion when they escape the cage regime but before the purely diffusive behavior is established. The rotational diffusion regime is also retarded by the presence of proline molecules. On the other hand, a strong coupling between proline and water diffusive dynamics which persists with decreasing temperature is directly observed using QENS. Not only are the temperature dependences of the diffusion coefficients of both components the same, but their absolute values also approach each other with increasing proline concentration. We compared our results with those reported using other techniques, in particular using dielectric spectroscopy (DS). A simple approach based on molecular hydrodynamics and a molecular treatment of DS allows rationalizing the a priori puzzling inconsistency between QENS and dielectric results regarding the dynamic coupling of the two components. The interpretation proposed is based on general grounds and therefore should be applicable to other biomolecular solutions.
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Affiliation(s)
- Paula Malo de Molina
- Centro de Física de Materiales (CFM) (CSIC-UPV/EHU) - Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, 20018 San Sebastián, Spain.
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Dmitrieva OA, Fedotova MV, Buchner R. Evidence for cooperative Na+ and Cl− binding by strongly hydrated l-proline. Phys Chem Chem Phys 2017; 19:20474-20483. [DOI: 10.1039/c7cp04335j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Strongly hydrated l-proline cooperatively binds Na+ and Cl− ions in aqueous solution.
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Affiliation(s)
- Olga A. Dmitrieva
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Marina V. Fedotova
- G.A. Krestov Institute of Solution Chemistry
- Russian Academy of Sciences
- 153045 Ivanovo
- Russian Federation
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie
- Universität Regensburg
- 93040 Regensburg
- Germany
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Yu D, Mole RA, Kearley GJ. Performance test on PELICAN – a multi-purpose time of flight cold neutron spectrometer. EPJ WEB OF CONFERENCES 2015. [DOI: 10.1051/epjconf/20158303019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Busch S, Lorenz CD, Taylor J, Pardo LC, McLain SE. Short-Range Interactions of Concentrated Proline in Aqueous Solution. J Phys Chem B 2014; 118:14267-77. [DOI: 10.1021/jp508779d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sebastian Busch
- Department
of Biochemistry, University of Oxford, Oxford, United Kingdom
| | | | | | - Luis Carlos Pardo
- Departament
de Física i Enginyeria Nuclear, Universitat Politècnica de Catalunya, 08028 Barcelona, Catalonia, Spain
| | - Sylvia E. McLain
- Department
of Biochemistry, University of Oxford, Oxford, United Kingdom
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