Dipole–dipole interactions between tryptophan side chains and hydration water molecules dominate the observed dynamic stokes shift of lysozyme

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

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Ein Wasserstoffisotopieeffekt im CuSO4 * 5H2O

Zeitschrift für Naturforschung A ◽

10.1515/zna-1969-1007 ◽

1969 ◽

Vol 24 (10) ◽

pp. 1502-1511

Author(s):

Karl Heinzinger

Keyword(s):

Water Vapor ◽

Aqueous Solutions ◽

Separation Factor ◽

Room Temperature ◽

Copper Ion ◽

Hydrogen Isotopes ◽

Bulk Water ◽

Water Molecules ◽

Hydration Water ◽

Sulfate Solutions

Abstract There are two kinds of water in CuSO4·5H2O differing by their binding in the crystal. The oxygen of four water molecules is bonded to the copper ion, that of the fifth molecule is hydrogen bonded. It is shown that the D/H ratios of these two kinds of water differ by 5.7%, the light isotope being enriched in the water molecules coordinated with the copper ion. The results show that there is no exchange of the hydrogen isotopes during the time needed for dehydration at room temperature which takes several days. The assumption has been confirmed that the water coordinated with the copper ion leaves the crystal first on dehydration at temperatures below 50 °C. Additional measurements of the separation factor for the hydrogen isotopes between water vapor and copper sulfate solutions allow conclusions on the fractionation of the hydrogen isotopes between bulk water and hydration water in aqueous solutions.

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WT and A53T α-synuclein systems: Melting Diagram and its new interpretation

10.1101/724922 ◽

2019 ◽

Author(s):

M. Bokor ◽

Á. Tantos ◽

P. Tompa ◽

K.-H. Han ◽

K. Tompa

Keyword(s):

Secondary Structure ◽

Structural Disorder ◽

Water Molecules ◽

Hydration Water ◽

Wild Type ◽

Water Binding ◽

Potential Barriers ◽

Intrinsically Disordered ◽

Mobile Water ◽

Binding Interfaces

AbstractParkinson’s disease is connected with abnormal α-synuclein (αS) aggregation. Energetics of potential barriers governing motions of hydration water is examined. Information about the distributions and heights of potential barriers is gained by a thermodynamical approach. The ratios of the heterogeneous water-binding interfaces measure proteins’ structural disorder. All αS forms possess secondary structural elements though they are intrinsically disordered. Monomers are functional at the lowest potential barriers, where mobile hydration water exists, with monolayer coverage of mobile hydration. The αS monomer contains 33% secondary structure and is more compact than a random coil. A53T αS monomer has a more open structure than the wild type. Monomers realize all possible hydrogen bonds. Half of the mobile hydration water amount for monomers is missing in αS oligomers and αS amyloids. Oligomers are ordered by 66%. Mobile water molecules in the first hydration shell of amyloids are the weakest bound compared to other forms. Wild type and A53T amyloids show identical, low-level hydration, and are considered as disordered to 75%.Statement of SignificanceAggregation of α-synuclein into oligomers, amyloid fibrils is a hallmark of Parkinson’s disease. A thermodynamic approach provides information on the heterogeneity of protein-water bonds in the wild type and A53T mutant monomers, oligomers, amyloids. This information can be related to ratios of heterogeneous water-binding interfaces, which measure the proteins’ structural disorder. Both α-synuclein monomers are intrinsically disordered. The monomers nevertheless have 33% secondary structure. They are functional as long as mobile water molecules surround them. They realize every possible H-bonds with water. Oligomers are like globular proteins with 66% ordered structure. Amyloids are disordered to 75% and are poorly hydrated with loosely bound water. Their hydration is identical. Oligomers, amyloids have only half as much hydrating mobile water as monomers.

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Hydration water molecules seen by NMR and by X-ray crystallography

Progress in Nuclear Magnetic Resonance Spectroscopy ◽

10.1016/0079-6565(95)01015-7 ◽

1995 ◽

Vol 27 (5-6) ◽

pp. 635-645 ◽

Cited By ~ 33

Author(s):

Martin Billeter

Keyword(s):

Water Molecules ◽

Hydration Water ◽

X Ray ◽

X Ray Crystallography

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Quadrupolar Relaxation of 27Al in Aqueous Solution. III. Discussion on Motions of Hydration Water Molecules

Journal of the Physical Society of Japan ◽

10.1143/jpsj.44.1946 ◽

1978 ◽

Vol 44 (6) ◽

pp. 1946-1952 ◽

Cited By ~ 1

Author(s):

Akira Takahashi

Keyword(s):

Aqueous Solution ◽

Water Molecules ◽

Hydration Water ◽

Quadrupolar Relaxation

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Calculated Raman Optical Activity Signatures of Tryptophan Side Chains

ChemPhysChem ◽

10.1002/cphc.200800448 ◽

2008 ◽

Vol 9 (15) ◽

pp. 2177-2180 ◽

Cited By ~ 41

Author(s):

Christoph R. Jacob ◽

Sandra Luber ◽

Markus Reiher

Keyword(s):

Optical Activity ◽

Side Chains ◽

Raman Optical Activity ◽

Tryptophan Side Chains

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Water–protein interactions from high–resolution protein crystallography

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2004.1498 ◽

2004 ◽

Vol 359 (1448) ◽

pp. 1191-1206 ◽

Cited By ~ 111

Author(s):

Masayoshi Nakasako

Keyword(s):

Hydrogen Bond ◽

Conformational Changes ◽

Protein Interactions ◽

Three Dimensional ◽

Water Molecules ◽

Aqueous Environment ◽

Hydration Water ◽

X Ray Crystallography ◽

Physico Chemical ◽

Domain Motions

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein–water interface have been investigated by cryogenic X–ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen–bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three–dimensional chain connection of a hydrogen–bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico–chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

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Identification of Electrolytes in Aqueous Solutions from Near-IR Spectra

Applied Spectroscopy ◽

10.1366/0003702963906096 ◽

1996 ◽

Vol 50 (4) ◽

pp. 444-448 ◽

Cited By ~ 18

Author(s):

Jie Lin ◽

Jing Zhou ◽

Chris W. Brown

Keyword(s):

Aqueous Solutions ◽

Ir Spectra ◽

Principal Component Regression ◽

Principal Component ◽

Transition Metal Ions ◽

Water Molecules ◽

Spectral Library ◽

Dipole Interactions ◽

Near Ir ◽

Solutions Of Electrolytes

Dissolution of electrolytes causes characteristic changes in the near-IR spectrum of water. These changes result from a decrease in the concentration of water; charge-dipole interactions between ions and water molecules; formation of hydrogen bonds between oxygen or nitrogen atoms in some ions and water molecules; production of H+ and OH− ions from dissociation and hydrolysis; absorptions due to OH, NH, and CH groups in some ions; and intrinsic colors of some transition metal ions. Changes in spectra were used for identification of electrolytes in aqueous solutions. Near-IR spectra of 71 solutions of single electrolytes were measured and used to develop a spectral library. This near-IR spectral library was processed with principal component regression (PCR) and used for the identification of single and multiple electrolytes in aqueous solutions with the use of their spectra. Most of the unknown electrolytes were identified correctly. For the others, very similar electrolytes were selected with one ion identified correctly. The near-IR spectral library of aqueous solutions of electrolytes can be used as a simple and fast approach for the identification of electrolytes.

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