J. Appl. Cryst.の発刊に際して

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer s...

Water Determines the Structure and Dynamics of Proteins

https://ucanr.edu/datastoreFiles/608-487.pdf

Protein structure and dynamics at high pressure.

http://www.ibp-ran.ru/download.php?trid=157

α-Lactalbumin: structure and function

Interactions of human serum albumin with chlorogenic acid and ferulic acid.

Fourier transform infrared spectroscopy in high-pressure studies on proteins.

Fourier transform infrared (FT-IR) spectroscopy combined with a resolution enhancement technique has been used to characterize pressure and thermal effects on the secondary structure of ribonuclease A. The experiments were performed at pD 7.0 with 50 mg/mL protein solution in D2O buffer. According to the observed changes in the amide I' band, secondary structure elements such as alpha-helices, beta-sheets, and turns are cooperatively disrupted by application of either pressures above 570 MPa at 30 degrees C or temperatures above 60 degrees C at 0.1 MPa. Pressure- and thermally-denatured ribonuclease A are fully unfolded and do not contain any residual secondary structures. Both the structural changes are intrinsically reversible, although the pressure-induced transition shows a hysteresis. It is found that nonnative turn structures are formed prior to the appearance of the native secondary structure in the folding from the pressure-unfolded state. The structural features upon the pressure-induced unfolding are additionally characterized by the interesting behavior of hydrogen-deuterium exchange at high pressure. Most of the backbone amide protons protected at atmospheric pressure, which are involved in the alpha-helices and beta-sheet, are exchanged with solvent deuterons in the pressure range where the two secondary structural elements are virtually identified as intact. There is a possibility that, for ribonuclease A, application of high pressure up to 570 MPa induces such a partially unfolded state as has native-like secondary structure but permits solvent to be highly accessible to the internal regions.

Pressure- and thermally-induced reversible changes in the secondary structure of ribonuclease A studied by FT-IR spectroscopy.

The chain-length dependence of the α-helix to β-sheet transition in poly(L-lysine) is studied by temperature-tuned FTIR spectroscopy. This study shows that heterogeneous samples of poly(L-lysine), comprising polypeptide chains with various lengths, undergo the α–β transition at an intermediate temperature compared to homogenous ingredients. This holds true as long as each individual fraction of the polypeptide is capable of adopting an antiparallel β-sheet structure. The tendency is that the longer chain is, the lower the α–β transition temperature is, which has been linked to the presence of distorted or solvated helices with turns or β sheets in elongating chains of poly(L-lysine). As such helical structures are apparently conducive to the α–β transition, this draws a comparison to the hypothesis of metastable protein conformational states being a common stage in amyloid-formation pathways. The antiparallel architecture of the β sheet is likely to reflect the pretransition interhelical interactions in poly(L-lysine). Namely, the chains are arranged in an antiparallel manner because of energetically favored antiparallel preassembly of dipolar α helices. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004

Chain‐length dependence of α‐helix to β‐sheet transition in polylysine: Model of protein aggregation studied by temperature‐tuned FTIR spectroscopy

Crystal growth of the trigonal form of isotactic poly(butene-1) (it-PB1) was successfully observed in the melt at atmospheric pressure. The growth rate of trigonal crystals was obtained by in situ optical microscopy. It is one hundredth that of it-PB1 tetragonal crystals. The growth rate of trigonal crystals, as well as that of tetragonal crystals, shows supercooling dependence derived from the nucleation theory. The value of the kinetic constant K of trigonal crystals is about 3.3 times larger than that of tetragonal crystals. The value of the pre-exponential factor G0 of trigonal crystals was found to be 41 times as large as that of tetragonal crystals. The difference between these K values can be attributed to the conformational entropy of the ethyl side groups in a nucleating stem. The discrepancy found in the values of G0 could be explained by introducing pinning and nucleation barriers, which originate from the crystal thickness δlc, which does not depend on the crystallization temperature. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 684–697, 2007

Isotactic poly(butene-1) trigonal crystal growth in the melt

The nucleation event of amyloid fibrils is one of the most crucial processes that dictate the timing and rate of the pathology of diseases; however, information regarding how protein molecules associate to produce fibril nuclei is currently limited. In order to explore this issue in more detail, we performed time-resolved small angle X-ray scattering (SAXS) measurements on insulin fibrillation, in combination with additional multidirectional analyses of thioflavin T fluorescence, FTIR spectroscopy, light scattering, and light transmittance, during the fibrillation process of bovine insulin. SAXS monitoring revealed that insulin molecules associated into rod-like prefibrillar aggregates in the very early stage of the reaction. After the formation of these early aggregates, they appeared to further coalesce mutually to form larger clusters, and the SAXS profiles subsequently showed the further time evolution of conformational development towards mature amyloid fibrils. Distinct types of structural units in terms of shape in a nano-scale order, cross-β content, and thioflavin T fluorescence intensity were observed in a manner that was dependent on the fibrillation pathways. These results suggest the presence of diverse substructures that characterize various fibrillation pathways, and eventually, manifest polymorphisms in mature amyloid fibrils.

/pdf/early-aggregation-preceding-the-nucleation-of-insulin-1wkf7nrnmr.pdf

Minoru Kato

Papers

Fourier transform infrared spectroscopy in high-pressure studies on proteins.

Pressure- and thermally-induced reversible changes in the secondary structure of ribonuclease A studied by FT-IR spectroscopy.

Chain‐length dependence of α‐helix to β‐sheet transition in polylysine: Model of protein aggregation studied by temperature‐tuned FTIR spectroscopy

Isotactic poly(butene-1) trigonal crystal growth in the melt

Early aggregation preceding the nucleation of insulin amyloid fibrils as monitored by small angle X-ray scattering