High-pressure protein crystal structure analysis of <i>Escherichia coli</i> dihydrofolate reductase complexed with folate and NADP<sup>+</sup>

Nagae, T.; Yamada, Hiroyuki; Watanabe, Nobuhisa

doi:10.1107/s2059798318009397

Cited by 19 publications

(23 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Collective structural changes can be both isotropic (compressive) and anisotropic (conformational) 39 . In general the compressibility of proteins is small 40 , 41 , but a compaction of cavities has been reported for several proteins in static high-pressure experiments 42 – 44 . It is thus interesting to analyse whether or not shock exposure affects the central channel and cavity volumes in Hb.CO 45 , 46 .…”

Section: Resultsmentioning

confidence: 98%

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

et al. 2021

View full text Add to dashboard Cite

X-ray free-electron lasers (XFELs) enable obtaining novel insights in structural biology. The recently available MHz repetition rate XFELs allow full data sets to be collected in shorter time and can also decrease sample consumption. However, the microsecond spacing of MHz XFEL pulses raises new challenges, including possible sample damage induced by shock waves that are launched by preceding pulses in the sample-carrying jet. We explored this matter with an X-ray-pump/X-ray-probe experiment employing haemoglobin microcrystals transported via a liquid jet into the XFEL beam. Diffraction data were collected using a shock-wave-free single-pulse scheme as well as the dual-pulse pump-probe scheme. The latter, relative to the former, reveals significant degradation of crystal hit rate, diffraction resolution and data quality. Crystal structures extracted from the two data sets also differ. Since our pump-probe attributes were chosen to emulate EuXFEL operation at its 4.5 MHz maximum pulse rate, this prompts concern about such data collection.

show abstract

Section: Resultsmentioning

confidence: 98%

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

et al. 2021

View full text Add to dashboard Cite

show abstract

“…In other words, pressure denaturation apparently occurs because the system will have a lower volume if water fills cavities inside the protein than if the cavities are compressed so that the more open solvated states become thermodynamically favored [6,7]. Supporting evidence includes high-pressure studies of crystal structures, which show that water is present in a large-cavity mutant of T4 lysozyme only at 1.5 kbar and above [8], and in cavities of mesophile isopropyl malate dehydrogenase (IPMDH) and dihydrofolate reductase (DHFR) only at 5 kbar and above [9,10]. Other differences include that the pressure unfolded state appears to be more compact than the thermally unfolded state [11] and that pressure unfolding is a slower process [12].…”

Section: Introductionmentioning

confidence: 99%

Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile

Huang

Rodgers

Hemley

et al. 2019

IJMS

View full text Add to dashboard Cite

Determining the effects of extreme conditions on proteins from “extremophilic” and mesophilic microbes is important for understanding how life adapts to living at extremes as well as how extreme conditions can be used for sterilization and food preservation. Previous molecular dynamics simulations of dihydrofolate reductase (DHFR) from a psychropiezophile (cold- and pressure-loving), Moritella profunda (Mp), and a mesophile, Escherichia coli (Ec), at various pressures and temperatures indicate that atomic fluctuations, which are important for enzyme function, increase with both temperature and pressure. Here, the factors that cause increases in atomic fluctuations in the simulations are examined. The fluctuations increase with temperature not only because of greater thermal energy and thermal expansion of the protein but also because hydrogen bonds between protein atoms are weakened. However, the increase in fluctuations with pressure cannot be due to thermal energy, which remains constant, nor the compressive effects of pressure, but instead, the hydrogen bonds are also weakened. In addition, increased temperature causes larger increases in fluctuations of the loop regions of MpDHFR than EcDHFR, and increased pressure causes both increases and decreases in fluctuations of the loops, which differ between the two.

show abstract

“…Therefore, we have chosen the X-ray structures of hen egg-white lysozyme (HEWL) 53 and Escherichia coli dihydrofolate reductase (DHFR). 54 Table 1 presents the relevant information about the native structures considered for this work. Pressure makes structures slightly more compact, as shown by a decrease in the radius of gyration, R g .…”

Section: Proteins Consideredmentioning

confidence: 99%

Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures

Río

Rey

2021

J. Phys. Chem. B

View full text Add to dashboard Cite

Structure-based models are coarse-grained representations of the interactions responsible for the protein folding process. In their simplest form, they use only the native contact map of a given protein to predict the main features of its folding process by computer simulation. Given their limitations, these models are frequently complemented with sequence-dependent contributions or additional information. Specifically, to analyze the effect of pressure on the folding/unfolding transition, special forms of these interaction potentials are employed, which may a priori determine the outcome of the simulations. In this work, we have tried to keep the original simplicity of structure-based models. Therefore, we have used folded structures that have been experimentally determined at different pressures to define native contact maps and thus interactions dependent on pressure. Despite the apparently tiny structural differences induced by pressure, our simulation results provide different thermodynamic and kinetic behaviors, which roughly correspond to experimental observations (when there is a possible comparison) of two proteins used as benchmarks, hen egg-white lysozyme and dihydrofolate reductase. Therefore, this work shows the feasibility of using experimental native structures at different pressures to analyze the global effects of this physical property on the protein folding process.

show abstract

High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP⁺

Cited by 19 publications

References 62 publications

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile

Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures

Contact Info

Product

Resources

About

High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP+

Cited by 19 publications

References 62 publications

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet

Effects of Pressure and Temperature on the Atomic Fluctuations of Dihydrofolate Reductase from a Psychropiezophile and a Mesophile

Behavior of Proteins under Pressure from Experimental Pressure-Dependent Structures

Contact Info

Product

Resources

About

High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP⁺