19. High-Pressure Biochemistry and Biophysics

Meersman, Filip; Daniel, Isabelle; Bartlett, Douglas H.; Winter, Roland; Hazael, Rachael; McMillan, Paul F.

doi:10.1515/9781501508318-021

Cited by 21 publications

(48 citation statements)

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“…Moreover, while the approach outlined here is in terms of enzymes, it can be used for other proteins, nucleic acids, and biomembranes, which are also affected by P-T-X. In particular, recent work on the pressure effects on these molecules, as reviewed in [16], makes such studies possible.…”

Section: Future Challengesmentioning

confidence: 99%

“…The effects of pressure P on mesophile proteins include compression, subunit dissociation, and unfolding, although pressure unfolding [18] tends to occur at higher pressures than where microbial communities have been found [16]. Exploring the effects of high pressure on monomeric enzyme function where subunit dissociation is not relevant is particularly intriguing because of the analogies to low temperature in that compression might reduce fluctuations.…”

Section: Future Challengesmentioning

confidence: 99%

“…Another timely advance has been in biophysical instrumentation, which have been developed mainly to study protein folding and stability [16] but could now be used to study flexibility. While typically enzymes are studied by perturbing temperature and chemical composition, which are easy to vary in the laboratory, recently special high-pressure cells have been made for standard biophysical instruments such as NMR spectroscopy [24], X-ray crystallography [25], and X-ray [26] and neutron [27] scattering as well as various optical spectroscopies and imaging [28], calorimetry [29] and biochemical assays [19], and calorimetry as well as biochemical assays.…”

Section: Future Challengesmentioning

confidence: 99%

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What makes proteins work: exploring life inP–T–X

Ichiye

2016

Phys. Biol.

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Although considerable progress has been made in the molecular biophysics of proteins, it is still not possible to reliably design an enzyme for a given function. The current understanding of enzyme function is that both structure and flexibility are important. Much attention has been focused recently on protein folding and thus structure, spurred on by insights from the folding funnel concept. For experimental studies of protein folding, variations in temperature (T) and chemical composition (X) of the solution have been traditionally exploited, although more recent studies using variations in pressure (P) made possible through new instrumentation have led to a deeper understanding of the energy landscape of protein folding. Other work has shown that flexibility is also essential for enzymes, although it is still not clear what type is important. Another avenue has been to take advantage of “Nature’s laboratory” by exploring homologous proteins from organisms that live in extreme conditions, or “extremophiles”. While the most studied extremophiles live at extremes of T and X, recent exploration of deep-sea environments has led to the discovery of organisms living under high P, or “piezophiles”. An exploration of targeted enzymes from organisms with various P-T-X growth conditions coupled with advances in biophysical instrumentation and computer simulations that allow studies of these enzymes at different P-T-X conditions may lead to a better understanding of “flexibility” and to general design criteria for active enzymes. Preface Kamal Shukla’s great contribution to science has been his vision that physical sciences could bring new insights to biological sciences, and that the marriage of methodologies, particularly theoretical/computational with experimental, was needed to tackle the complexities of biology. Furthermore, his openness to new methods and different ideas outside the current fad has helped make his vision a reality. In my remarks below, I have not tried to limit myself to projects that I know Kamal had sponsored, nor have I tried to highlight all that he has sponsored. Instead, everything I mention has been influenced directly or indirectly by his efforts. Perhaps the indirect influences are most telling, because they would not have happened without Kamal.

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Section: Future Challengesmentioning

confidence: 99%

Section: Future Challengesmentioning

confidence: 99%

Section: Future Challengesmentioning

confidence: 99%

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What makes proteins work: exploring life inP–T–X

Ichiye

2016

Phys. Biol.

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“…[1][2][3] Throughout most of the Earth's history, life has experienced a range of pressures, such as static pressures in subsurface environments that could have served as refuge where microbial life on Earth started and where it still flourishes to date. [1][2][3] Throughout most of the Earth's history, life has experienced a range of pressures, such as static pressures in subsurface environments that could have served as refuge where microbial life on Earth started and where it still flourishes to date.…”

Section: Introductionmentioning

confidence: 99%

“…In fact, beyond the well-investigated oceanic and continental surface settings, the less accessible deep sea, sub-seafloor and continental subsurface may represent the largest habitats by volume on Earth for microorganisms. 3,5 Lipid bilayers display various phase transitions including a chain melting (gel-to-fluid) transition. 2,4 The basic structural element of biological membranes consists of lamellar lipid bilayers, and the composition of the lipid chains, the headgroup and hence the physical-chemical properties of the membrane can vary significantly in cellular membranes.…”

Section: Introductionmentioning

confidence: 99%

Exploring the structure and phase behavior of plasma membrane vesicles under extreme environmental conditions

Seeliger

Erwin

Rosin

et al. 2015

Phys. Chem. Chem. Phys.

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Not only drastic temperature- but also pressure-induced perturbations of membrane organization pose a serious challenge to the biological cell. Although high hydrostatic pressure significantly influences the structural properties and thus functional characteristics of cells, this has not prevented life from invading the high pressure habitats of marine depths where pressures up to the 100 MPa level are encountered. Here, the temperature- and pressure-dependent structure and phase behavior of giant plasma membrane vesicles have been explored in the absence and presence of membrane proteins using a combined spectroscopic and microscopic approach. Demixing into extended liquid-ordered and liquid-disordered domains is observed over a wide range of temperatures and pressures. Only at pressures beyond 200 MPa a physiologically unfavorable all gel-like ordered lipid phase is reached at ambient temperature. This is in fact the pressure range where the membrane-protein function has generally been observed to cease, thereby shedding new light on the possible origin of this observation.

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Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures

et al. 2016

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Biophysics under extreme conditions is the fundamental platform for scrutinizing life in unusual habitats,s uch as those in the deep sea or continental subsurfaces,but also for putative extraterrestrial organisms.T herefore,a ni mportant thermodynamic variable to explore is pressure.Itisshown that the combination of infrared spectroscopywith simulation is an exquisite approach for unraveling the intricate pressure response of the solvation pattern of TMAOi nw ater,w hichi s expected to be transferable to biomolecules in their native solvent. Pressure-enhanced hydrogen bonding was found for TMAOi nw ater.T MAOi samolecule knownt os tabilize proteins against pressure-induced denaturation in deep-sea organisms.Anever-increasing number of microorganisms are known that flourish only when subjected to extreme environmental conditions,including high pressures in the kilobar regime. [1][2][3][4] In fact, the deep sea, the sub-seafloor,a nd the continental subsurface together provide the largest microbial habitats on Earth. [5] Laboratory experiments in the multi-gigapascal (10 kbar) range even point to survival at higher pressures than achieved on Earth. [6,7] Although it is well-known that organisms living in such extreme conditions must have strategies to adapt to those conditions,t he underlying molecular adaptation mechanisms still remain largely unknown. [1][2][3][4] One such strategy involves the intracellular accumulation of small molecules,t ermed piezolytes,t hat stabilize protein structures at extreme pressures. [6,7] Tr imethylamine N-oxide (TMAO), in particular,i sk nown to efficiently offset the perturbing effects of high hydrostatic pressure in deep-sea animals. [8,9] Although the consensus view on the stabilizing effect of TMAOu nder ambient conditions implies that it functions as aso-called molecular crowder that depletes from protein surfaces, [10][11][12] there exists no coherent molecular picture of the stabilizing effect of TMAOu nder extreme-pressure conditions,d espite the fact that experi-ments have revealed its strong potencya lso at high pressures. [13] Moreover,even the molecular-level effect of TMAO on the pressure-dependent structure and dynamics of water remains unknown. [14] It is the realm of an emerging field, "extreme biophysics", to elucidate the (bio)molecular foundations that allow for life far away from the usual physiological conditions which govern ambient life. [15][16][17][18][19][20][21][22][23] Although temperature effects have been studied extensively over the last 30 years,e xtreme pressures are much more difficult to access in the laboratory. This difficulty constitutes ac ritical bottleneck because pressure,b eing ac rucial thermodynamic variable next to temperature and concentration, could otherwise be used as ag ateway to gain fundamental insight into the structure, dynamics,a nd hence function of these systems. [15][16][17][18][19][20][21][22][23] In at hrust to push forward extreme biophysics,w ef ocus herein on Fourier transform infrared (FTIR) spectroscopy as ap robe t...

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19. High-Pressure Biochemistry and Biophysics

Cited by 21 publications

References 0 publications

What makes proteins work: exploring life inP–T–X

What makes proteins work: exploring life inP–T–X

Exploring the structure and phase behavior of plasma membrane vesicles under extreme environmental conditions

Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures

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