Pressure effects on intra- and intermolecular interactions within proteins

Boonyaratanakornkit, Boonchai B.; Park, Chan Beum; Clark, Douglas S.

doi:10.1016/s0167-4838(01)00347-8

Cited by 315 publications

(234 citation statements)

References 93 publications

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“…Anesthetic binding to proteins within internal cavities also leads to an increase in protein stability and further shifts the population of conformational sub-states [41][42][43][44]. Pressure can also induce a stabilization through a compression of hydrophobic cavities resulting in increased van der Waals contacts and shifts conformational sub-states [45,46]. Internal cavities play thus a fundamental role in sampling the different conformational sub-states.…”

Section: Discussionmentioning

confidence: 99%

Functional relevance of the internal hydrophobic cavity of urate oxidase

Colloc’h

Prangé

2014

FEBS Letters

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a b s t r a c tUrate oxidase from Aspergillus flavus is a 135 kDa homo-tetramer which has a hydrophobic cavity buried within each monomer and located close to its active site. Crystallographic studies under moderate gas pressure and high hydrostatic pressure have shown that both gas presence and high pressure would rigidify the cavity leading to an inhibition of the catalytic activity. Analysis of the cavity volume variations and functional modifications suggest that the flexibility of the cavity would be an essential parameter for the active site efficiency. This cavity would act as a connecting vessel to give flexibility to the neighboring active site, and its expansion under pure oxygen pressure reveals that it might serve as a transient reservoir on its pathway to the active site.

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Section: Discussionmentioning

confidence: 99%

Functional relevance of the internal hydrophobic cavity of urate oxidase

Colloc’h

Prangé

2014

FEBS Letters

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“…Quaternary structures are more affected than the tertiary and secondary structures. Recent reviews deal with this problem (8,9).…”

Section: Pressure Effects On Protein Structuresmentioning

confidence: 99%

The powerful high pressure tool for protein conformational studies

Marchal

Torrent

Masson

et al. 2005

Braz J Med Biol Res

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The pressure behavior of proteins may be summarized as a the pressure-induced disordering of their structures. This thermodynamic parameter has effects on proteins that are similar but not identical to those induced by temperature, the other thermodynamic parameter. Of particular importance are the intermolecular interactions that follow partial protein unfolding and that give rise to the formation of fibrils. Because some proteins do not form fibrils under pressure, these observations can be related to the shape of the stability diagram. Weak interactions which are differently affected by hydrostatic pressure or temperature play a determinant role in protein stability. Pressure acts on the 2º, 3º and 4º structures of proteins which are maintained by electrostatic and hydrophobic interactions and by hydrogen bonds. We present some typical examples of how pressure affects the tertiary structure of proteins (the case of prion proteins), induces unfolding (ataxin), is a convenient tool to study enzyme dissociation (enolase), and provides arguments to understand the role of the partial volume of an enzyme (butyrylcholinesterase). This approach may have important implications for the understanding of the basic mechanism of protein diseases and for the development of preventive and therapeutic measures.

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“…Nevertheless, sufficiently high temperature may also distort protein structure and cause unfolding or denaturation (25)(26)(27). Another thermodynamic parameter, pressure, also plays an important role in protein structure and dynamics (28)(29)(30)(31)(32)(33). It changes the protein volume (33) and affects protein intermolecular and intramolecular structures explicitly (28,32).…”

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confidence: 99%

Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile

Shrestha

Bhowmik

Copley

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens is a large oligomeric protein derived from a hyperthermophilic microorganism that is found near hydrothermal vents deep under the sea, where the pressure is up to 100 MPa (1 kbar). It has attracted great interest in biophysical research because of its high activity under extreme conditions in the seabed. In this study, we use the quasielastic neutron scattering (QENS) technique to investigate the effects of pressure on the conformational flexibility and relaxation dynamics of IPPase over a wide temperature range. The β-relaxation dynamics of proteins was studied in the time ranges from 2 to 25 ps, and from 100 ps to 2 ns, using two spectrometers. Our results indicate that, under a pressure of 100 MPa, close to that of the native environment deep under the sea, IPPase displays much faster relaxation dynamics than a mesophilic model protein, hen egg white lysozyme (HEWL), at all measured temperatures, opposite to what we observed previously under ambient pressure. This contradictory observation provides evidence that the protein energy landscape is distorted by high pressure, which is significantly different for hyperthermophilic (IPPase) and mesophilic (HEWL) proteins. We further derive from our observations a schematic denaturation phase diagram together with energy landscapes for the two very different proteins, which can be used as a general picture to understand the dynamical properties of thermophilic proteins under pressure.protein dynamics | energy landscape | denaturation phase diagram | quasielastic neutron scattering | mode coupling theory T he biological functions of proteins, such as enzyme catalysis, are often understood from their crystallographic structures (1). On the other hand, it is crucial to take into account dynamic behavior to fully comprehend these functions (2, 3). In vivo, proteins are in constant motion among different conformations (3-5). The thermal energy, which is of the order of k B T per atom, where k B is the Boltzmann constant and T is the absolute temperature, triggers biomolecules to sample different conformations around the average structure. These conformations are also known as conformational substates (CSs) (5). Fluctuations among these CSs play an important role in protein function (3,5). These lead to the concept of a multidimensional potential energy landscape (EL) that specifies a complete description of CSs in proteins (6-9). The existence of an EL was proposed by H. Frauenfelder and others in the 1970s and has been validated both by computations and by experiments (6-12).Proteins show various dynamic phenomena over a wide range of timescales, from picoseconds to milliseconds (13). A fast dynamic process, on a timescale of a picosecond to 10 ns, also known as β-relaxation, occurs due to small amplitude fluctuations in atoms/ molecules, such as loop motions and side-chain rotations (14). The energy barrier or activation energy (E A ) between different CSs for this process is smaller than k B T (15). On t...

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Pressure effects on intra- and intermolecular interactions within proteins

Cited by 315 publications

References 93 publications

Functional relevance of the internal hydrophobic cavity of urate oxidase

Functional relevance of the internal hydrophobic cavity of urate oxidase

The powerful high pressure tool for protein conformational studies

Effects of pressure on the dynamics of an oligomeric protein from deep-sea hyperthermophile

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