Protein adaptation to high hydrostatic pressure: Computational analysis of the structural proteome

Avagyan, Samvel; Vasilchuk, Daniel; Makhatadze, George I.

doi:10.1002/prot.25839

Cited by 15 publications

(12 citation statements)

References 68 publications

(161 reference statements)

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“…Pressure, similar to temperature, is an important thermodynamic parameter that can profoundly affect molecular systems (64). HHP represents a distinctive form of stress associated with volume changes that alter numerous physiological and biochemical processes, such as protein unfolding and dissociation, lipid bilayer phase transition, and ligand binding (65,66). Pressure studies on biomolecules are generally performed between 0.1 and 1,500 MPa (23).…”

Section: Effects Of High Hydrostatic Pressure On Biomacromoleculesmentioning

confidence: 99%

Research and application of hydrostatic high pressure in tumor vaccines (Review)

Yan

Lin

et al. 2021

Oncol Rep

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It is well known that hydrostatic pressure (HP) is a physical parameter that is now regarded as an important variable for life. High hydrostatic pressure (HHP) technology has influenced biological systems for more than 100 years. Food and bioscience researchers have shown great interest in HHP technology over the past few decades. The development of knowledge related to this area can better facilitate the application of HHP in the life sciences. Furthermore, new applications for HHP may come from these current studies, particularly in tumor vaccines. Currently, cancer recurrence and metastasis continue to pose a serious threat to human health. The limited efficacy of conventional treatments has led to the need for breakthroughs in immunotherapy and other related areas. Research into tumor vaccines is providing new insights for cancer treatment. The purpose of this review is to present the main findings reported thus far in the relevant scientific literature, focusing on knowledge related to HHP technology and tumor vaccines, and to demonstrate the potential of applying HHP technology to tumor vaccine development.

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Section: Effects Of High Hydrostatic Pressure On Biomacromoleculesmentioning

confidence: 99%

Research and application of hydrostatic high pressure in tumor vaccines (Review)

Yan

Lin

et al. 2021

Oncol Rep

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“…This method has been benchmarked against experimental data and shown to reproduce well the total volume changes upon protein unfolding [25][26] . It uses structural information obtained from all-atom explicit solvent molecular dynamics simulations starting with x-ray coordinates in order to compute the volume changes upon protein unfolding [26][27][28] .…”

Section: Knowledge Of the Value Of Vtse Relative To The Valuesmentioning

confidence: 99%

The Volumetric Properties of the Transition State Ensemble for Protein Folding

Avagyan

Makhatadze

2021

Preprint

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Hydrostatic pressure together with the temperature is an important environmental variable that plays an essential role in biological adaptation of extremophilic organisms. In particular, the effects of hy-drostatic pressure on the rates of the protein folding/unfolding reaction are determined by the magni-tude and sign of the activation volume changes. Here we provide computational description of the ac-tivation volume changes for folding/unfolding reaction, and compare them with the experimental data for six different globular proteins. We find that the volume of the transition state ensemble is always in-between the folded and unfolded states. Based on this, we conclude that hydrostatic pressure will invariably slow down protein folding and accelerate protein unfolding.

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“…1 In our previous work, we explored the idea that organisms adapted to high-pressure environments acquired adaptations in protein sequences that make proteins more pressure stable than proteins from their nonpiezophilic counterparts. 2 We applied a computational method to predict volume changes upon protein unfolding 1,3 to proteomes of piezophilic and nonpiezophilic organisms. This was done to test the hypothesis that the proteins of piezophiles will undergo volume changes that are less negative or even positive, when compared to the proteins of nonpiezophiles.…”

Section: ■ Introductionmentioning

confidence: 99%

Effects of Hydrostatic Pressure on the Thermodynamics of CspB-Bs Interactions with the ssDNA Template

Avagyan

Makhatadze

2021

Biochemistry

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Understanding the thermodynamic mechanisms of adaptation of biomacromolecules to high hydrostatic pressure can help shed light on how piezophilic organisms can survive at pressures reaching over 1000 atmospheres. Interaction of proteins with nucleic acids is one of the central processes that allow information flow encoded in the sequence of DNA. Here, we report the results of a study on the interaction of cold shock protein B from Bacillus subtilis (CspB-Bs) with heptadeoxythymine template (pDT7) as a function of temperature and hydrostatic pressure. Experimental data collected at different CspB-Bs:pDT7 ratios were analyzed using a thermodynamic linkage model that accounts for both protein unfolding and CspB-Bs:pDT7 binding. The global fit to the model provided estimates of the stability of CspB-Bs, ΔG Prot o , the volume change upon CspB-Bs unfolding, ΔV Prot , the association constant for CspB-Bs:pDT7 complex, K a o , and the volume changes upon pDT7 single-stranded DNA (ssDNA) template binding, ΔV Bind . The protein, CspB-Bs, unfolds with an increase in hydrostatic pressure (ΔV Prot < 0). Surprisingly, our study showed that ΔV Bind < 0, which means that the binding of CspB-Bs to ssDNA is stabilized by an increase in hydrostatic pressure. Thus, CspB-Bs binding to pDT7 represents a case of linked equilibrium in which folding and binding react differently upon an increase in hydrostatic pressure: protein folding/unfolding equilibrium favors the unfolded state, while protein−ligand binding equilibrium favors the bound state. These opposing effects set a "maximum attainable" pressure tolerance to the protein−ssDNA complex under given conditions.

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Protein adaptation to high hydrostatic pressure: Computational analysis of the structural proteome

Cited by 15 publications

References 68 publications

Research and application of hydrostatic high pressure in tumor vaccines (Review)

Research and application of hydrostatic high pressure in tumor vaccines (Review)

The Volumetric Properties of the Transition State Ensemble for Protein Folding

Effects of Hydrostatic Pressure on the Thermodynamics of CspB-Bs Interactions with the ssDNA Template

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