Protposer: The web server that readily proposes protein stabilizing mutations with high PPV

García-Cebollada, Helena; Sancho, Javier

doi:10.1016/j.csbj.2022.05.008

Cited by 4 publications

(3 citation statements)

References 132 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, protein engineering focused predominantly on determining free energy changes rather than enthalpy or heat capacity changes, which is not ideal for the purpose of performing a fine dissection of protein energetics. Ultimately, despite the large number of mutational experiments that have been carried out and that continue to feed the protein stability databases (Nikam et al, 2021 ; Xavier et al, 2021 ) used to train protein stability predictors (Dehouck et al, 2011 ; García‐Cebollada et al, 2022 ; Liu & Kuhlman, 2006 ; Schymkowitz et al, 2005 ), the relative contribution of the different physical interactions to protein stability remains unclear.…”

Section: Discussionmentioning

confidence: 99%

Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable

Galano‐Frutos,

Sancho

2024

Protein Science

Self Cite

View full text Add to dashboard Cite

Protein folding energetics can be determined experimentally on a case‐by‐case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein–protein and solvent–solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.

show abstract

Section: Discussionmentioning

confidence: 99%

Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable

Galano‐Frutos,

Sancho

2024

Protein Science

Self Cite

View full text Add to dashboard Cite

show abstract

“…Besides, protein engineering has predominantly focused on determining free energy changes rather than enthalpy or heat capacity changes, which is not ideal for the purpose of performing a fine dissection of protein energetics. Altogether, despite the large number of mutational experiments done, which keep feeding databases 52,53 used to train protein stability predictors 54,55 , the relative contribution of the different elementary interactions to protein stability remains unclear.…”

Section: Discussionmentioning

confidence: 99%

Molecular Interactions and Forces that Make Proteins Stable: A Quantitative Inventory from Atomistic Molecular Dynamics Simulations

Galano‐Frutos

Sancho

2023

Preprint

Self Cite

View full text Add to dashboard Cite

Protein design requires a deep control of protein folding energetics, which can be determined experimentally on a case-by-case basis but is not understood in sufficient detail. Calorimetry, protein engineering and biophysical modeling have outlined the fundamentals of protein stability, but these approaches face difficulties in elucidating the specific contributions of the intervening molecules and elementary interactions to the folding energy balance. Recently, we showed that, using Molecular Dynamics (MD) simulations of native proteins and their unfolded ensembles, one can calculate, within experimental error, the enthalpy and heat capacity changes of the folding reaction. Analyzing MD simulations of four model proteins (CI2, barnase, SNase and apoflavodoxin) whose folding enthalpy and heat capacity changes have been successfully calculated, we dissect here the energetic contributions to protein stability made by the different molecular players (polypeptide and solvent molecules) and elementary interactions (electrostatic, van der Waals and bonded) involved. Although the proteins analyzed differ in length (65-168 amino acid residues), isoelectric point (4.0-8.99) and overall fold, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformation is enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and it is nearly equally destabilized by interactions between protein and solvent molecules. From the perspective of elementary physical interactions, the native conformation is stabilized by van de Waals and coulombic interactions and is destabilized by bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by protein-solvent interactions or, from the alternative perspective, by coulombic interactions.

show abstract

“…Beyond MD, there is a big family of computationally cheaper, easier-to-master bioinformatics tools, often available as web servers. These are sequence- and structure-based tools for predicting protein stability and the effects of mutations [ 135 , 136 , 137 , 138 , 139 ], proposing mutations for improving stability [ 140 , 141 ], and developing nanoscale protein materials [ 142 ]. During past years, FoldX [ 143 ] and Rosetta [ 144 ] were of particular popularity [ 145 , 146 , 147 , 148 ].…”

Section: Determination Of Protein Stabilitymentioning

confidence: 99%

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions

Masson

Lushchekina

2022

Molecules

View full text Add to dashboard Cite

The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.

show abstract

Protposer: The web server that readily proposes protein stabilizing mutations with high PPV

Cited by 4 publications

References 132 publications

Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable

Energy, water, and protein folding: A molecular dynamics‐based quantitative inventory of molecular interactions and forces that make proteins stable

Molecular Interactions and Forces that Make Proteins Stable: A Quantitative Inventory from Atomistic Molecular Dynamics Simulations

Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions

Contact Info

Product

Resources

About