Browse
Submit Data
Databases
API
Help

Dataset Information

8 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.

ABSTRACT: The denaturant dependence of hydrogen-deuterium exchange (HDX) is a powerful measurement to identify the breaking of individual H-bonds and map the free energy surface (FES) of a protein including the very rare states. Molecular dynamics (MD) can identify each partial unfolding event with atomic-level resolution. Hence, their combination provides a great opportunity to test the accuracy of simulations and to verify the interpretation of HDX data. For this comparison, we use Upside, our new and extremely fast MD package that is capable of folding proteins with an accuracy comparable to that of all-atom methods. The FESs of two naturally occurring and two designed proteins are so generated and compared to our NMR/HDX data. We find that Upside's accuracy is considerably improved upon modifying the energy function using a new machine-learning procedure that trains for proper protein behavior including realistic denatured states in addition to stable native states. The resulting increase in cooperativity is critical for replicating the HDX data and protein stability, indicating that we have properly encoded the underlying physiochemical interactions into an MD package. We did observe some mismatch, however, underscoring the ongoing challenges faced by simulations in calculating accurate FESs. Nevertheless, our ensembles can identify the properties of the fluctuations that lead to HDX, whether they be small-, medium-, or large-scale openings, and can speak to the breadth of the native ensemble that has been a matter of debate.

SUBMITTER: Peng X

PROVIDER: S-EPMC8757463 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Tracing a protein's folding pathway over evolutionary time using ancestral sequence reconstruction and hydrogen exchange.

Project description:The conformations populated during protein folding have been studied for decades; yet, their evolutionary importance remains largely unexplored. Ancestral sequence reconstruction allows access to proteins across evolutionary time, and new methods such as pulsed-labeling hydrogen exchange coupled with mass spectrometry allow determination of folding intermediate structures at near amino-acid resolution. Here, we combine these techniques to monitor the folding of the ribonuclease H family along the evolutionary lineages of T. thermophilus and E. coli RNase H. All homologs and ancestral proteins studied populate a similar folding intermediate despite being separated by billions of years of evolution. Even though this conformation is conserved, the pathway leading to it has diverged over evolutionary time, and rational mutations can alter this trajectory. Our results demonstrate that evolutionary processes can affect the energy landscape to preserve or alter specific features of a protein's folding pathway.

| S-EPMC6158009 | biostudies-literature

The free energy of dissociation of oligomeric structure in phycocyanin is not linear with denaturant.

Project description:Using SEC HPLC and fluorescence anisotropy, absorption spectra were assigned to the specific oligomeric structures found with phycocyanin. The absorption spectra were used to quantify the population of each oligomeric form of the protein as a function of both urea concentration and temperature. Phycocyanin hexamers dissociate to trimers with equilibrium constants of 10(-6) to 10(-5). Phycocyanin trimers dissociate to monomers with equilibrium constants of 10(-15) to 10(-12). Both dissociation constants increase linearly with increasing urea concentration, and deltaG(o) values calculated from the equilibrium constants fit best with an exponential function. Our findings appear in contrast with the commonly used linear extrapolation model, deltaG(urea)(o) = deltaG(water)(o) + A[denaturant], in which a linear relationship exists between the free energy of protein unfolding or loss of quaternary structure and the denaturant concentration. Our data examines a smaller range of denaturant concentration than generally used, which might partially explain the inconsistency.

| S-EPMC2519023 | biostudies-literature

Tuning the Wettability and Surface Free Energy of Poly(vinylphenol)Thin Films by Modulating Hydrogen-Bonding Interactions.

Project description:The ability to tune the surface properties of a polymer film in a simple and effective manner is important for diverse biological, industrial, and environmental applications. In this work, we investigated whether or not the surface free energy of poly(vinyl phenol; PVPh) can be tuned by adjusting the casting solvent and the thermal treatment time, which alters the proportions of intra-and intermolecular hydrogen bonding interactions. Compared to the untreated sample, in tetrahydrofuran (THF) system, the thermal treatment resulted in a lower proportion of intermolecular hydrogen bonds and a concomitant decrease in the surface free energy (from 39.3 to 18.8 mJ/m2). In contrast, the thermal treatment in propylene glycol methyl ether acetate (PGMEA) and ethyl-3-ethoxypropionate (EEP) systems increased the proportion of intermolecular hydrogen bonds and the surface free energy of the polymer thin films, from 45.0 to 54.3 mJ/m2 for PGMEA and from 45.5 to 52.9 mJ/m2 for EEP. Controlling intermolecular hydrogen-bonding interactions is a unique and easy method for tuning the surface free energies of polymer substances.

| S-EPMC7182822 | biostudies-literature

Prediction of native-state hydrogen exchange from perfectly funneled energy landscapes.

Project description:Simulations based on perfectly funneled energy landscapes often capture many of the kinetic features of protein folding. We examined whether simulations based on funneled energy functions can also describe fluctuations in native-state protein ensembles. We quantitatively compared the site-specific local stability determined from structure-based folding simulations, with hydrogen exchange protection factors measured experimentally for ubiquitin, chymotrypsin inhibitor 2, and staphylococcal nuclease. Different structural definitions for the open and closed states based on the number of native contacts for each residue, as well as the hydrogen-bonding state, or a combination of both criteria were evaluated. The predicted exchange patterns agree with the experiments under native conditions, indicating that protein topology indeed has a dominant effect on the exchange kinetics. Insights into the simplest mechanistic interpretation of the amide exchange process were thus obtained.

| S-EPMC3203634 | biostudies-literature

Improving spectral validation rates in hydrogen-deuterium exchange data analysis.

Project description:HX-MS data generated to support the testing and development of the HX data analysis applications in Mass Spec Studio.

2021-02-22 | PXD022831 | Pride

Validation of Free Energy Methods in AMBER.

Project description:Herein we provide high-precision validation tests of the latest GPU-accelerated free energy code in AMBER. We demonstrate that consistent free energy results are obtained in both the gas phase and in solution. We first show, in the context of thermodynamic integration (TI), that the results are invariant with respect to "split" (e.g., stepwise decharge-vdW-recharge) versus "unified" protocols. This brought to light a subtle inconsistency in previous versions of AMBER that was traced to the improper treatment of 1-4 vdW and electrostatic interactions involving atoms across the softcore boundary. We illustrate that under the assumption that the ensembles produced by different legs of the alchemical transformation between molecules A and B in the gas phase and aqueous phase are very small, the inconsistency in the relative hydration free energy ΔΔGhydr[A → B] = ΔGaq[A → B] - ΔGgas[A → B] is minimal. However, for general cases where the ensembles are shown to be substantially different, as expected in ligand-protein binding applications, these errors can be large. Finally, we demonstrate that results for relative hydration free energy simulations are independent of TI or multistate Bennett's acceptance ratio (MBAR) analysis, invariant to the specific choice of the softcore region, and in agreement with results derived from absolute hydration free energy values.

| S-EPMC7686255 | biostudies-literature

Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

Project description:Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

| S-EPMC3157700 | biostudies-literature

Mapping the energy landscape of repeat proteins using NMR-detected hydrogen exchange.

Project description:Repeat proteins contain tandem arrays of a simple structural motif. In contrast to globular proteins, repeat proteins are stabilized only by interactions between residues that are relatively close together in the sequence, with no "long-range" interactions. Our work focuses on the tetratricopeptide repeat (TPR), a 34 amino acid helix-turn-helix motif found in tandem arrays in many natural proteins. Earlier, we reported the design and characterization of a series of consensus TPR (CTPR) proteins, which are built as arrays of multiple tandem copies of a 34 amino acid consensus sequence. Here, we present the results of extensive hydrogen exchange (HX) studies of the folding-unfolding behavior of two CTPR proteins (CTPR2 and CTPR3). We used HX to detect and characterize partially folded species that are populated at low frequency in the nominally folded state. We show that for both proteins the equilibrium folding-unfolding transition is non-two-state, but sequential, with the outermost helices showing a significantly higher probability than inner helices of being unfolded. We show that the experimentally observed unfolding behavior is consistent with the predictions of a simple Ising model, in which individual helices are treated as "spin-equivalents". The results that we present have general implications for our understanding of the thermodynamic properties of repeat proteins.

| S-EPMC3282110 | biostudies-literature

Bubble formation and scale dependence in free-surface air entrainment.

Project description:The air bubble entrainment and self-aeration phenomena in free-surface water flows reveal a rich interplay of fundamental science and engineering, and the size distribution of the entrained bubbles enhances the air-water gas flux, improves the gas transfer, and influences the cavitation erosion protection in high-speed flows. In the present study, we investigate the bubble-formation mechanism of free-surface air entrainment and the related microscopic bubble scale in the laboratory. This paper provides a quantitative description of bubble entrainment. The entrapment deformation of the local free surface over a period follows a power-law scaling and entrains a bubble when the entrapped surface becomes enclosed in the unstable movement period. Both the size scale and shape character of the entrapped free surface determine the size and skewness of the distribution of the air bubble. The entrapment deformation process confirms that the instability behaviour of the local air-water interface results in the onset of bubble entrainment. Further research is necessary to elucidate the instability criterion dominated by the interface instability and promote a new understanding of multiphase flow generation and development.

| S-EPMC6662671 | biostudies-literature

Predicting gene ontology functions from protein's regional surface structures.

Project description:BACKGROUND: Annotation of protein functions is an important task in the post-genomic era. Most early approaches for this task exploit only the sequence or global structure information. However, protein surfaces are believed to be crucial to protein functions because they are the main interfaces to facilitate biological interactions. Recently, several databases related to structural surfaces, such as pockets and cavities, have been constructed with a comprehensive library of identified surface structures. For example, CASTp provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities. RESULTS: A novel method was proposed to predict the Gene Ontology (GO) functions of proteins from the pocket similarity network, which is constructed according to the structure similarities of pockets. The statistics of the networks were presented to explore the relationship between the similar pockets and GO functions of proteins. Cross-validation experiments were conducted to evaluate the performance of the proposed method. Results and codes are available at: http://zhangroup.aporc.org/bioinfo/PSN/. CONCLUSION: The computational results demonstrate that the proposed method based on the pocket similarity network is effective and efficient for predicting GO functions of proteins in terms of both computational complexity and prediction accuracy. The proposed method revealed strong relationship between small surface patterns (or pockets) and GO functions, which can be further used to identify active sites or functional motifs. The high quality performance of the prediction method together with the statistics also indicates that pockets play essential roles in biological interactions or the GO functions. Moreover, in addition to pockets, the proposed network framework can also be used for adopting other protein spatial surface patterns to predict the protein functions.

| S-EPMC2233648 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data