Average Solvent Accessibility Research Articles

Mechanism insights into liquid polarity regulation for enhanced dewatering of waste-activated sludge: Specifically focusing on the solid-liquid affinity reduction depending on phase-transfer and conformational features of amphiphilic protein

This study proposed that decreasing liquid polarity could weaken the intermolecular polar force at solid-liquid interface of waste-activated sludge (WAS). Accordingly, a process for enhanced sludge dewatering through liquid polarity regulation was established. The liquid polarity was quantified by dielectric constant and the decrease of liquid dielectric constant below 50 was found to significantly improve the solid-liquid separation performance of WAS in terms of filterability by >70%. The differential scanning calorimeter (DSC) coupled with mass spectrum (MS) identified that 60 °C was the appropriate temperature for liquid amendment (i.e., acetonitrile) recovery from filtered sludge cake, and the corresponding energy consumption was calculated to be at most 799.0 J/g, which was substantially lower than that of water evaporation by sludge drying. The NaCl addition with 75% of saturated concentration could non-thermally recover 91.7 ± 4.9% of acetonitrile amendment from filtrate by salting-out. The great potentials in energy saving and recycle of chemicals make the newly proposed approach act as alternatives for the conventional process (i.e., mechanically dewatering + drying). Regarding the mechanism of liquid polarity regulation for enhanced WAS dewatering, the solid-liquid interfacial free energy was found to be reduced by 39.4% with the liquid dielectric constant decreasing from 78.50 to 41.00. Also, Tandem Mass Tags (TMT) proteomics tracked the phase-transfer of amphiphilic proteins with decreasing liquid polarity, which found that the solubilization of proteins involved in the Gene Ontology (GO) classifications of “membrane protein complex” and “membrane protein complex/outer membrane” could facilitate the enhanced solid-liquid separation of WAS. The conformational analysis on those differential proteins was further conducted to reveal the structure attributes of amphiphilic proteins for the phase-transfer feature. The proteins with more exposed amino acid residues (i.e., average solvent accessibility index over 1.8) tended to dissolve in the liquid phase with lower polarity, which was accompanied with the reduced interfacial free energy of WAS. On the contrary, the proteins with buried amino acid residues (e.g., the central hydrophobic β-sheet is surrounded by the hydrophilic α-helix) precipitated in the solid phase with the decreasing liquid polarity. All these findings are expected to create a novel option for dewatering WAS with recyclable liquid conditioning agents, and provide the improved mechanistic insights into the migration of interfacial compositions controlling the dewaterability of WAS.

Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins.

The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0–155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0–29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.

Charge-Surface Correlation in Electrospray Ionization of Folded and Unfolded Proteins

Electrospray-ionization mass spectrometry (ESI-MS) is widely used for protein studies. It has been shown that the extent of protein ionization under nondenaturing conditions correlates well with the solvent-accessible surface area of the tridimensional structure, for either folded monomers or multimeric complexes. The goal of this study was to test whether this relation holds for unfolded proteins as well. In order to overcome the paucity of structural data, the server ProtSA was used to model the conformational ensembles of proteins in the unfolded state and generate estimates of the average solvent accessibility. The results are analyzed along with literature data or original measurements by ESI-MS. It is found that the charge-to-surface relation holds for proteins in the unfolded state, free from solvent effects. A double-log plot is derived, in close agreement with published data for folded proteins. These results suggest that the solvent-accessible surface area is a key factor determining the extent of protein ionization by electrospray, independent of the conformational state. This conclusion helps rationalizing conformational effects in protein ESI-MS. The here reported relation can be used to predict the average solvent accessibility and, hence, the state of folding of unknown proteins from ESI-MS data.

On nucleotide solvent accessibility in RNA structure

Sequence dependence of solvent accessibility in globular and membrane proteins is well established. However, this important structural property has been poorly investigated in nucleic acids. On the other hand investigation of structural determinants of transcriptional and post-transcriptional processes in gene expression are also in a primitive stage and there is a need to explore novel sequence and structural features of both DNA and RNA, which may explain both basic and regulatory mechanisms at various stages of expression. We have recently shown that the nucleotide accessibility in double-stranded DNA molecules strongly depends on sequence context and can be predicted using neighbor information. In this work, we investigate statistics, neighbor-dependence and predictability of nucleotide solvent accessibility for various types of RNA molecules (single-stranded, double-stranded, protein-unbound and protein-bound). It was found that average solvent accessibility of different RNA trinucleotides varies considerably. Interestingly, important translational signals (initiatory AUG codon, Shine-Dalgharno site) were characterized by high solvent accessibility that could be important for its selection in evolution. We also analyzed a relationship between nucleotide accessibility and synonymous codon usage bias in some genomes and find that the two properties are directly related. We believe that the analysis and prediction of nucleotide solvent accessibility opens new avenues to explore more biologically meaningful relationship between RNA structure and function.

Computational analysis and determination of a highly conserved surface exposed segment in H5N1 avian flu and H1N1 swine flu neuraminidase

BackgroundCatalytic activity of influenza neuraminidase (NA) facilitates elution of progeny virions from infected cells and prevents their self-aggregation mediated by the catalytic site located in the body region. Research on the active site of the molecule has led to development of effective inhibitors like oseltamivir, zanamivir etc, but the high rate of mutation and interspecies reassortment in viral sequences and the recent reports of oseltamivir resistant strains underlines the importance of determining additional target sites for developing future antiviral compounds. In a recent computational study of 173 H5N1 NA gene sequences we had identified a 50-base highly conserved region in 3'-terminal end of the NA gene.ResultsWe extend the graphical and numerical analyses to a larger number of H5N1 NA sequences (514) and H1N1 swine flu sequences (425) accessed from GenBank. We use a 2D graphical representation model for the gene sequences and a Graphical Sliding Window Method (GSWM) for protein sequences scanning the sequences as a block of 16 amino acids at a time. Using a protein sequence descriptor defined in our model, the protein sliding scan method allowed us to compare the different strains for block level variability, which showed significant statistical correlation to average solvent accessibility of the residue blocks; single amino acid position variability results in no correlation, indicating the impact of stretch variability in chemical environment. Close to the C-terminal end the GSWM showed less descriptor-variability with increased average solvent accessibility (ASA) that is also supported by conserved predicted secondary structure of 3' terminal RNA and visual evidence from 3D crystallographic structure.ConclusionThe identified terminal segment, strongly conserved in both RNA and protein sequences, is especially significant as it is surface exposed and structural chemistry reveals the probable role of this stretch in tetrameric stabilization. It could also participate in other biological processes associated with conserved surface residues. A RNA double hairpin secondary structure found in this segment in a majority of the H5N1 strains also supports this observation. In this paper we propose this conserved region as a probable site for designing inhibitors for broad-spectrum pandemic control of flu viruses with similar NA structure.

A tale of two tails: why are terminal residues of proteins exposed?

It is widely known that terminal residues of proteins (i.e. the N- and C-termini) are predominantly located on the surface of proteins and exposed to the solvent. However, there is no good explanation as to the forces driving this phenomenon. The common explanation that terminal residues are charged, and charged residues prefer to be on the surface, cannot explain the magnitude of the phenomenon. Here, we survey a large number of proteins from the PDB in order to explore, quantitatively, this phenomenon, and then we use a lattice model to study the mechanisms involved. The location of the termini was examined for 425 small monomeric proteins (50-200 amino acids) and it was found that the average solvent accessibility of termini residues is 87.1% compared with 49.2% of charged residues and 35.9% of all residues. Using a cutoff of 50% of the maximal possible exposure, 80.3% of the N-terminal and 86.1% of the C-terminal residues are exposed compared to 32% for all residues. In addition, terminal residues are much more distant from the center of mass of their proteins than other residues. Using a 2D lattice, a large population of model proteins was studied on three levels: structural selection of compact structures, thermodynamic selection of conformations with a pronounced energy gap and kinetic selection of fast folding proteins using Monte-Carlo simulations. Progressively, each selection raises the proportion of proteins with termini on the surface, resulting in similar proportions to those observed for real proteins.

Effects of Anion Proximity in Peptide Primary Sequence on the Rate and Mechanism of Leucine Oxidation

Hydroxyl radical surface mapping is a useful tool for investigating protein structure and folding. The rate of protein side-chain oxidation by the hydroxyl radical is known to be affected primarily by the chemical reactivity of the side chain and the accessibility of the reactive site to the radical. Efforts have been made to determine the inherent rate of stable product formation of each amino acid side chain, so that the rate of oxidation of an amino acid can be used to accurately estimate the average solvent accessibility of the amino acid side chain in the folded protein. However, the effects of nearby primary sequence on peptide oxidation have not been studied. Here, we examine the amounts of various oxidation products of a small peptide consisting of one leucine and one aspartic acid separated by zero to five glycine residues, as well as with modification of the N- and C-terminus. We find that the relative amounts of certain oxidation products can be heavily influenced by the primary structure of the surrounding peptide. The formation of many products, including hydroxylation, is inhibited by proximity to negative charges, while the formation of other products showed more complicated responses to changing primary sequence.

Dimensionality of amino acid space and solvent accessibility prediction with neural networks

Solvent accessibility prediction from amino acid sequences has been pursued by several researchers. Such a prediction typically starts by transforming the amino acid category (or type) information into numerical representations. All twenty amino acids can be completely and uniquely represented by 20-dimensional vectors. Here, we investigate if the amino acid space defined in this way really requires twenty dimensions. We tried to develop corresponding representations in fewer dimensions. A method for searching optimal codification schema in an arbitrary space using neural networks was developed. The method is used to obtain optimal encoding of amino acids at various levels of dimensionality, and applied to optimize the amino acid codifications for the prediction of the solvent accessibility values of the proteins using feed-forward neural networks. The traditional 20-dimensional codification seems to be redundant in solving the solvent accessibility prediction problem, since a 1-dimensional codification is able to achieve almost the same degree of accuracy as the 20-dimensional codification. Optimal coding in much fewer dimensions could be used to make the predictions of accessible surface area with almost the same degree of accuracy as that obtained by a fully unique 20-dimensional coding. The 1-dimensional amino acid codification for solvent accessibility prediction obtained by a purely mathematical way based on neural networks is highly correlated with a physical property of the amino acids, namely their average solvent accessibility. The method developed to find the optimal codification is general, although the codification thus produced is dependent on the type of estimated property.

Look-up tables for protein solvent accessibility prediction and nearest neighbor effect analysis.

We developed dictionaries of two-, three-, and five-residue patterns in proteins and computed the average solvent accessibility of the central residues in their native proteins. These dictionaries serve as a look-up table for making subsequent predictions of solvent accessibility of amino acid residues. We find that predictions made in this way are very close to those made using more sophisticated methods of solvent accessibility prediction. We also analyzed the effect of immediate neighbors on the solvent accessibility of residues. This helps us in understanding how the same residue type may have different accessible surface areas in different proteins and in different positions of the same protein. We observe that certain residues have a tendency to increase or decrease the solvent accessibility of their neighboring residues in C- or N-terminal positions. Interestingly, the C-terminal and N-terminal neighbor residues are found to have asymmetric roles in modifying solvent accessibility of residues. As expected, similar neighbors enhance the hydrophobic or hydrophilic character of residues. Detailed look-up tables are provided on the web at www.netasa.org/look-up/.

Statistical Models for Discerning Protein Structures Containing the DNA-binding Helix-Turn-Helix Motif

A method for discerning protein structures containing the DNA-binding helix-turn-helix (HTH) motif has been developed. The method uses statistical models based on geometrical measurements of the motif. With a decision tree model, key structural features required for DNA binding were identified. These include a high average solvent-accessibility of residues within the recognition helix and a conserved hydrophobic interaction between the recognition helix and the second alpha helix preceding it. The Protein Data Bank was searched using a more accurate model of the motif created using the Adaboost algorithm to identify structures that have a high probability of containing the motif, including those that had not been reported previously.

Ethanol-induced conformational transitions in holo-alpha-lactalbumin: spectral and calorimetric studies.

Conformational transitions of holo-alpha-lactalbumin in a hydro-ethanolic cosolvent system was studied by spectrofluorescence, CD in near- and far-uv regions, and high-sensitivity differential scanning calorimetry. Experimental results allow us to propose that in isothermal conditions alpha-lactalbumin undergoes a number of conformational transitions with increasing ethanol concentration: N<=>I<=>D<=>H. The existence of I-state was deduced from spectrofluorometric and near-uv CD data. In this state the aromatic chromophores of the amino acid side chains are more accessible to the solvent displaying higher local mobility. The H-state was detected from far-uv CD spectra as a state corresponding to the content of alpha-helices higher than originally found in native protein. However, calorimetric measurements provide data revealing only the two-state mechanism of alpha-lactalbumin unfolding in both water and in aqueous ethanol solutions. This indicates that the energy levels of N- and I-states as well as of D- and H-states are similar. Thermodynamics of the unfolding of alpha-lactalbumin in hydroethanolic solutions was analyzed with the help of the linear model of solvent denaturation. Unfolding increments of enthalpy, entropy, and Gibbs energy of transfer of the protein from a reference aqueous solution to hydro-ethanolic solutions of different concentrations were determined from the calorimetric data. They are linear functions of molar ethanol fraction. The slope of the unfolding increment of Gibbs energy of transfer was calculated from data on transfer of amino acid residues taking into account the average solvent accessibility of amino acid residues in the native structure of small globular proteins, using the additive group contribution method.

Simultaneous Monitoring of the Environment of Tryptophan, Tyrosine, and Phenylalanine Residues in Proteins by Near-Ultraviolet Second-Derivative Spectroscopy

A method for deconvolution of the near-uv second-derivative spectra of proteins into their component tryptophan, tyrosine, and phenylalanine spectra is described. In this approach, the second-derivative spectra of tryptophan and tyrosine model compounds are numerically shifted to create a set of reference spectra corresponding to anticipated peak positions in protein environments of different polarity. The relative contributions of these individual standard spectra are varied until the best fit to the experimental protein spectrum is obtained. Separate addition of tryptophan and tyrosine standard spectra, weighted by their contributions as determined in the fitting procedure, yields an accurate representation of the spectra of these residues in proteins. The position of the intersection of these spectra with the wavelength axis is used as a measure of spectral position in ethylene glycol perturbation experiments in which the average solvent accessibility is assessed by relating the observed shifts in the tryptophan and tyrosine spectra to the shifts observed for corresponding model compounds. The phenylalanine peak positions in the set of 16 proteins studied are determined as described previously [H. Mach et al. (1991) Arch. Biochem. Biophys. 287, 33-40]. For all three aromatic residues in proteins, no consistent correlation between absolute spectral band positions and average solvent accessibility is observed, suggesting a significant influence of other local (e.g., electrostatic) effects on near-uv spectra of proteins. The maximum spectral shift observed between solvent-exposed model compounds and side chains entirely buried in apolar protein core was found to be approximately 5 nm for tyrosine, 4 nm for tryptophan, and 2 nm for phenylalanine residues.

Mechanism of surface peptide proton exchange in bovine pancreatic trypsin inhibitor salt effects and O-protonation

The acid-catalyzed hydrogen exchange rate constants k H, and the base-catalyzed rate constants k OH, have been determined (in the preceding paper) for the 25 most rapidly exchanging NH groups of bovine pancreatic trypsin inhibitor. Most of these NH groups are at the protein-solvent interface. The correlation of k H, but not k OH, with the static accessibility and hydrogen bonding of the peptide carbonyl O atom indicates that the mechanism of acid catalysis in proteins involves O-protonation. Agreement between the ionic strength dependence observed for k H and k OH and the ionic strength dependence calculated for an O-protonation mechanism supports this conclusion. N-protonation for acid catalysis, as well as N-deprotonation for base catalysis, have traditionally been assumed in the mechanism of the chemical step in peptide amide proton exchange. A preference for the alternative O-protonation mechanism has far-reaching implications in the interpretation of protein hydrogen exchange kinetics. With an O-protonation mechanism, acid-catalyzed rates of surface NH groups are primarily a function of the average solvent accessibility of the carbonyl O atoms in the dynamic solution structure, while base-catalyzed rates of surface NH groups measure solvent accessibility of the peptide N. The relative dynamic accessibilities of peptide O atoms, as measured by relative values of k H (corrected for electrostatic effects), correlate with O static accessibilities in the crystal structure. A lower correlation of static accessibility of N atoms with k OH is observed for surface NH groups in peptide groups in which the carbonyl O is not hydrogen bonded. For some surface NH groups, the observed pH of minimum rate, pH min, deviates widely from the pH min of model compounds. This is explained as the combined result of electrostatic effects and of the differences in accessibility of the carbonyl O and N atoms that result in a change in the relative values of k H and k OH as compared to those of model peptides. A mechanism whereby exchange of interior sites is catalyzed by interactions of catalysis ions with protein surface atoms via charge transfer is suggested.