Protein Solvent Accessible Surface Research Articles

Laser-free Hydroxyl Radical Protein Footprinting to Perform Higher Order Structural Analysis of Proteins.

Hydroxyl Radical Protein Footprinting (HRPF) is an emerging and promising higher order structural analysis technique that provides information on changes in protein structure, protein-protein interactions, or protein-ligand interactions. HRPF utilizes hydroxyl radicals (▪OH) to irreversibly label a protein's solvent accessible surface. The inherent complexity, cost, and hazardous nature of performing HRPF have substantially limited broad-based adoption in biopharma. These factors include: 1) the use of complicated, dangerous, and expensive lasers that demand substantial safety precautions; and 2) the irreproducibility of HRPF caused by background scavenging of ▪OH that limit comparative studies. This publication provides a protocol for operation of a laser-free HRPF system. This laser-free HRPF system utilizes a high energy, high-pressure plasma light source flash oxidation technology with in-line radical dosimetry. The plasma light source is safer, easier to use, and more efficient in generating hydroxyl radicals than laser-based HRPF systems, and the in-line radical dosimeter increases the reproducibility of studies. Combined, the laser-free HRPF system addresses and surmounts the mentioned shortcomings and limitations of laser-based techniques.

Role of pH in structural changes for Pin1 protein: an insight from molecular dynamics study.

Pin1 protein is closely associated with the pathogenesis of cancers and Alzheimer's disease (AD). Previously, we have shown the acid-induced denaturation of Pin1 was determined by means of fluorescence emission, synchronous fluorescence etc., indicating an intermediate state around chromophores in Pin1 at about 4.0. Molecular dynamics simulations for the wild type Pin1 and its mutants were performed to explore the role of pH in the conformation changes of Pin1 protein. Our present study shows that one protein domain (PPIase domain) is more sensitive than the other one (WW domain) in Pin1 protein, and also our study shows that the integrality of the two conserve tryptophan in one domain (WW) is important in response to low pH. We arrive at the last result with the analysis of the protein root mean square distance and the analysis of the radius of gyration. The analysis of protein solvent accessible surface area values have proven our previous experiment result that there is an intermediate state around tryptophan residues at about pH4.0. Moreover, acidic states of the protein can break the alpha-helixes in Pin1, especially the alpha-helix α3 close to active sites; as a result, Pin1 loses most of its activity at low pH. The results help us to understand the role of pH in Pin1, provide us insights into the conformation change at the atomic-level and emphasize the important role of decreased pH in the pathogenesis of some Pin1-related diseases, and support the therapeutic approach for the related Pin1 diseases by targeting acidosis and modifying the intracellular pH gradients.

Obtaining protein solvent accessible surface area when structural data is unavailable using osmotic pressure

AbstractHere, we provide an algorithm that predicts solvent accessible surface area (SASA) using concentrated solution osmotic pressure data. Sheep hemoglobin monomer and β‐lactoglobulin are used for verification. Additionally, SASA for structurally unknown calf lens α‐crystallin aggregate is predicted. Using osmotic pressure data, the predicted SASA value for sheep hemoglobin, 22,398 ± 1,244 Å2, was in excellent agreement with computational model predictions (24,304 Å2‐26,100 Å2). Similarly, predicted SASA values for bovine β‐lactoglobulin in pH solutions of pH 5.1, 6.0, and 8.0, were 5,765 ± 1,031 Å2, 6,656 ± 1,082 Å2, and 9,141 ± 1,060 Å2, respectively, were in good agreement with the computationally determined SASA value (7,500 Å2–8,628 Å2). Predicted SASA for the aggregate of calf lens α‐crystallin (800 kDa) was found to be 417,691 ± 16,790 Å2. These results illustrate that this novel method can provide an important experimental alternative in estimating SASA for proteins and, possibly, their complexes in solution. © 2011 American Institute of Chemical Engineers AIChE J, 2012

Fast accurate evaluation of protein solvent exposure.

Protein solvation energies are often taken to be proportional to solvent-accessible surface areas. Computation of these areas is numerically demanding and may become a bottleneck for folding and design applications. Fast graph-based methods, such as dead-end elimination (DEE), become possible if all energies, including solvation energies, are expressed as single-residue and pair-residue terms. To this end, Street and Mayo originated a pair-residue approximation for solvent-accessible surface areas (Street AG, Mayo SL. Pairwise calculation of protein solvent accessible surface areas. Fold Des 1998;3:253-258). The dominant source of error in this method is the overlapping burial of side-chain surfaces in the protein core. Here we report a new pair-residue approximation, which greatly reduces this overlap error by the use of optimized generic side-chains. We have tested the generic-side-chain method for the ten proteins studied by Street and Mayo and for 377 single-domain proteins from the CATH database (Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH-A hierarchic classification of protein domain structures. Structure 1997;5:1093-1108). With little additional cost in computation, the new method consistently reduces error for total areas and residue-by-residue areas by more than a factor of two. For example, the residue-by-residue error (for buried area) is reduced from 7.42 A(2) to 3.70 A(2). This difference translates into a solvation energy difference of approximately 0.2 kcal/mol per residue, amounting to a reduction in root-mean-square energy error of 2 kcal/mol for a 100 residue chain, a potentially critical difference for both protein folding and design applications.

A Dissection of Specific and Non-specific Protein–Protein Interfaces

We compare the geometric and physical–chemical properties of interfaces involved in specific and non-specific protein–protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are illustrated by 70 protein–protein complexes and by subunit contacts in 122 homodimeric proteins; non-specific interactions are illustrated by 188 pairs of monomeric proteins making crystal-packing contacts selected to bury more than 800 Å 2 of protein surface. A majority of these pairs have 2-fold symmetry and form “crystal dimers” that cannot be distinguished from real dimers on the basis of the interface size or symmetry. The chemical and amino acid compositions of the large crystal-packing interfaces resemble the protein solvent-accessible surface. These interfaces are less hydrophobic than in homodimers and contain much fewer fully buried atoms. We develop a residue propensity score and a hydrophobic interaction score to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and we derive indexes to evaluate the atomic packing, which we find to be less compact at non-specific than at specific interfaces. We test the capacity of these parameters to identify homodimeric proteins in crystal structures, and show that a simple combination of the non-polar interface area and the fraction of buried interface atoms assigns the quaternary structure of 88% of the homodimers and 77% of the monomers in our data set correctly. These success rates increase to 93–95% when the residue propensity score of the interfaces is taken into consideration.

Pairwise calculation of protein solvent-accessible surface areas

The tractability of many algorithms for determining the energy state of a system depends on the pairwise nature of an energy expression. Some energy terms, such as the standard implementation of the van der Waals potential, satisfy this criterion whereas others do not. One class of important potentials that are not pairwise involves benefits and penalties for burying hydrophobic and/or polar surface areas. It has been found previously that, in some cases, a pairwise approximation to these surface areas correlates with the true surface areas. We set out to generalize the applicability of this approximation. We develop a pairwise expression with one scalable parameter that closely reproduces both the true buried and the true exposed solvent-accessible surface areas. We then refit our previously published coiled-coil stability data to give solvation parameters of 26 cal/mol A2 favoring hydrophobic burial and 100 cal/mol A2 opposing polar burial. An accurate pairwise approximation to calculate exposed and buried protein solvent-accessible surface area is achieved.

Protein hydration and unfolding – insights from experimental partial specific volumes and unfolded protein models

The partial specific volume of a protein is an experimental quantity containing information about solute-solvent interactions and protein hydration. We use a hydration-shell model to partition the partial specific volume into an intrinsic volume occupied by the protein and a change in the volume occupied by the solvent resulting from the solvent interactions with the protein. We seek to extract microscopic information about protein hydration and unfolding from experimental volume measurements without using computer simulations. We employ the idea that the protein-solvent interaction will be proportional to the surface area of the protein. A linear relationship is obtained when the difference between the experimental protein partial specific volume and its intrinsic volume is plotted as a function of the protein solvent-accessible surface area. The effect of using different protein volume definitions on the analysis of protein volumetric properties is discussed. Volumetric data are used to test a model for the unfolded state of proteins and to make predictions about the denatured state. The linear relationship between hydration-shell volume change and accessible surface area reflects the similar surface properties (fractional composition of nonpolar, polar and charged surface) among a diverse set of proteins. This linear relationship is found to be independent of how the solution is partitioned into solute and solvent components. The interpretation of hydration shell versus bulk water properties is found to be very model dependent, however. The maximally exposed unfolded protein model is found to be inconsistent with experimental volume changes of unfolding.

A flexible triangulation method to describe the solvent-accessible surface of biopolymers.

A relatively simple protein solvent-accessible surface triangulation method for continuum electrostatics applications employing the boundary element method is presented. First, the protein is placed onto a three-dimensional lattice with a specified lattice spacing. To each lattice point, a box is assigned. Boxes located in the solvent region and in the interior of the protein are removed from the set. Improper connections between boxes and the possible existence of cavities in the interior of the protein which would destroy the proper connectivity of the triangulated surface are taken care of. The remaining set of boxes define the outer contour of the protein. Each free face exposed to the solvent of the remaining set of boxes is triangulated after the surface defined by the free faces has been smoothed to follow the shape of the macromolecule more accurately. The final step consists of a mapping of triangle vertices onto a set of surface points which define the solvent-accessible surface. Normal vectors at triangle vertices are obtained also from the free faces which define the orientation of the surface. The algorithm was tested for six molecules including four proteins; a dipeptide, a helical peptide consisting of 25 residues, calbindin, lysozyme, calmodulin and cutinase. For each molecule, total areas have been calculated and compared with the result computed from a dotted solvent-accessible surface. Since the boundary element method requires a low number of vertices and triangles to reduce the number of unknowns for reasons of efficiency, the number of triangles should not be too high. Nevertheless, credible results are obtained for the total area with relative errors not exceeding 12% for a large lattice spacing (0.30 nm) while close to zero for a smaller lattice spacing (down to 0.16 nm). The output of the triangulation computer program (written in C++) is rather simple so that it can be easily converted to any format acceptable for any molecular graphics programs.

Solvent accessibility properties of complex proteins.

AN important factor in the thermodynamics of protein folding is the partition of amino acid residues between the solvent environment and the protein core. The extent of the interaction between the folded polypeptide and the surrounding medium can be measured by determining the solvent accessible surface area as defined by Lee and Richards1. In this communication we present the results of solvent accessibility calculations for the large (195,000 Mr) dimeric enzyme phosphorylase a and other multidomain, multisubunit proteins. These results are discussed in the light of the generalisations concerning protein solvent—accessible surface area and shape which have been based on data derived from low molecular weight proteins.