Hydrophobic Core Of Protein Research Articles

CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

Recent results suggest that during evolution certain substitutions at protein sites may occur in a coordinated manner due to interactions between amino acid residues. Information on these coordinated substitutions may be useful for analysis of protein structure and function. CRASP is an Internet-available software tool for the detection and analysis of coordinated substitutions in multiple alignments of protein sequences. The approach is based on estimation of the correlation coefficient between the values of a physicochemical parameter at a pair of positions of sequence alignment. The program enables the user to detect and analyze pairwise relationships between amino acid substitutions at protein sequence positions, estimate the contribution of the coordinated substitutions to the evolutionary invariance or variability in integral protein physicochemical characteristics such as the net charge of protein residues and hydrophobic core volume. The CRASP program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/.

Exploring sequence/folding space: folding studies on multiple hydrophobic core mutants of ubiquitin.

The stability, dynamic, and structural properties of ubiquitin and two multiple hydrophobic core mutants were studied. One of the mutants (U4) has seven substitutions in the hydrophobic core (M1L, I3L, V5I, I13F, L15V, V17M, and V26L). On average, its side chains are larger than the wild-type, and it can thus be thought of as having an overpacked core. The other mutant (U7) has two substitutions (I3V and I13V). On average, it has smaller side chains than the wild-type, and it can therefore be considered to be underpacked. The three proteins are well-folded and show similar backbone dynamics (T(1), T(2), and HNOE values), indicating that the regular secondary structure extends over the same residue ranges. The crystallographic structure of U4 was determined. The final R(factor) and R(free) are 0.198 and 0.248, respectively, at 2.18 A resolution. The structure of U4 is very similar to wild-type ubiquitin. Remarkably, there are almost no changes in the positions of the C(alpha) atoms along the entire backbone, and the hydrogen-bonding network is maintained. The mutations of the hydrophobic core are accommodated by small movements of side chains in the core of mutated and nonmutated residues. Unfolding and refolding kinetic studies revealed that U4 unfolds with the highest rates; however, its refolding rate constants are very similar to those of the wild-type protein. Conversely, U7 seems to be the most destabilized protein; its refolding rate constant is smaller than the other two proteins. This was confirmed by stopped-flow techniques and by H/D exchange methodologies. This work illustrates the possibility of repacking the hydrophobic core of small proteins and has important implications in the de novo design of stable proteins.

Redesigning the Folding Energetics of a Model Three-helix Bundle Protein by Site-directed Mutagenesis

Because of their limited size and complexity, de novo designed proteins are particularly useful for the detailed investigation of folding thermodynamics and mechanisms. Here, we describe how subtle changes in the hydrophobic core of a model three-helix bundle protein (GM-0) alter its folding energetics. To explore the folding tolerance of GM-0 toward amino acid sequence variability, two mutant proteins (GM-1 and GM-2) were generated. In the mutants, cavities were created in the hydrophobic core of the protein by either singly (GM-1; L35A variant) or doubly (GM-2; L35A/I39A variant) replacing large hydrophobic side chains by smaller Ala residues. The folding of GM-0 is characterized by two partially folded intermediate states exhibiting characteristics of molten globules, as evidenced by pressure-unfolding and pressure-assisted cold denaturation experiments. In contrast, the folding energetics of both mutants, GM-1 and GM-2, exhibit only one folding intermediate. Our results support the view that simple but biologically important folding motifs such as the three-helix bundle can reveal complex folding plasticity, and they point to the role of hydrophobic packing as a determinant of the overall stability and folding thermodynamic of the helix bundle.

Clustering of Large Hydrophobes in the Hydrophobic Core of Two-stranded α-Helical Coiled-Coils Controls Protein Folding and Stability

The de novo design and biophysical characterization of two 60-residue peptides that dimerize to fold as parallel coiled-coils with different hydrophobic core clustering is described. Our goal was to investigate whether designing coiled-coils with identical hydrophobicity but with different hydrophobic clustering of non-polar core residues (each contained 6 Leu, 3 Ile, and 7 Ala residues in the hydrophobic core) would affect helical content and protein stability. The disulfide-bridged P3 and P2 differed dramatically in alpha-helical structure in benign conditions. P3 with three hydrophobic clusters was 98% alpha-helical, whereas P2 was only 65% alpha-helical. The stability profiles of these two analogs were compared, and the enthalpy and heat capacity changes upon denaturation were determined by measuring the temperature dependence by circular dichroism spectroscopy and confirmed by differential scanning calorimetry. The results showed that P3 assembled into a stable alpha-helical two-stranded coiled-coil and exhibited a native protein-like cooperative two-state transition in thermal melting, chemical denaturation, and calorimetry experiments. Although both peptides have identical inherent hydrophobicity (the hydrophobic burial of identical non-polar residues in equivalent heptad coiled-coil positions), we found that the context dependence of an additional hydrophobic cluster dramatically increased stability of P3 (Delta Tm approximately equal to 18 degrees C and Delta[urea](1/2) approximately equal to 1.5 M) as compared with P2. These results suggested that hydrophobic clustering significantly stabilized the coiled-coil structure and may explain how long fibrous proteins like tropomyosin maintain chain integrity while accommodating polar or charged residues in regions of the protein hydrophobic core.

The effect of an HMG-CoA reductase inhibitor on arteriosclerotic nanoplaque formation and size in a biosensor model

Proteoheparan sulfate can be adsorbed to a methylated silica surface in a monomolecular layer via its transmembrane hydrophobic protein core domain. Due to electrostatic repulsion, its anionic glycosaminoglycan side chains are stretched out into the blood substitute solution, thereby representing a receptor site for specific lipoprotein binding through basic amino acid-rich residues within their apolipoproteins. The binding process was studied by ellipsometric techniques. Low-density lipoprotein (LDL) was found to deposit strongly at the proteoheparan sulfate-coated surface, particularly in the presence of Ca 2+, apparently through complex formation ‘proteoglycan–LDL–calcium’. This ternary complex build-up may be interpreted as arteriosclerotic nanoplaque formation on the molecular level responsible for the arteriosclerotic primary lesion. HDL bound to heparan sulfate proteoglycan protected against LDL deposition and completely suppressed calcification of the proteoglycan–lipoprotein complex. In addition, HDL was able to decelerate the ternary complex deposition and to disrupt newly formed nanoplaques. Therefore, HDL attached to its proteoglycan receptor sites is thought to raise a multidomain barrier, selection and control motif for transmembrane and paracellular lipoprotein uptake into the arterial wall. The molecular arteriosclerosis model was tested on its reliability in a biosensor application in order to unveil possible acute pleiotropic effects of the lipid lowering drug fluvastatin. The very low-density lipoprotein (VLDL)/intermediate-density lipoprotein (IDL)/LDL and VLDL/IDL/LDL/HDL plasma fractions from a high-risk patient with dyslipoproteinemia and type 2 diabetes mellitus showed beginning arteriosclerotic nanoplaque formation already at a normal blood Ca 2+ concentration, with a strong increase at higher Ca 2+ concentrations. Nanoplaque formation and size of the HDL-containing lipid fraction remained well below that of the LDL-containing lipid fraction. Fluvastatin, whether applied acutely to the patient (one single 80 mg slow release matrix tablet) or in a 2-months medication regimen, markedly slowed down this process of ternary aggregational nanoplaque build-up and substantially inhibited nanoplaque size development at all Ca 2+ concentrations used. The acute action resulted without any significant change in lipid concentrations of the patient. Furthermore, after nanoplaque generation, fluvastatin, similar to HDL, was able to reduce nanoplaque formation and size. These immediate effects of fluvastatin have to be taken into consideration while interpreting the clinical outcome of long-term studies.

Structural Consequences of a Cancer-causing BRCA1-BRCT Missense Mutation

The integrity of the carboxyl-terminal BRCT repeat region is critical for BRCA1 tumor suppressor function; however, the molecular details of how a number of clinically derived BRCT missense mutations affect BRCA1 function remain largely unknown. Here we assess the structural response of the BRCT tandem repeat domain to a well characterized, cancer-associated single amino acid substitution, Met-1775 --> Arg-1775. The structure of BRCT-M1775R reveals that the mutated side chain is extruded from the protein hydrophobic core, thereby altering the protein surface. Charge-charge repulsion, rearrangement of the hydrophobic core, and disruption of the native hydrogen bonding network at the interface between the two BRCT repeats contribute to the conformational instability of BRCT-M1775R. Destabilization and global unfolding of the mutated BRCT domain at physiological temperatures explain the pleiotropic molecular and genetic defects associated with the BRCA1-M1775R protein.

Simplicial Neighborhood Analysis of Protein Packing (SNAPP): A Computational Geometry Approach to Studying Proteins

Publisher Summary This chapter describes the application of computational geometry methodology to protein-structure analysis and comparison. The Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method is applied to the problem of automatically identifying recurrent substructures in a large database of diverse protein structures. The chapter presents a novel approach to mapping protein cores with application to fold recognition via structural templates. It also describes the use of the SNAPP methodology for recognizing functional patterns characteristic of three unique protein families. SNAPP employs Delaunay tessellation to identify recurrent tertiary packing motifs that may be characteristic of protein structural and functional families. This method includes automatic identification of elementary tertiary packing motifs recurring in a large database of protein structures, automatic identification of global patterns of protein structure organization by recognizing the protein's hydrophobic core, and identification of functional signature motifs in a family of proteins that can assist structure-based annotation.

Biosensing of arteriosclerotic nanoplaque formation and interaction with an HMG-CoA reductase inhibitor.

Proteoheparan sulphate can be adsorbed to a methylated silica surface in a monomolecular layer via its transmembrane hydrophobic protein core domain. As a result of electrostatic repulsion, its anionic glycosaminoglycan side chains are stretched out into the blood substitute solution, thereby representing one receptor site for specific lipoprotein binding through basic amino acid-rich residues within their apolipoproteins. The binding process was studied by ellipsometric techniques suggesting that high-density lipoprotein (HDL) has a high binding affinity and a protective effect on interfacial heparan sulphate proteoglycan layers with respect to low-density lipoprotein (LDL) and Ca2+ complexation. Low-density lipoprotein was found to deposit strongly at the proteoheparan sulphate-coated surface, particularly in the presence of Ca2+, apparently through complex formation 'proteoglycan-LDL-calcium'. This ternary complex build-up may be interpreted as arteriosclerotic nanoplaque formation on the molecular level responsible for the arteriosclerotic primary lesion. On the other hand, HDL bound to heparan sulphate proteoglycan protected against LDL deposition and completely suppressed calcification of the proteoglycan-lipoprotein complex. In addition, HDL was able to decelerate the ternary complex deposition. Therefore, HDL attached to its proteoglycan receptor sites is thought to raise a multidomain barrier, selection and control motif for transmembrane and paracellular lipoprotein uptake into the arterial wall. Although much remains unclear regarding the mechanism of lipoprotein depositions at proteoglycan-coated surfaces, it seems clear that the use of such systems offers possibilities for investigating lipoprotein deposition at a 'nanoscopic' level under close to physiological conditions. In particular, Ca2+-promoted LDL deposition and the protective effect of HDL even at high Ca2+ and LDL concentrations agree well with previous clinical observations regarding risk and beneficial factors for early stages of atherosclerosis. Considering this, the system was tested on its reliability in a biosensor application in order to unveil possible acute pleiotropic effects of the lipid lowering drug fluvastatin. The very low-density lipoprotein (VLDL)/intermediate-density lipoprotein (IDL)/LDL plasma fraction from a high risk patient with dyslipoproteinaemia and type 2 diabetes mellitus showed beginning arteriosclerotic nanoplaque formation already at a normal blood Ca2+ concentration, with a strong increase at higher Ca2+ concentrations. Fluvastatin, whether applied to the patient (one single 80 mg slow release matrix tablet) or acutely in the experiment (2.2 micromol L-1), markedly slowed down this process of ternary aggregational nanoplaque complexation at all Ca2+ concentrations used. This action resulted without any significant change in lipid concentrations of the patient. Furthermore, after ternary complex build-up, fluvastatin, similar to HDL, was able to reduce nanoplaque adsorption and size. These immediate effects of fluvastatin have to be taken into consideration while interpreting the clinical outcome of long-term studies.

The acute effect of fluvastatin on lipoprotein deposition in a model substrate for ellipsometry studies at an endothelial membrane equivalent

Proteoheparan sulfate can be adsorbed to a methylated silica surface in a monomolecular layer via its transmembrane hydrophobic protein core domain. Due to electrostatic repulsion, its anionic glycosaminoglycan side chains are stretched out into the blood substitute solution representing one receptor site for specific lipoprotein binding through basic amino acid-rich residues within their apolipoproteins. The binding process was studied by ellipsometric techniques. LDL was found to deposit strongly at the proteoheparan sulfate, particularly in the presence of Ca 2+ thus creating the complex formation proteoglycan — low-density lipoprotein — calcium. This ternary complex build-up may be interpreted as arteriosclerotic nanoplaque formation on the molecular level responsible for the arteriosclerotic primary lesion. Although much remains unclear regarding the mechanism of lipoprotein depositions at proteoglycan-coated surfaces, it seems clear that the use of such systems offers possibilities for investigating lipoprotein deposition at a nanoscopic level under close to physiological conditions. Therefore, we tested the system on its reliability in a biosensor application in order to unveil possible acute pleiotropic effects of the lipid lowering drug fluvastatin. Already with a normal blood Ca 2+ concentration, the VLDL/IDL/LDL plasma fraction from a high-risk patient with dyslipoproteinemia and type 2 diabetes mellitus showed beginning arteriosclerotic nanoplaque formation that massively increased at higher Ca 2+ concentrations. Fluvastatin, whether applied to the patient (one single 80 mg slow release matrix tablet) or acutely in the experiment (2.2 μmol/l), markedly slowed down this process of ternary aggregational nanoplaque complexation at all Ca 2+ concentrations used. This action resulted without any change in lipid concentrations of the patient. Furthermore, after ternary complex build-up, fluvastatin was able to reduce nanoplaque adsorption and size. These immediate effects of fluvastatin have to be taken into consideration while interpreting the results of long-term studies. Altogether, the proteoglycan coated hydrophobic silica surface used in these experiments, mimics the endothelial cell membrane in quite a perfect manner with respect to lipoprotein interactions at the blood-endothelium-matrix interface.

The triplet-state lifetime of indole in aqueous and viscous environments: significance to the interpretation of room temperature phosphorescence in proteins.

The interpretation of room temperature phosphorescence studies of proteins requires an understanding of the mechanisms governing the tryptophan triplet-state lifetimes of residues fully exposed to solvent and those deeply buried in the hydrophobic core of proteins. Since solvents exposed tryptophans are expected to behave similarly to indole free in solution, it is important to have an accurate measure of the triplet state lifetime of indole in aqueous solution. Using photon counting techniques and low optical fluence (J/cm(2)), we observed the triplet-state lifetime of aqueous, deoxygenated indole and several indole derivatives to be approximately 40 micros, closely matching the previous reports by Bent and Hayon based on flash photolysis (12 micros; Bent, D. V.; Hayon, E. J. Am. Chem. Soc. 1975, 97, 2612-2619) but much shorter than the 1.2 ms lifetime observed more recently (Strambini, G. B.; Gonnelli, M. J. Am. Chem. Soc. 1995, 117, 7646-7651). However, we have now been able to reproduce the long lifetime reported by the latter workers for aqueous indole solutions and show that it likely arises from geminate recombination of the indole radical cation and solvated electron, a conclusion based on studies of the indole radical cation in water (Bent and Hayon, 1975). The evidence for this comes from a fast rise in the phosphorescence emission and measurements of a corresponding enhanced quantum yield in unbuffered solutions. This species can be readily quenched, and the corresponding fast rise disappears, leaving a monoexponential 40 micros decay, which we argue is the true indole triplet lifetime. The work is put in the context of room temperature phosphorescence studies of proteins.

X-ray Structure and Ligand Binding Study of a Moth Chemosensory Protein

Chemosensory proteins (CSPs) are believed to be involved in chemical communication and perception. Such proteins, of M(r) 13,000, have been isolated from several sensory organs of a wide range of insect species. Several CSPs have been identified in the antennae and proboscis of the moth Mamestra brassicae. One of them, CSPMbraA6, a 112-amino acid antennal protein, has been expressed in large quantities and is soluble in the Escherichia coli periplasm. X-ray structure determination has been performed in parallel with ligand binding assays using tryptophan fluorescence quenching. The protein has overall dimensions of 25 x 30 x 32 A and exhibits a novel type of alpha-helical fold with six helices connected by alpha-alpha loops. A narrow channel extends within the protein hydrophobic core. Fluorescence quenching with brominated alkyl alcohols or fatty acids and modeling studies indicates that CSPMbraA6 is able to bind such compounds with C12-18 alkyl chains. These ubiquitous proteins might have the role of extracting hydrophobic linear compounds (pheromones, odors, or fatty acids) dispersed in the phospholipid membrane and transporting them to their receptor.

Stacking and T-shape competition in aromatic-aromatic amino acid interactions.

The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

Lipoprotein–proteoglycan interactions at a silica surface membrane

Abstract Proteoheparan sulfate can be adsorbed to a methylated silica surface in a monomolecular layer via its transmembrane hydrophobic protein core domain. Due to electrostatic repulsion, its anionic polysugar side chains are stretched out into the blood substitute solution representing a receptor site for specific lipoprotein binding through basic amino acid-rich residues within their apolipoproteins. The binding process was studied by ellipsometric techniques showing that low density lipoprotein (LDL) strongly deposited at the proteoheparan sulfate, particularly in the presence of Ca2+. On the other hand, high density lipoprotein (HDL) bound to heparan sulfate proteoglycan (HS-PG) protected against LDL docking even at high LDL and Ca2+ concentrations and completely suppressed calcification of the proteoglycan–lipo–protein complex. These findings correlate well with those obtained from clinical investigations on risk factors for arteriosclerosis. The most important patient-oriented finding was the at least four times higher affinity constant of HDL binding to the proteoglycan receptor as compared to LDL docking. Therefore, under normal in vivo conditions most of the proteoglycan receptors are occupied by HDL and in this way shielded against LDL binding. Since competition is the dominant rule at the receptor site, the ternary complex HS-PG/LDL/Ca2+ aggregation can be reversed by HDL. Altogether, the proteoglycan coated hydrophobic silica surface used in these experiments, mimics the endothelial cell membrane in quite a perfect manner with respect to lipoprotein interactions at the blood–endothelium–matrix interface.

Packing is a key selection factor in the evolution of protein hydrophobic cores.

The energy derived from optimized van der Waals interactions in closely packed, folded proteins has been proposed to be of similar energetic magnitude to hydrophobicity in stabilizing the native state. If packing is this energetically important, it should influence the evolution of protein core sequences. To test this hypothesis, the occurrence of various amino acid side chains in the major hydrophobic core of staphylococcal nuclease and 42 homologous proteins was determined. Most such positions in this protein family are usually isoleucine, leucine, or valine. Previously we have constructed and measured the stabilities of 12 single, 44 double, 64 triple, and 32 quadruple mutants, representing all possible permutations of these three side chains at two overlapping sets of four positions in the core of staphylococcal nuclease. The stabilities and interaction energies of those mutants with various combinations of the most common, or consensus, sequence were compared to the stabilities of all other mutants. Mutants which had the consensus side-chain combinations were not necessarily the most stable, but usually were found to have the best interaction energies. In other words, these proteins were far more stable than would be predicted from simply summing the observed energetic effects of the component single mutations, apparently reflecting particularly favorable packing interactions that are possible for the most common side chains. An additional 12 mutants which tested possible alternate explanations of the results were constructed. The stabilities and interaction energies of these mutants also support the conclusion that packing is a crucial determinant guiding the sequence evolution of protein cores.

Synthesis and physical properties of protein core mimetics.

A series of mimetic cores composed of a synthetic scaffold and amino acids have been constructed and their properties investigated in chloroform. A relative measure of H-bond strength was obtained by comparing temperature coefficients derived from variable-temperature (1)H NMR experiments. Although most templates had a strong H-bond, only a single template composed of D- and L-phenylalanines was able to form two strong H-bonds. Templates containing D- and L-leucines formed only a single H-bond. The results of these studies suggest that aromatic edge-to-face interactions provide greater stabilization energy than aliphatic-aromatic interactions in the tightly packed hydrophobic cores of proteins. Partial structures of the templates were derived by analyzing a series of two-dimensional (1)H NMR spectra and performing molecular mechanics calculations using AMBER and MMFF94 force fields.

A receptor-based biosensor for lipoprotein docking at the endothelial surface and vascular matrix

Proteoheparan sulfate can be adsorbed to a methylated silica surface in a monomolecular layer via its transmembrane hydrophobic protein core domain. Due to electrostatic repulsion, its anionic glycosaminoglycan side chains are stretched out into the blood substitute solution, representing a receptor site for specific lipoprotein binding through basic amino acid-rich residues within their apolipoproteins. The binding process was studied by ellipsometric techniques showing that HDL has a high binding affinity to the receptor and a protective effect on interfacial heparan sulfate proteoglycan layers, with respect to LDL and Ca 2+ complexation. LDL was found to deposit strongly at the proteoheparan sulfate, particularly in the presence of Ca 2+, thus creating the complex formation ‘proteoglycan–low density lipoprotein–calcium’. This ternary complex build-up may be interpreted as arteriosclerotic nanoplaque formation on the molecular level responsible for the arteriosclerotic primary lesion. On the other hand, HDL bound to heparan sulfate proteoglycan protected against LDL docking and completely suppressed calcification of the proteoglycan–lipoprotein complex. In addition, HDL and aqueous garlic extract were able to reduce the ternary complex deposition and to disintegrate HS-PG/LDL/Ca 2+ aggregates. Although much remains unclear regarding the mechanism of lipoprotein depositions at proteoglycan-coated surfaces, it seems clear that the use of such systems offers possibilities for investigating lipoprotein deposition at a ‘nanoscopic’ level under close to physiological conditions. In particular, Ca 2+-promoted LDL deposition and the protective effect of HDL, even at high Ca 2+ and LDL concentrations, agree well with previous clinical observations regarding risk and beneficial factors for early stages of atherosclerosis. Therefore, we believe that the system can be of some use in investigations, e.g. of the interplay between different lipoproteins in arteriosclerotic plaque formation, as well as in high throughput screening of candidate drugs to atherosclerosis in a biosensor application.

Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations

Mutational experiments show how changes in the hydrophobic cores of proteins affect their stabilities. Here, we estimate these effects computationally, using four-body likelihood potentials obtained by simplicial neighborhood analysis of protein packing (SNAPP). In this procedure, the volume of a known protein structure is tiled with tetrahedra having the center of mass of one amino acid side-chain at each vertex. Log-likelihoods are computed for the 8855 possible tetrahedra with equivalent compositions from structural databases and amino acid frequencies. The sum of these four-body potentials for tetrahedra present in a given protein yields the SNAPP score. Mutations change this sum by changing the compositions of tetrahedra containing the mutated residue and their related potentials. Linear correlation coefficients between experimental mutational stability changes, Δ(Δ G unfold), and those based on SNAPP scoring range from 0.70 to 0.94 for hydrophobic core mutations in five different proteins. Accurate predictions for the effects of hydrophobic core mutations can therefore be obtained by virtual mutagenesis, based on changes to the total SNAPP likelihood potential. Significantly, slopes of the relation between Δ(Δ G unfold) and Δ SNAPP for different proteins are statistically distinct, and we show that these protein-specific effects can be estimated using the average SNAPP score per residue, which is readily derived from the analysis itself. This result enhances the predictive value of statistical potentials and supports previous suggestions that “comparable” mutations in different proteins may lead to different Δ(Δ G unfold) values because of differences in their flexibility and/or conformational entropy.

Determination of the Potential of Mean Force of Aromatic Amino Acid Complexes in Various Solvents Using Molecular Dynamics Simulations: The Case of the Tryptophan−Histidine Pair

An analysis of structural properties of the tryptophan−histidine (TRP−HIS) pair in vacuo and in various solvents (water, dimethyl sulfoxide, methanol, and carbon tetrachloride) has been done using classical molecular dynamics simulations with atomistic potential models for both solute and solvent molecules. The potential of mean force (PMF) was determined as a function of the TRP centroid−HIS centroid distance and of the angle between the ring planes. We show that T-shaped structures are favored in nonpolar solvents, whereas they are completely destabilized in solvents forming strong hydrogen bonds. Amphiphilic solvents such as methanol and dimethyl sulfoxide destabilize both the T-shaped and stacked arrangements. The results are consistent with previous analysis on protein crystallographic databases, where the stacked structures are found mainly on the protein surface exposed to the solvent, while T-shaped arrangements are preferentially found in the hydrophobic protein core. Finally, comparison of expli...

Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

AbstractEmploying introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001

De novo design and characterization of an apolar helical hairpin peptide at atomic resolution: Compaction mediated by weak interactions.

Design of helical super secondary structural motifs is expected to provide important scaffolds to incorporate functional sites, thus allowing the engineering of novel miniproteins with function. An alpha,beta-dehydrophenylalanine containing 21-residue apolar peptide was designed to mimic the helical hairpin motif by using a simple geometrical design strategy. The synthetic peptide folds into the desired structure as assessed crystallographically at 1.0-A resolution. The two helices of the helical-hairpin motif, connected by a flexible (Gly)(4) linker, are docked to each other by the concerted influence of weak interactions. The folding of the peptide without binary patterning of amino acids, disulfide bonds, or metal ions is a remarkable observation. The results demonstrate that preferred interactions among the hydrophobic residues selectively discriminate their putative partners in space, leading to the unique folding of the peptide, also a hallmark of the unique folding of hydrophobic core in globular proteins. We demonstrate here the engineering of molecules by using weak interactions pointing to their possible further exploitation in the de novo design of protein super secondary structural elements.