Distribution Of Amino Acid Residues Research Articles

Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.

Exploring CRY1 Protein Residue Associations with Diurnal and Nocturnal Behaviors Across Vertebrate Species

Background/Aim: Core clock genes exert influence over a spectrum of behavioral consequences and physiological processes. In mammals, distinct transcription-translation feedback loops oscillate approximately every 24 hours, aligning peripheral tissues with the dark-light cycle. Consequently, species manifest diverse activity patterns in their daily routines; for instance, diurnal species exhibit sleep during dark periods and heightened activity during light periods. Over the course of evolution, subtle changes in protein sequences can lead to divergent phenotypic traits. This study aims to scrutinize core clock protein residues to identify significant amino acid sites that might underlie diurnal or non-diurnal tendencies from an evolutionary standpoint. Methods: We performed multiple sequence alignment on coding sequences of vertebrate core clock protein, CRY1, orthologs obtained from the NCBI database. This was achieved using the Constraint-based Multiple Alignment Tool (COBALT). Vertebrate species were classified into diurnal (n=127) and nocturnal (n=92) categories. Statistical methods were applied to analyze the non-random distribution of amino acid residues between the two groups. Results: Our analysis of the CRY1 protein provides initial insights into specific amino acid residues exhibiting non-random associations with both nocturnal and diurnal behaviors. Notably, we identified five residues subject to purifying selection and 21 residues under positive selection within CRY1 orthologs. These residues span across exons 1, 4, and 9-12, predominantly concentrated in the tail region. Conclusion: This preliminary investigation highlights the importance of particular amino acids within core clock proteins, offering valuable insights into their functional significance. The observed discrepancies in conservation patterns between diurnal and nocturnal groups underscore the potential disruption of essential folding processes or post-translational mechanisms by mutations in these regions. This research marks a pioneering advancement in understanding the phenotypic outcomes of core clock proteins and their direct correlation with behavioral traits within evolutionary contexts, potentially linking to sleep disorders.

Elucidating binding mechanisms of caffeic acid and resveratrol by beta-lactoglobulin: Insights into hydrophobic interactions and complex formation

Employing β-lactoglobulin (β-Lg) as a bioactive carrier substantially enhances the stability of small molecule active compounds. This research examines the intricate interaction mechanisms between β-Lg and caffeic acid (CA) as well as resveratrol (RES). Utilizing UV and fluorescence spectral analysis, it was discovered that both CA and RES exhibit a notable fluorescence quenching effect on β-Lg, predominantly characterized by static quenching. Thermodynamic assessments revealed that hydrophobic interactions primarily drive the formation of complexes between the two small molecules and β-Lg. Concerning binding affinity, β-Lg/CA displayed a stronger association compared to β-Lg/RES. Synchronous fluorescence spectroscopy outcomes demonstrated alterations in the hydrophobic microenvironment of aromatic amino acids. Particle size evaluations indicated a reduction in the size of both complexes, suggesting that CA and RES effectively enhance the dispersion of complexes within the solution. Molecular docking and molecular dynamics simulations substantiated that upon binding with proteins, small molecules remain stably situated within the hydrophobic cavity of β-Lg, without considerable secondary structure modifications. Based on the MM/PBSA method, the energy contribution distribution of amino acid residues disclosed that ILE56, PHE105, and 58LEU contribute maximally to β-Lg/CA, while MET107, ILE84, and VAL41 contribute most significantly to β-Lg/RES.Regarding antioxidant activity, the following hierarchy was observed: β-Lg/RES > β-Lg/CA > RES > CA. The insights gained from this investigation offer invaluable information for developing polyphenol protection systems and designing advanced β-lactoglobulin carriers.

Determination of HIV Tropism in Patients with Antiretroviral Therapy Failure in Arkhangelsk Region

The aim of the study was to determine the tropism of the human immunodeficiency virus in patients with virological failure of antiretroviral therapy (ART) from the Arkhangelsk Region based on the analysis of the env gene V3 loop nucleotide sequence.Materials and methods. We used blood plasma samples obtained from 76 HIV-infected persons from the Arkhangelsk Region with virological failure of antiretroviral therapy. The nucleotide sequences of the HIV env gene C2-V3-C3 region were studied by PCR followed by sequencing. The genotype of the studied strains was determined based on the analysis of their phylogenetic relations with reference sequences from the international GenBank database, as well as using specialized programs. To predict viral tropism, the Garrido rule and the online bioinformatic tool Geno2Pheno[coreceptor] were used. The Geno2Pheno[coreceptor] algorithm, determines the false positive rate (FPR) based on the analysis of the env gene V3 loop nucleotide sequence. Results and discussion. Significantly lower representation of R5X4/X4-tropic HIV variants in long-term infected persons with subsubtype A6 virus compared to subtype B virus has been shown. For all FPR cut-off algorithms, a significant correlation between subtype and HIV tropism was observed (p=0.0014 and p=0.013 for FPR 10 % and FPR 20 %, respectively). While among subtype B strains, at least 57 % were identified as R5X4/X4-tropic variants (for an FPR of 10 %), including two strains classified as X4-tropic; among HIV subsubtype A6 even at an FPR of 20 %, the frequency of R5X4/X4-tropic samples only slightly exceeded 22 %. It can be assumed that the dynamics of changes in HIV tropism depends on the virus subtype. Significant differences in the distribution of amino acid residues of the V3 region sequences in the examined group between R5-tropic and R5X4/X4-tropic strains of subsubtype A6 for positions 18 (χ2=7.616, p=0.0058), 21 (χ2=7.281, p=0.007), 24 (χ2=5.587, p=0.0181), and 34 (χ2=5.144, p=0.0233) have been demonstrated. Among the R5X4/X4-tropic strains of the A6 subsubtype, amino acid substitutions were registered at positions 6, 19, 21, 26, 29, 30, which were not found in the R5-tropic A6 strains. The high occurrence frequency of a number of mutations previously described as presumably associated with resistance to maraviroc and similar drugs may indicate a natural polymorphism characteristic of the A6 subsubtype, which does not correlate with resistance to CCR5 co-receptor antagonists.

Do molecular dynamics force fields accurately model Ramachandran distributions of amino acid residues in water?

Molecular dynamics (MD) is a powerful tool for studying intrinsically disordered proteins, however, its reliability depends on the accuracy of the force field. We assess Amber ff19SB, Amber ff14SB, OPLS-AA/M, and CHARMM36m with respect to their capacity to capture intrinsic conformational dynamics of 14 guest residues x (=G, A, L, V, I, F, Y, DP, EP, R, C, N, S, T) in GxG peptides in water. The MD-derived Ramachandran distribution of each guest residue is used to calculate 5 J-coupling constants and amide I' band profiles to facilitate a comparison to spectroscopic data through reduced χ2 functions. We show that the Gaussian model, optimized to best fit the experimental data, outperforms all MD force fields by an order of magnitude. The weaknesses of the MD force fields are: (i) insufficient variability of the polyproline II (pPII) population among the guest residues; (ii) oversampling of antiparallel at the expense of transitional β-strand region; (iii) inadequate sampling of turn-forming conformations for ionizable and polar residues; and (iv) insufficient guest residue-specificity of the Ramachandran distributions. Whereas Amber ff19SB performs worse than the other three force fields with respect to χ2 values, it accounts for residue-specific pPII content better than the other three force fields. Additional testing of residue-specific RSFF1 and Amber ff14SB combined with TIP4P/2005 on six guest residues x (=A, I, F, DP, R, S) reveals that residue specificity derived from protein coil libraries or an improved water model alone do not result in significantly lower χ2 values.

The combined use of amide I bands in polarized Raman, IR, and vibrational dichroism spectra for the structure analysis of peptide fibrils and disordered peptides and proteins

AbstractRaman spectroscopy is generally a versatile tool to explore the structure of proteins and peptides in solution. However, in spite of the development of ultraviolet (UV) resonance Raman spectroscopy as a tool that allows for the investigation of samples with lower concentrations, Raman has not played the same role as infrared (IR) spectroscopy with regard to secondary structure analysis. Reported UV Raman studies have recently focused on the ψ‐dependence of amide III as a useful tool for the structural analysis even of disordered peptides. Amide I based structural analysis generally uses visible excitation. Rather than describing the traditional secondary structure analysis of proteins, this review focusses on work that used Raman in conjunction with other vibrational spectroscopies such as IR and vibrational circular dichroism to probe the conformational distribution of amino acid residues in unfolded peptides and the self‐assembling of peptides into fibrils. We argue against the use of spectral decomposition into Gaussian bands particularly if this type of analysis is exclusively applied to either IR or Raman band profiles. The article emphasizes the delocalized excitonic character of amide I wavefunctions which has to be accounted for in any attempt to use the respective bands for structure analysis.

Harnessing the power of electrophoresis and chromatography: Offline coupling of reverse phase liquid chromatography-capillary zone electrophoresis-tandem mass spectrometry for peptide mapping for monoclonal antibodies

RPLC-MS/MS is the present workhorse for bottom-up proteomics-based characterization. However it suffers from limited peak capacity and challenges with respect to detection of small and hydrophilic peptides. CZE-MS/MS offers an orthogonal alternative to RPLC-MS/MS but has limited sensitivity due to low sample loading. In the present work, for the first time, offline coupling of an RPLC–CZE–MS/MS has been demonstrated for peptide mapping of a monoclonal antibody-based therapeutic product. The performance of this platform has been compared to the state-of-the-art RPLC-MS/MS and CZE-MS/MS approaches. Fifteen fractions were isolated from a mAb tryptic digest using RPLC, and each fraction was analyzed by CZE-ESI-MS/MS. Results indicate that not only the RPLC–CZE–MS/MS platform identified a larger number of distinct peptides (372) than the RPLC-MS/MS (219) and CZE-MS/MS (177) platforms, it also offered significantly superior sequence coverage (99.55% vs. 89.76% and 94.21% for the heavy chain and 98.6% vs. 92.06% and 95.79% for the light chain). Also, the distribution of amino acid residues with post translational modifications was 413 for RPLC–CZE–MS/MS, 150 for RPLC-MS/MS and 94 for CZE-MS/MS. In fact, the RPLC–CZE–MS/MS system performed better than the combined datasets from RPLC-MS/MS or CZE-MS/MS. Our study shows that the traditionally used one-dimensional (1D) RPLC-MS/MS and CZE-MS/MS-based platforms may not be enough for characterization of complex molecules such as monoclonal antibodies. The proposed approach should be an essential addition to the analytical toolkit for in-depth primary structural characterization of mAbs.

Anticooperative Nearest-Neighbor Interactions between Residues in Unfolded Peptides and Proteins

Growing evidence suggests that the conformational distributions of amino acid residues in unfolded peptides and proteins depend on the nature of the nearest neighbors. To explore whether the underlying interactions would lead to a breakdown of the isolated pair hypothesis of the classical random coil model, we further analyzed the conformational propensities that were recently obtained for the two guest residues (x,y) of GxyG tetrapeptides. We constructed a statistical thermodynamics model that allows for cooperative as well as for anticooperative interactions between adjacent residues adopting either a polyproline II or a β-strand conformation. Our analysis reveals that the nearest-neighbor interactions between most of the central residues in the investigated GxyG peptides are anticooperative. Interaction Gibbs energies are rather large at high temperatures (350 K), at which point many proteins undergo thermal unfolding. At room temperature, these interaction energies are less pronounced. We used the obtained interaction parameter in a Zimm-Bragg/Ising-type approach to calculate the temperature dependence of the ultraviolet circular dichroism (CD) of the MAX3 peptide, which is predominantly built by KV repeats. The agreement between simulation and experimental data was found to be satisfactory. Finally, we analyzed the temperature dependence of the CD and 3J(HNHα) parameters of the amyloid β1–9 fragment. The results of this analysis and a more qualitative consideration of the temperature dependence of denatured proteins probed by CD spectroscopy further corroborate the dominance of anticooperative nearest-neighbor interactions. Generally, our results show that unfolded peptides—and most likely also proteins—exhibit some similarity with antiferromagnetic systems.

Anti-cooperative Nearest Neighbor Coupling Determines the Statistical Coil State of Peptides and Proteins at High Temperatures

The interest in the unfolded state of peptides and proteins stems partially from the observation that conformational distributions of amino acid residues are more restricted and residue specific than expected for an ideal random coil. Moreover, multiple lines of evidence suggest that contrary to the isolated pair hypothesis the conformational propensity of a distinct residue depends on the properties of its neighbors. We analyzed the recently reported conformational propensities of the two guest residues of GxyG peptides in terms of a statistical thermodynamics model that allows for cooperative as well as anti-cooperative interactions between adjacent residues adopting either a polyproline II (pPII) or a β-strand conformation. Our analysis revealed that the nearest neighbor interactions between most of the central residues in the investigated GxyG peptides is anti-cooperative. Interaction Gibbs energies become significant at high temperature (350 K) at which most proteins undergo thermal unfolding. At room temperature, these interaction energies are less pronounced. We utilized the obtained interaction parameters in an Ising-type approach to calculate the temperature dependence of the UV circular dichroism (CD) of the so-called MAX3 peptide that is predominantly built by KV-repeats. The agreement between simulation and experimental data is very good. Finally, we analyzed the temperature dependence of the CD spectra and selected 3J(HNHα ) parameters of the Aβ(1-9) fragment. The results corroborated the occurrence of anti-cooperative nearest neighbor interactions. A comparison of CD spectra of unfolded and intrinsically disordered proteins with predictions of our model suggests that anti-cooperative interactions govern their experimentally obtained temperature dependence. Generally, our results suggest that unfolded peptides and proteins behave like antiferromagnetic systems in the presence of a magnetic field of intermediate strength.

Cobra Cytotoxins: Structural Organization and Antibacterial Activity

Cardiotoxins (cytotoxins, CT) are β-structured proteins isolated from the venom of cobra. They consist of 59-61 amino acid residues, whose antiparallel chains form three 'fingers'. In contrast to neurotoxins with an overall similar fold, CTs are amphiphilic. The amphiphilicity is caused by positively charged lysine and arginine residues flanking the tips of the loops that consist primarily of hydrophobic amino acids. A similar distribution of amino acid residues is typical for linear (without disulfide bonds) cationic cytolytic peptides from the venoms of other snakes and insects. Many of them are now considered to be lead compounds in combatting bacterial infections and cancer. In the present review, we summarize the data on the antibacterial activity of CTs and compare it to the activity of linear peptides.

Allergens of mites

Mite allergens belong to the group of inhalant allergens and represent antigenic substances which are particutlarly important in the pathogenesis of respiratory system diseases and skin diseases. The most common diseases associated with chronic exposure to these aeroallergens include: allergic rhinitis, bronchial asthma and atopic dermatitis. Mite allergens are simple proteins or glycoproteins with different molecular structures and various biochemical functions. The sensitizing capacity of these proteins is connected from their physicochemical properties. Individual allergens perform, among others, the functions of structural proteins, act as enzymes, transport lipids, bind metal ions, and are capable of glycosylation. In addition, mite allergenic proteases degrade proteins of the skin epithelium-resulting in a weakening of its natural protective barrier-and induce the immune response. The proteases also induce the release of pro-inflammatory cytokines: interleukin-4 (IL-4), interleukin 6 (IL-6), interleukin 8 (IL-8), eotaxin, and granulocyte-macrophage colony-stimulating factor-GM-CSF. The article presents the tertiary structure of major and mid-range mite allergens and their classification. Based on literature reports concerning the chemical structure of allergenic proteins, it was emphasized that the structural differences between homologous proteins with allergenic pozoproperties relate to the distribution of amino acid residues on the surface of the molecule. IgE binding affinity and the similarities and differences in the amino acid sequence of the allergens were also the basis for determining cross-reactivity of allergenic proteins. The paper shows an example of this phenomenon, describing the existence of common allergens for various mite species.

Nearest Neighbor Interactions Attenuate Intrinsic Amino Acid Conformational Preferences: A Combined Vibrational and NMR Study

Contrary to the isolated pair hypothesis, a pivotal ingredient of the random coil model, conformational distributions of amino acid residues in unfolded proteins cannot be considered as isolated from their nearest neighbors. To enable structural predictions of unfolded proteins or peptides (IDPs) knowledge about intrinsic propensities of amino acid residues must be complemented by information on nearest-neighbor interactions. To explore this influence, we preformed a joint vibrational and 2D-NMR spectroscopy study of selected “GxyG” host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y={A,K,LV}. The choice of D and S (L and V) for the x (y) position was motivated by their documented ability to drastically change the distribution of alanine in xAy tripeptides of truncated coil libraries. The observed spectral information were analyzed in terms of superpositions of 2D-Gaussian functions in the Ramachandran space, representing sub-ensembles of pPII-, β-strand-, helical-, and turn-like conformations. Results reveal that “turn forming residues” and hydrophobic residues have very strong effects on the conformation of their nearest neighbors. A direct comparison of the conformational distribution for S and D in GSAG ,GSLG, and GDAG with corresponding distributions in GxG peptiess reveals that hydrophobic neighbors cause drastic reductions of turn propensities. As a neighbor, K eliminates the asx turn propensity of D. In addition, insertion of these 'turn forming' residues (S, and D) causes conformational redistributions of L, A, and K from pPII to more extended β strand-like conformations while at the same time increasing the overall turn content. Concomitantly, the positions of pPII and particularly of β distributions are shifted to lower ψ values. Taken together, our results indicate that Dx and Sx motifs might act as conformational randomizers in proteins, attenuating intrinsic propensities of neighboring residues.

Monitoring the antigenic evolution of human influenza A viruses to understand how and when viruses escape from existing immunity

BackgroundThe World Health Organization (WHO) organizes consultations in February and September of each year, spearheaded by an advisory group of experts to analyze influenza surveillance data generated by the WHO Global Influenza Surveillance and Response System (GISRS). The purpose of these consultations is to recommend the composition on influenza virus vaccines for the northern and southern hemispheres, respectively. The latest news of influenza viruses is made available to the public and updated on the WHO website. Although WHO discloses the manner in which it has made the recommendation, usually by considering epidemiological and clinical information to analyze the antigenic and genetic characteristics of seasonal influenza viruses, most individuals do not possess an understanding of antigenic drift and when it occurs.FindingsWe have constructed a web server, named Fluctrl, and implemented a pipeline whereby HA sequence data is downloaded from the Influenza Virus Resource at NCBI along with their isolation information including isolation year and location, which are parsed and managed in MySQL database. By analyzing the frequency of each amino acid residue of the HA1 domain expressed by the viruses on annual basis, users are able to obtain evolutionary dynamics of human influenza viruses corresponding with epidemics. Users are able to upload and analyze their HA1 sequences for generating evolutionary dynamics. In addition, a distribution of amino acid residues at a particular site is represented geographically to trace the location where antigenic variants are seeded.ConclusionsFluctrl is constructed for monitoring the antigenic evolution of human influenza A viruses. This tool is intended to inform the general public how and when influenza viruses evade the human body's immunity. Furthermore, leveraging the geographic information, the original locations of emerging influenza viruses can be traced. Fluctrl is freely accessible at http://sb.nhri.org.tw/fluctrl.

How do Nearest-Neighbor Interactions Effect the Conformational Distributions in Peptides?

For structural predictions of intrinsically disordered proteins (IDPs), knowledge about intrinsic propensities of amino acids must be complimented by information on nearest-neighbor interactions. To explore the influence of nearest-neighbors on conformational distributions of amino acid residues, we preformed a joint vibrational and 2D-NMR study of selected GxyG host-guest peptides: GDyG, GSyG, GxLG, GxVG, where x/y={A,K,LV}. The choice of D and S (L/V) for the x (y) position was motivated by their documented ability to drastically change the distribution of alanine in xAy tripeptide sequences in truncated coil libraries. Five J-coupling constants and amide I’ profiles of the respective IR, polarized Raman and Vibrational Circular Dichroism spectra were analyzed using a superposition of 2D-Gaussian functions in Ramachandran space representing sub-ensembles of pPII-, β-strand-, helical-, and turn-like conformations. Our analysis of the amide I' profiles exploits excitonic coupling between the local amide I′ modes in the tetra-peptides. Our results reveal that D and S particularly alter the conformation of their downstream neighbor. In a recent study, these amino acids were shown to have an unusually high preference for type I’/IIβ and asx-turns. A direct comparison of the ensemble obtained for serine in GSAG, GSLG and GSG reveals that A and L cause the asx-turn population to be mitigated in favor of more extended pPII/ β structures. Upon insertion of these ‘turn-forming’ residues, alanine's conformational ensemble is modestly changed (shift from pPII to β), while the position of pPII and particularly of β is shifted to lower ψ-values. DFT calculations indeed show that the forced reduction in ψ for A increases the H-bond distance for serine in the asx-turn conformation. Taken together, our results indicate that Dx and Sx-motifs might act as conformational randomizers in proteins, attenuating intrinsic propensities of neighboring residues.

Global conformations of proteins as predicted from the modeling of their CZE mobility data

Estimations of protein global conformations in well-specified physicochemical microenvironments are obtained through global structural parameters defined from polypeptide-scale analyses. For this purpose protein electrophoretic mobility data must be interpreted through a physicochemical CZE model to obtain estimates of protein equivalent hydrodynamic radius, effective and total charge numbers, hydration, actual ionizing pK and pH-near molecule. The electrical permittivity of protein domain is also required. In this framework, the solvent drag on proteins is obtained via the characteristic friction power coefficient associated with the number of amino acid residues defining the global chain conformation in solution. Also, the packing dimension related to the spatial distribution of amino acid residues within the protein domain is evaluated and discussed. These scaling coefficients together with the effective and total charge number fractions of proteins provide relevant interpretations of protein global conformations mainly from collapsed globule to hybrid chain regimes. Also, protein transport properties may be estimated within this framework. In this regard, the central role played by the friction power coefficient in the evaluation of these properties is highlighted.

Enhancement of Dissolution Rates of Amorphous Silica by Interaction with Bovine Serum Albumin at Different pH Conditions

AbstractProteins and protein-like molecules are abundant in various geochemical environments; they form complexes with mineral surfaces and with dissolved organic matter. To evaluate the effect of proteins on rates of dissolution of minerals, experiments on the dissolution of amorphous silica in solutions containing various concentrations of bovine serum albumin (BSA) were performed in this study. The dissolution experiments were carried out by a batch method using solutions of 0.1 mM NaCl with 0.00, 0.05, 0.1, 0.2, 0.5, and 1.0 mg/mL of BSA at three different pH conditions, 6, 5, and 4. The results of the experiments demonstrated that BSA exhibited strong rate-enhancement effects on the dissolution of amorphous silica and were dependent on BSA concentration and the solution pH. At pH 6, the dissolution rates of amorphous silica appeared to increase successively by ~1.6, 2.2, 2.4, 2.5, and 2.9 times with increasing BSA concentrations of 0.05, 0.1, 0.2, 0.5, and 1.0 mg/mL, respectively. The rates of dissolution increased by greater degrees, ~3.1–5.8 and 4.9–13.0 times at pH 5 and 4, respectively. According to the calculated charge distributions of amino acid residues of the BSA molecule, the dissolution rates of amorphous silica were likely to be enhanced by attractive electrostatic interactions of the positively charged side chains of lysine, arginine, and histidine residues with the negatively charged >SiO− sites on the amorphous silica surface. The negatively charged side chains such as glutamic acid and aspartic acid residues may inhibit the attractive interaction, depending on the degree of deprotonation.

Influence of structural features on the self-assembly of short ionic oligopeptides

We investigated the self-aggregation of 12 short ionic oligopeptides constituted by 4-7 amino acid residues to establish useful structure-property relationships that might be exploited in the biomedical field by using the concept of molecular Lego. We show that the critical aggregation concentration (CAC) of tetrapeptides decreases with increasing hydrophobicity of neutral residues. Additionally, the dependence of the CAC of isomeric oligopeptides on the distribution of amino acid residues confirms the high tendency to self-organization of molecules with alternating ionic and neutral residues. Indeed, atomic force microscopy (AFM) images recorded on oligopeptide solutions above the CAC show the presence of either fibrillar or spherical aggregates depending on oligopeptide structure and concentration, steric hindrance, solution pH, and time. The potential of the investigated oligopeptides in tissue engineering applications is supported by their in vitro cytocompatibility.

Solvent Accessible Surface Area of Amino Acid Residues in Globular Proteins: Correlation of Apparent Transfer Free Energies with Experimental Hydrophobicity Scales

It is known that the distribution of amino acid residues in globular proteins between surface and interior is in certain correlation with various experimental scales based on partitioning of amino acids or their analogs between water and organic solvents. These scales are often used in various quantitative structure-activity relationship (QSAR) studies as well as for evaluation of stability of proteins. In this work we have analyzed the distribution of residues based on their solvent accessible surface area in more than 8000 protein structures. Using extensive statistical sampling, we have computed residue apparent free energies of transfer between protein interior and surface applying various criteria for classifying residues as exposed or buried. The correlation of these statistical energies with several experimental hydrophobicity scales is discussed. We propose three types of statistical apparent transfer free energy scales and show that each of these scales is in better correlation with one of the experimental hydrophobicity scales (water/vapor, water/cyclohexane, and water/octanol transfer scales). The data are interpreted through the application of theoretical considerations by Finkelstein et al. (Protein Struct. Funct. Genet. 1995, 23, 142) based on random energy model of heteropolymer globules. The deviation of apparent transfer free energies from experimental scales is discussed and analyzed. The variations of amino acid distribution in proteins with the size of protein structure is discussed and the final protein set is chosen to minimize these variations.

Animal Toxins Acting on Voltage-Gated Potassium Channels

Animal venoms are rich natural sources of bioactive compounds, including peptide toxins acting on the various types of ion channels, i.e. K(+), Na(+), Cl(-) and Ca(2+). Among K+ channel-acting toxins, those selective for voltage-gated K(+) (Kv) channels are widely represented and have been isolated from the venoms of numerous animal species, such as scorpions, sea anemones, snakes, marine cone snails and spiders. The toxins characterized hitherto contain between 22 and 60 amino acid residues, and are cross-linked by two to four disulfide bridges. Depending on their types of fold, toxins can be classified in eight structural categories, which showed a combination of beta-strands, helices, or a mixture of both. The main architectural motifs thereof are referred to as alpha/beta scaffold and inhibitor cystine knot (ICK). A detailed analysis of toxin structures and pharmacological selectivities indicates that toxins exhibiting a similar type of fold can exert their action on several subtypes of Kv channels, whereas a particular Kv channel can be targeted by toxins that possess unrelated folds. Therefore, it appears that the ability of structurally divergent toxins to interact with a particular Kv channel relies onto a similar spatial distribution of amino acid residues that are key to the toxin-channel interaction (rather than the type of toxin fold). The diversity of Kv channel blockers and their therapeutic value in the potential treatment of a number of specific human diseases, especially autoimmune disorders, inflammatory neuropathies and cancer, are reviewed.

Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly

Complete determination of a membrane protein structure requires knowledge of the protein position within the lipid bilayer. As the number of determined structures of membrane proteins increases so does the need for computational methods which predict their position in the lipid bilayer. Here we present a coarse-grained molecular dynamics approach to lipid bilayer self-assembly around membrane proteins. We demonstrate that this method can be used to predict accurately the protein position in the bilayer for membrane proteins with a range of different sizes and architectures.