Different Types Of Amino Acids Research Articles

A Modified Amino Acid Network Model Contains Similar and Dissimilar Weight

For a more detailed description of the interaction between residues, this paper proposes an amino acid network model, which contains two types of weight—similar weight and dissimilar weight. The weight of the link is based on a self-consistent statistical contact potential between different types of amino acids. In this model, we can get a more reasonable representation of the distance between residues. Furthermore, with the network parameter, average shortest path length, we can get a more accurate reflection of the molecular size. This amino acid network is a “small-world” network, and the network parameter is sensitive to the conformation change of protein. For some disease-related proteins, the highly central residues of the amino acid network are highly correlated with the hot spots. In the compound with the related drug, these residues either interacted directly with the drug or with the residue which is in contact with the drug.

Sequence Evolution Correlates with Structural Dynamics

Biochemical activity and core stability are essential properties of proteins, maintained usually by conserved amino acids. Structural dynamics emerged in recent years as another essential aspect of protein functionality. Structural dynamics enable the adaptation of the protein to binding substrates and to undergo allosteric transitions, while maintaining the native fold. Key residues that mediate structural dynamics would thus be expected to be conserved or exhibit coevolutionary patterns at least. Yet, the correlation between sequence evolution and structural dynamics is yet to be established. With recent advances in efficient characterization of structural dynamics, we are now in a position to perform a systematic analysis. In the present study, a set of 34 enzymes representing various folds and functional classes is analyzed using information theory and elastic network models. Our analysis shows that the structural regions distinguished by their coevolution propensity as well as high mobility are predisposed to serve as substrate recognition sites, whereas residues acting as global hinges during collective dynamics are often supported by conserved residues. We propose a mobility scale for different types of amino acids, which tends to vary inversely with amino acid conservation. Our findings suggest the balance between physical adaptability (enabled by structure-encoded motions) and chemical specificity (conferred by correlated amino acid substitutions) underlies the selection of a relatively small set of versatile folds by proteins.

Detection of collagen through FTIR and HPLC from the body and foot of Donax cuneatus Linnaeus, 1758.

To make more effective use of available marine resources, acid soluble collagen (ASC) was isolated from body and foot of wedge clam Donax cuneatus Linnaeus, 1758 with acetic acid and was characterized for their potential and commercial applications. The yield of ASC was 17% and 23% respectively. SDS PAGE, UV and FTIR spectroscopy showed that both were type I mainly with slight differences. HPLC was used for identifying the presence of different types of amino acids, where glycine was more or less 20% in both the samples and takes the lead amino acid position and presence of imino acids (11.8 and 12.6%) has been the characteristic feature of type I collagen.

Biomimetic formation of Titania Thin Films: Effect of Amino Acids on the Deposition Process

Different types of amino acids have been used as additives to control the aqueous deposition of titanium dioxide thin films on single-crystal Si wafers. Thin titania films can be obtained through a chemical bath deposition (CBD) process using TiCl₄ as a precursor in an aqueous solution at temperatures below 100 °C. The addition of amino acids to the deposition solution was shown to reduce the thickness and roughness of the films and to increase their density. These protein building blocks were employed to modify the deposition rate as well as the size of aggregates that form the film. The thickness, crystallinity, morphology and composition of the grown films were characterized by a variety of techniques, including XRD, XPS, AFM and SEM. The consequences of the type of the amino acid additive (and its concentration in the solution) on the microstructural evolutions of the deposed films are thus revealed and discussed on the basis of the organic-inorganic interactions in solution and at the film surface.

Hydrophobic, Hydrophilic, and Charged Amino Acid Networks within Protein

The native three-dimensional structure of a single protein is determined by the physicochemical nature of its constituent amino acids. The 20 different types of amino acids, depending on their physicochemical properties, can be grouped into three major classes: hydrophobic, hydrophilic, and charged. The anatomy of the weighted and unweighted networks of hydrophobic, hydrophilic, and charged residues separately for a large number of proteins were studied. Results showed that the average degree of the hydrophobic networks has a significantly larger value than that of hydrophilic and charged networks. The average degree of the hydrophilic networks is slightly higher than that of the charged networks. The average strength of the nodes of hydrophobic networks is nearly equal to that of the charged network, whereas that of hydrophilic networks has a smaller value than that of hydrophobic and charged networks. The average strength for each of the three types of networks varies with its degree. The average strength of a node in a charged network increases more sharply than that of the hydrophobic and hydrophilic networks. Each of the three types of networks exhibits the “small-world” property. Our results further indicate that the all-amino-acids networks and hydrophobic networks are of assortative type. Although most of the hydrophilic and charged networks are of the assortative type, few others have the characteristics of disassortative mixing of the nodes. We have further observed that all-amino-acids networks and hydrophobic networks bear the signature of hierarchy, whereas the hydrophilic and charged networks do not have any hierarchical signature.

Computational alanine scanning mutagenesis—An improved methodological approach

Alanine scanning mutagenesis of protein-protein interfacial residues can be applied to a wide variety of protein complexes to understand the structural and energetic characteristics of the hot-spots. Binding free energies have been estimated with reasonable accuracy with empirical methods, such as Molecular Mechanics/Poisson-Boltzmann surface area (MM-PBSA), and with more rigorous computational approaches like Free Energy Perturbation (FEP) and Thermodynamic Integration (TI). The main objective of this work is the development of an improved methodological approach, with less computational cost, that predicts accurately differences in binding free energies between the wild-type and alanine mutated complexes (DeltaDeltaG(binding)). The method was applied to three complexes, and a mean unsigned error of 0.80 kcal/mol was obtained in a set of 46 mutations. The computational method presented here achieved an overall success rate of 80% and an 82% success rate in residues for which alanine mutation causes an increase in the binding free energy > 2.0 kcal/mol (warm- and hot-spots). This fully atomistic computational methodological approach consists in a computational Molecular Dynamics simulation protocol performed in a continuum medium using the Generalized Born model. A set of three different internal dielectric constants, to mimic the different degree of relaxation of the interface when different types of amino acids are mutated for alanine, have to be used for the proteins, depending on the type of amino acid that is mutated. This method permits a systematic scanning mutagenesis of protein-protein interfaces and it is capable of anticipating the experimental results of mutagenesis, thus guiding new experimental investigations.

Amphoteric surfactants containing ?-hydroxy ester group and an amino acid residue

A series of amphoteric surfactants containing α -hydroxy ester group and an amino acid residue were prepared with the addition of epoxy derivatives (which were prepared from epoxidation of alkyl methacrylate) to different types of amino acids (glycine, alanine, valine, isoleucine, phenylalanine, tyrosine, serine, threonine, aspartic and anthranilic acid).The structures of the prepared compounds were confirmed by infrared spectra, proton magnetic resonance spectra, Mass spectra and elementary analysis. Surface tension, Kraft point, foaming power, critical micelle concentration emulsion and Ca ++ stabilities were determined. Antimicrobial activity and biodegradability were also screened.

An unexpected inversion of enantioselectivity in direct asymmetric aldol reactions on a unique L-proline/ γ-Al 2O 3 catalyst

L-proline adsorbed on γ-Al 2O 3 unexpectedly switches the enantioselectivity of the direct asymmetric aldol reaction of acetone with p-nitrobenzaldehyde from 68% ee ( R configuration for free L-proline catalyst) with 80% yield to 21% ee ( S configuration) with 78% yield. The inversion of enantioselectivity was also observed in the direct asymmetric aldol reactions of acetone with several other aromatic aldehydes catalyzed by the L-proline adsorbed on γ-Al 2O 3. This inversion phenomenon is found to be general for different types of amino acids adsorbed on γ-Al 2O 3. The hydroxyl groups on γ-Al 2O 3 are found to be involved in the inversion induction of enantioselectivity in these direct asymmetric aldol reactions.

Pyrolytic behaviour of microcystins and microcystin-spiked algal blooms

This work describes the pyrolytic behaviour of microcystin (MC) standards using both conventional analytical pyrolysis (Py-GC–MS) and thermochemolysis with tetramethylammonium hydroxide (TMAH). In both cases, the pyrolytic patterns of the MCs at low pyrolysis temperature were structure-dependant, which confirms that pyrolytic techniques are suitable to readily distinguish between different types of MCs. However, the different types of amino acids conforming the structure of the MCs were distinguished only after TMAH/thermochemolysis. In order to examine the suitability of such techniques as a potential tool in the analysis of MC in cyanobacterial algae blooms, pyrolytic experiments using cyanobacterial cultures spiked with the microcystin LR (MC-LR) were also performed. The results suggest that pyrolytic techniques could be used for the rapid and safe detection of toxins in cyanobacterial blooms. Although promissory, further work directed to technique optimization would be necessary before this methodology is used as a routine detection method.

Hydrophobic compaction, curvature of space and deciphering protein sequences

I n the July 2000 issue of the Bulletin de la SFP [1), Yves-Henri Sanejouand and Georges Trinquier presented an overview of the surprising ability of simple topological models (cubic nets) to explain the fundamental three-dimensional (3D) folding properties of the polymers that we call proteins, those essential components oflife. Here, through a number ofdifferent examples, I will illustrate another equally surprising aspect of another apparent simplicity, that relating to hydrophobic compaction, which governs the folding of these macromolecules and which directly serves as a useful tool to decipher genes, thereby opening new prospects in this post-genomic era. A protein is a linear, unbranched polymer consisting of anywhere from a few dozen to a few thousand links. Nature has limited the chemical diversity of proteins, with the occasional exception, to twenty different types (the twenty common amino acids). All amino acids share the same backbone, differing in terms of their side chains (Fig. 1). Seven amino acids have an aliphatic or aromatic side chain, making them stronglyhydrophobic: V (valine), I (isoleucine), L (leucine), F (phenylalanine), M (methionine), Y (tyrosine) and W (tryptophane). Six have a strongly hydrophilic side chain: D (aspartic acid), E (glutamic acid),N (asparagine), Q (glutamine), K (lysine) and R (arginine), while the other seven have intermediate properties: A (alanine), C (cysteine), T (threonine), G (glycine), P (proline), S (serine), and H (histidine). This distribution ofhydrophobicitylhydrophilicity offers a clever range ofblocks with which to build macromolecules exhibiting remarkable physicochemical properties. Under normal conditions, any fairly long polypeptide (from a few dozen to a few hundred amino acids) folds spontaneously in the presence ofwater into globular domains with a stable threedimensional architecture; some can also fold specifically (often in helical form) within lipid membranes. It is the dichotomy between hydrophobicitylhydrophilicity that acts as the driving force for these processes (e.g. (2)), as it does for many other physicochemical situations in the world around us. The succession of different types of amino acids along the polymer, which is specific to each protein, is called the primary structure, or sequence. This information is sufficient for the polypeptide chain to adopt a stable and unique three-dimensional structure in.a suitable medium (mainly water), with the occasional exception (Fig. 1). Yet not all the positions of a given sequence have the same influence on the cooperative process of folding. As a result, ancestral proteins have undergone considerable modification during evolution, amino acid after amino acid, without altering their resulting three-dimensional structure nor affecting their associated biological function(s). Thus, it is not infrequent that proteins with only a very low number of chemically conserved homologous positions along the polypeptide chain (cf. Fig.4A),i.e. a very low level of sequence identity (10 % for example), are in fact close cousins within a same structural or functional family. The result is that, while the number of natural sequences in

Vaterite Stabilization in CaCO3 Crystal Growth by Amino Acid

Calcium carbonate crystals were grown in a CaCl2–Na2CO3 solution containing an amino acid. We have employed 12 different types of amino acids as additives. The concentrations of noncharged-polar amino acids and those of the acidic ones in CaCO3 precipitates are one or two orders higher than those of all of the other types. These two types of amino acids tend to stabilize the vaterite phase which is unstable without amino acid additives. The vaterite forms as cauliflower-like grains consisting of many tiny grains (<0.1 µm). The vaterite content in CaCO3 precipitates is correlated to the concentration of amino acids in the precipitates. The physicochemical interactions between amino acids and CaCO3 are discussed on the basis of the Frontier orbitals obtained by the semi-empirical molecular orbitals calculation of the Zerner's intermediate neglect of differential overlap method.

Alteration in ion channel function of mouse nicotinic acetylcholine receptor by mutations in the M4 transmembrane domain.

The effect of structural alterations of the M4 transmembrane segment in the Torpedo californica AChR has shown that substitution of specific residues can be critical to the channel gating (Lasalde et al., 1996). In a previous study we found that phenylalanine and tryptophan substitutions at the alphaC418 residue in the M4 transmembrane segment of the Torpedo californica AChR significantly altered ion channel function (Lee et al., 1994; Ortiz-Miranda et al., 1997). Cassette mutagenesis was used to mutate the Cys residue at the corresponding C418 position in the alpha subunit of mouse AChR. A total of nine mutations on the mouse alphaC418 position were tested, including the alphaC418A, alphaC418V, alphaC418L, alphaC418S, alphaC418M, alphaC418W, alphaC418H, alphaC418E and alphaC418G mutants. All the mutants tested were functional except the alphaC418G which was not expressed on the surface of the oocyte. The data obtained from macroscopic and single channel currents demonstrate that different types of amino acids can be accommodated at this presumably lipid-exposed position without loss of ion-channel function. As with the Torpedo AChR, the mutation of Cys to Trp dramatically decreased the EC(50) for acetylcholine and increased channel open time. The lack of expression of the mouse alphaC418G suggest that there are some differences in folding, oligomerization and perhaps transport to the surface membrane for this mutant between the Torpedo and the mammalian AChR.

Characterization of the substrate specificity of alpha1,3galactosyltransferase utilizing modified N-acetyllactosamine disaccharides.

alpha1,3galactosyltransferase (alpha1,3GalT) catalyzes the synthesis of a range of glycoconjugates containing the Galalpha1,3Gal epitope which is recognized by the naturally occurring human antibody, anti-Gal. This enzyme may be a useful synthetic tool to produce a range of compounds to further investigate the binding site of anti-Gal and other proteins with a Galalpha1,3Gal binding site. Thus, the enzyme has been probed with a series of type 2 disaccharide-C8(Galbeta1-4GlcNAc-C8) analogs. The enzyme tolerated acceptors with modifications at C2 and C3 of the N-acetylglucosamine residue, producing a family of compounds with a nonreducing alpha1,3 linked galactose. Compounds that did not serve as acceptors were evaluated as inhibitors. Interestingly, the type 1 disaccharide-C8, Galbeta1-3GlcNAc-C8, was a good inhibitor of the enzyme (Ki = 270 microM vs. Km = 190 microM for Galbeta1-4GlcNAc-C8). A potential photoprobe, based on a modified type 2 disaccharide (octyl 3-amino-3-deoxy-3-N-(2-diazo-3, 3, 3-trifluoropropionyl-beta-D-galactopyranosyl-(1, 4)-2-acetamindo-2-deoxy-beta-D-glycopyranoside, (DTFP-LacNAc-C8)), was evaluated as an inhibitor of alpha1,3GalT. alpha1,3GalT bound DTFP-LacNAc-C8 with an affinity (Ki = 300 microM) similar to that displayed by the enzyme for LacNAc-C8. Additional studies were done to determine the enzyme's ability to transfer a range of sugars from UDP-sugar donors. The results of these experiments demonstrated that alpha1,3GalT has a strict specificity for UDP-Gal. Finally, inactivation studies with various amino acid modifiers were done to obtain information on the importance of different types of amino acids for alpha1,3GalT activity.

Nature of Driving Force for Protein Folding: A Result From Analyzing the Statistical Potential

In a statistical approach to protein structure analysis, Miyazawa and Jernigan (MJ) derived a $20\times 20$ matrix of inter-residue contact energies between different types of amino acids. Using the method of eigenvalue decomposition, we find that the MJ matrix can be accurately reconstructed from its first two principal component vectors as $M_{ij}=C_0+C_1(q_i+q_j)+C_2 q_i q_j$, with constant $C$'s, and 20 $q$ values associated with the 20 amino acids. This regularity is due to hydrophobic interactions and a force of demixing, the latter obeying Hildebrand's solubility theory of simple liquids.

16] Affinity labels for NAD(P)-specific sites

Publisher Summary Locating the coenzyme site within a known nicotinamide adenine dinucleotide phosphate (NADP)-dependent dehydrogenase and identifying the amino acid contributors to that coenzyme site are critical steps in understanding the relationship of structure to function in the nicotinamide coenzyme-requiring enzymes. In some cases, the coenzyme site has been located by recognition of an amino acid sequence motif commonly found in crystalline nucleotide-binding enzymes. Affinity labeling provides an alternate approach to identify the coenzyme site of an enzyme while it is in solution. In this approach, a reagent is designed that has a close structural resemblance to the natural coenzyme, but also features a functional group capable of reacting covalently and indiscriminantly with many different types of amino acids. This approach is aimed at forming a reversible complex of the enzyme and affinity label and, once bound at the coenzyme site, the affinity label reacts irreversibly with an amino acid accessible from that site.

Interaction of pyridoxal 5'-phosphate with tryptophan-139 at the subunit interface of dimeric D-amino acid transaminase.

The crystal structure of dimeric bacterial D-amino acid transaminase shows that the indole rings of the two Trp-139 side chains face each other in the subunit interface about 10 angstroms from the coenzyme, pyridoxal 5'-phosphate. To determine whether it has a role in the catalytic efficiency of the enzyme or interacts with the coenzyme, Trp-139 has been substituted by several different types of amino acids, and the properties of these recombinant mutant enzymes have been compared to the wild-type enzyme. In the native wild-type holoenzyme, the fluorescence of one of the three Trp residues per monomer is almost completely quenched, probably due to its interaction with PLP since in the native wild-type apoenzyme devoid of PLP, tryptophan fluorescence is not quenched. Upon reconstitution of this apoenzyme with PLP, the tryptophan fluorescence is quenched to about the same extent as it is in the native wild-type enzyme. The site of fluorescence quenching is Trp-139 since the W139F mutant in which Trp-139 is replaced by Phe has about the same amount of fluorescence as the wild-type enzyme. The circular dichroism spectra of the holo and the apo forms of both the wild-type and the W139F enzymes in the far-ultraviolet show about the same degree of ellipticity, consistent with the absence of extensive global changes in protein structure. Furthermore, comparison of the circular dichroism spectrum of the W139F enzyme at 280 nm with the corresponding spectral region of the wild-type enzyme suggests a restricted microenvironment for Trp-139 in the latter enzyme. The functional importance of Trp-139 is also demonstrated by the finding that its replacement by Phe, His, Pro, or Ala gives mutant enzymes that are optimally active at temperatures below that of the wild-type enzyme and undergo the E-PLP --> E-PMP transition as a function of D-Ala concentration with reduced efficiency. The results suggest that a fully functional dimeric interface with the two juxtaposed indole rings of Trp-139 is important for optimal catalytic function and maximum thermostability of the enzyme and, furthermore, that there might be energy transfer between Trp-139 and coenzyme PLP.

Effect of chemical modification on some structural and functional properties of pennisetin, a major seed storage protein from pearl millet

Nine different types of amino acids of pennisetin, a major storage protein in pearl millet, were modified separately and the effect of this modificatio

Evaluation of homology modeling of HIV Protease

The model of human immunodeficiency virus (HIV-1) protease which was based on the crystal structure of Rous sarcoma virus (RSV) protease has been compared to the recently determined crystal structure of chemically synthesized HIV-1 protease. The overall difference between the model and crystal structure was 1.4 A root mean square (rms) deviation for 86 superimposed C alpha atoms. The position of the flexible flap differs in the model and six residues at the amino terminus were incorrectly placed. With these exceptions, all atoms of the model and crystal structure agree to 2.1 A rms deviation. The conformation of some surface bends in the model agrees less well with the crystal structure. Identical amino acids in RSV and HIV proteases were modeled more reliably than different types of amino acids. The amino acids which form the substrate binding site were modeled most accurately to 1.2 A rms deviation for all atoms compared to the crystal structure. This suggests that functionally significant regions of related proteins can be modeled with high accuracy. The model gave correct predictions for residues making interactions with the substrate, and therefore could be used to design inhibitors. The model based on the RSV protease structure is more similar to the experimental structure than are previous models based on the structures of non-viral aspartic proteases.

A computer model to dynamically simulate protein folding: studies with crambin.

The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximating the effect of each side chain. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealing has been used to dynamically sample the conformations available to this simple model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence-dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide pairing, are reproduced by the simulation, suggesting the model may accurately simulate the folding process.

The 14-fold periodicity in alpha-tropomyosin and the interaction with actin.

A Fourier analysis of the distributions of different types of amino acids in the sequence of tropomyosin shows strong 14th-order peaks in the profiles of both negatively charged and non-polar amino acids, with a period of 1923 residues and an overall repeat length of 275 ± 2 amino acids, which is shorter than the sequence length of 284 amino acids. Both peaks are statistically significant and confirm Parry's work (1974, 1975b). The regularities are analysed in terms of an assumed supercoil structure in which two α-helices lie parallel and in register to form a supercoil with a pitch of 137 A. These molecules are then assumed to overlap end-to-end by eight to nine amino acids so that the periodicity is continuous along an extended filament of linked tropomyosin molecules. The periodic features are stronger in the outer surface of the molecule away from the core of the supercoil. The sequence divides into 14 bands which each have a narrow zone of net positive charge and a broader negatively charged zone. Overlapping every positive zone is a hydrophobic zone which always has at least one non-polar group on the outer surface. Anomalies in the charge distribution are found near the molecular ends and close to Cys190. These are attributed to the end-to-end overlap site and the troponin binding site. In the thin filament the 137 A pitch supercoil would make seven half-twists relative to the twisted actin helix along a 385 A length, so that a pair of adjacent bands would be oriented equivalently with respect to a pair of actins 28 A apart. We therefore suggest that the bands (each containing one zone of each type) should be divided alternately into two series, α and β. Every pair of bands is 3913 residues long and each of the seven pairs corresponds with one segment of the 42-residue gene duplication repeat observed previously in the sequence. The disparity between the periods of 42 and 3913 is overcome by deletions and insertions. The 3913-residue periodicity is not simply a consequence of the supercoil structure or gene duplication but is probably a result of adaptation to the spatial periodicity of the actin helix in muscle. Although the α and β bands are alike in general, they differ systematically in detail and the α bands are more regular than the β. We propose that the seven α and seven β bands are alternative sets of sites which bind equivalently to complementary groups of sites on seven actins in the “relaxed” and “active” states of muscle, respectively. In each band the negative zone probably attaches to actin by magnesium bridges and the hydrophobic zone by direct contacts with the narrow outer edge of the supercoil. Since the supercoil twists 90 ° relative to actin on passing between adjacent α and β bands, a quarter rotation of the whole tropomyosin molecule would detach one set of seven sites and attach the other, allowing a highly co-operative switch mechanism.