Molecular dynamics of oligopeptides. A comparative study of the interactions of amino acid residues in dipeptide structures

A comparative study of the molecular dynamics of dipeptides consisting of natural amino acid residues has been carried out. Molecular dynamics protocols were used that do not violate the principle of equidistribution of energy by degrees of freedom. Autocorrelation functions of complex exponential curves from dihedrals were used for the comparative analysis. The interactions of amino acid residues were classified by their influence on the dynamic properties of neighboring amino acid residues.     

Lactate dehydrogenase from the tetraploid weatherfish Misgurnus fossilis during temperature adaptation: determination of structural differences in two forms of the enzyme by molecular modeling methods

A structural analysis of two lactate dehydrogenase M4 protein forms has been performed. These structures are the protein products of two lactate dehydrogenase gene (LDH-A) copies in the weatherfish Misgurnus fossilis genome after thermal adaptation (acclimation) to 5 degrees C and 18 degrees C. The localization of three earlier identified amino acid substitutions (Gly214Val, Leu304Ile, Asp312Glu) has been determined, and the molecular dynamics simulation and computer modeling of two forms of the enzyme from skeletal muscles LDH-M4 have been carried out. After molecular dynamics trajectory calculations carried out at 5, 18, and 25 degrees C, the intersubunit distances for all structures used in calculations have been determined. It has been found that the Gly214Val substitution localized in the intersubunit region leads to a new intersubunit interaction, which plays a role in the stabilization of tetrameric enzyme structure after the adaptation to 18 degrees C.     

Molecular dynamics study of femtosecond events in photoactive yellow protein after photoexcitation of the chromophore

Molecular dynamics simulations were carried out to study what happens in a photoreceptor protein, photoactive yellow protein (PYP), immediately after the vertical transition of the chromophore from the ground to the excited state. A photon absorption simulation was performed to investigate the movement of amino acid residues upon photoexcitation. To calculate the excited state of the chromophore, SCF-CI calculation was carried out with INDO/S Hamiltonian. We observed that some amino acid residues have strong interactions with the chromophore. Most of these amino acid residues are conserved in PYPs from three different species of bacteria. This observation indicates the biological importance of these residues. Proteins 32:268–275, 1998. © 1998 Wiley-Liss, Inc.     

Molecular dynamics of oligopeptides. A comparative study of residue interactions in dipeptides

The molecular dynamics of dipeptides of natural amino acids were examined using protocols that do not violate the principle of equal distribution of energy over the degrees of freedom. Comparative analysis involved autocorrelation functions of complex exponentials from dihedrals. The mutual influence of residues was classified by the effects on the dynamic properties of the neighbors.     

Investigations of the thermostability of rubredoxin models using molecular dynamics simulations.

The affects of differences in amino acid sequence on the temperature stability of the three-dimensional structure of the small beta-sheet protein, rubredoxin (Rd), was revealed when a set of homology models was subjected to molecular dynamics simulations at relatively high temperatures. Models of Rd from the hyperthermophile, Pyrococcus furiosus (Pf), an organism that grows optimally at 100 degrees C, were compared to three mesophilic Rds of known X-ray crystal structure. Simulations covering the limits of known Rd thermostabilities were carried out at temperatures of 300 K, 343 K, 373 K, and 413 K. They suggest that Rd stability is correlated with structural dynamics. Because the dynamic behavior of three Pf Rd models was consistently different from the dynamic behavior of the three mesophilic Rd structures, detailed analysis of the temperature-dependent dynamic behavior was carried out. The major differences between the models of the protein from the hyperthermophile and the others were: (1) an obvious temperature-dependent transition in the mesophilic structures not seen with the Pf Rd models, (2) consistent AMBER energy for the Pf Rd due to differences in nonbonded interaction terms, (3) less variation in the average conformations for the Pf Rd models with temperature, and (4) the presence of more extensive secondary structure for the Pf Rd models. These unsolvated dynamics simulations support a simple, general hypothesis to explain the hyperthermostability of Pf Rd. Its structure simplifies the conformational space to give a single minimum accessible over an extreme range of temperatures, whereas the mesophilic proteins sample a more complex conformational space with two or more minima over the same temperature range.     

Conformational studies of anthrax polypeptide, subtilis polypeptide, and synthetic poly- -L-glutamic acid

Poly-γ-L -glutamic acid has been synthesized by the activated pentachlorophenyl ester polymerization method and the molecule weight of the polymer was found to be 16,000. Comparative conformational studies on the synthetic and on the native polyglutamic acid mbtained from B. anthracis and B. subtilis were carried out using optical rotatory dispersion, circular dichroism, peptide absorption spectrum, and titration data. These results show that poly-γ-glutamic acid does not exhibit any conformational order under the conditions of investigation. At low degrees of ionization, restriction of conformational freedom via random “hypercoiling” of the chain appears likely.     

Involvement of K+ channels and calcium-dependent pathways in the action of T3 on amino acid accumulation and membrane potential in Sertoli cells of immature rat testis

The purpose of this study was to investigate the involvement of calcium in K+ currents and its effects on amino acid accumulation and on the membrane potential regulated by tri-iodo-L-thyronine (T3) in Sertoli cells. Immature rat testes were pre-incubated for 30 min in Krebs-Ringer bicarbonate buffer and incubated for 60 min in the presence of [14C]methylaminoisobutyric acid with and without T3 or T4 (dose-response curve). Specific channel blockers or chelating agents were added at different concentrations during pre-incubation and incubation periods to study the basal amino acid accumulation and a selected concentration of each drug was chosen to analyze the influence on the stimulatory hormone action. All amino acid accumulation experiments were carried out in a Dubnoff metabolic incubator at 32 degrees C, pH 7.4 and gassed with O2:CO2 (95:5; v/v). Seminiferous tubules from immature Sertoli cell-enriched testes were used for the electrophysiology experiments. Intracellular recording of the Sertoli cells was carried out in a chamber perfused with KRb with/without T3, T4 or blockers and the membrane potential was monitored. We found that T3 and T4 stimulated alpha-[1-14C] methylaminoisobutyric acid accumulation in immature rat testes and induced a membrane hyperpolarization in Sertoli cells. The action of T3 on amino acid accumulation and on the hyperpolarizing effect was inhibited by the K(+)-ATP channel blocker tolbutamide as well as the voltage-dependent Ca2+ channel blocker verapamil. These results clearly demonstrate for the first time the existence of an ionic mechanism related to Ca2+ and K+ fluxes in the rapid, nongenomic action of T3.     

Low temperature cultivation of Escherichia coli carrying a rice lipoxygenase L-2 cDNA produces a soluble and active enzyme at a high level

Using a T7 RNA polymerase promoter system, rice lipoxygenase L-2 cDNA was expressed in E. coli as a fusion protein with 18 amino acid residues at the amino terminal end of the original enzyme. Incubation at 37 degrees C for 3 h in the presence of the inducer resulted in the production of inactive lipoxygenase. However, when induction was carried out at 15 degrees C for 16 h, active lipoxygenase, amounting to 3% of the total soluble protein, was produced. The enzyme was purified by ammonium sulfate precipitation and Mono-Q column chromatography to homogeneity at a yield of 80%. Expression of this protein should permit future site-directed mutagenesis of the gene and crystallization of the enzyme.     

Molecular dynamics of oligopeptides. 4. Dynamic characteristics of frequently and rarely occurring dipeptide fragments of proteins

The existence of differences in the dynamic organization of frequently and the rarely occurring dipeptide fragments in globular and membrane proteins was shown. The dynamic isomorphism and the collective degrees of freedom in these fragments were analyzed. A topological classification of the maps of the levels of free energy for pairs of dihedral angles of the main chain and side residues was carried out.     

Free energy calculations for the relative binding affinity between DNA and lambda-repressor

The change in the binding free energy between DNA and lambda-repressor resulting from a base substitution, thymine (T)-->deoxyuracil (abbreviated as U), was evaluated by the free energy perturbation method on the basis of molecular dynamics simulations for the DNA-lambda-repressor complex in water with all degrees of freedom and including long-range Coulomb interactions. The binding free energy change that we calculated (1.47 +/- 0.40 kcal/mol) was in good agreement with an experimental value (1.8 kcal/mol). We clarified why the small difference between T and U (CH(3) in T is replaced with H in U) caused such a significant change in the binding free energy: The substitution of CH(3) in T with H in U lowered the dissociated-state free energy level due to the gain of the hydration free energy. Furthermore, the T-->U substitution raised the free energy level in the associated state due to the loss of the favored van der Waals (vdW) interactions with the lambda-repressor amino acid residues. In other words, the amino acid residues of lambda-repressor can recognize the CH(3) in T through the vdW interactions with the CH(3). This recognition is enhanced in a water environment, because the hydrophobic CH(3) prefers the amino acid residues of lambda-repressor to water molecules.     

Improvement of oxidative and thermostability of N-carbamyl-d-amino Acid amidohydrolase by directed evolution

N-Carbamyl-D-amino acid amidohydrolase (N-carbamoylase), which is currently employed in the industrial production of unnatural D-amino acid in conjunction with D-hydantoinase, has low oxidative and thermostability. We attempted the simultaneous improvement of the oxidative and thermostability of N-carbamoylase from Agrobacterium tumefaciens NRRL B11291 by directed evolution using DNA shuffling. In a second generation of evolution, the best mutant 2S3 with improved oxidative and thermostability was selected, purified and characterized. The temperature at which 50% of the initial activity remains after incubation for 30 min was 73 degrees C for 2S3, whereas it was 61 degrees C for wild-type enzyme. Treatment of wild-type enzyme with 0.2 mM hydrogen peroxide for 30 min at 25 degrees C resulted in a complete loss of activity, but 2S3 retained about 79% of the initial activity under the same conditions. The K(m) value of 2S3 was estimated to be similar to that of wild-type enzyme; however k(cat) was decreased, leading to a slightly reduced value of k(cat)/K(m), compared with wild-type enzyme. DNA sequence analysis revealed that six amino acid residues were changed in 2S3 and substitutions included Q23L, V40A, H58Y, G75S, M184L and T262A. The stabilizing effects of each amino acid residue were investigated by incorporating mutations individually into wild-type enzyme. Q23L, H58Y, M184L and T262A were found to enhance both oxidative and thermostability of the enzyme and of them, T262A showed the most significant effect. V40A and G75S gave rise to an increase only in oxidative stability. The positions of the mutated amino acid residues were identified in the structure of N-carbamoylase from Agrobacterium sp. KNK 712 and structural analysis of the stabilizing effects of each amino acid substitution was also carried out.     

Conformational preferences of amino acid side chains in collagen

Conformational energy computations were carried out on collagenlike triple-stranded conformations of several poly(tripeptide)s with the general structure CH₃CO? (Gly? X? Y)₃? NHCH₃. The sequences considered had various amino acid residues in position X or Y of the central tripeptide, with either Pro or Ala as a neighbor, i.e., Gly-X-Pro, Gly-X-Ala, Gly-Pro-Y, and Gly-Ala-Y. Minimum-energy conformations were computed for the side chains, and their distributions were compared for the four sequences. The residues used were Abu (= α-aminobutyric acid), Leu, Phe, Ser, Asp, Asn, Val, Ile, and Thr. The conformational energy of a ? Ch₂? CH₃ side chain in Abu was mapped as a function of the dihedral angle χ¹. Intrastrand interactions with neighboring residues do not affect the conformations of a side chain in position Y, and they have a minor effect on it in the X-Ala sequence, but they strongly restrict the conformational freedom of the side chain in the X-Pro sequence. Conversely, interstrand interactions do not affect side chains in position X, but they strongly restrict the conformational freedom of a side chain in position Y if there is a nearby Pro residue in a neighboring strand. Hydrogen bonds with the backbone can be formed in some conformations of long polar side chains, such as Asp, Asn, or Gln. All amino acid residues can be accommodated in collagen. Because of the interactions mentioned above, steric and energetic constraints can be correlated with observed preferences of certain amino acids for positions X or Y in collagen. Hence, these preferences may be explained, in part, in terms of differences in the conformational freedom of the side chains in the triple-stranded structure.     

Ribonucleotide reductase activity during the cell cycle of Saccharomyces cerevisiae

A fluorometric amino acid analyzer using fluorescamine for the assay of the full array of natural amino acids including proline on a single column is reported. The proline determination was carried out by specific introduction of a solution of N-chlorosuccinimide into the flow system. Single column fluorometric amino acid analysis was carried out in a significantly shorter time and with a sensitivity almost two orders of magnitude greater than that obtained with a commerical colorimetric ninhydrin amino acid analyzer.     

Deltorphin analogs restricted via a urea bridge: structure and opioid activity.

Eight cyclic heptapeptides related to the full sequence of deltorphin have been synthesized. The synthesis of linear peptides containing diamino acid residues in positions 2 and 4 was carried out on a 4-methylbenzhydrylamine resin. Depending on protection procedures, the N-protected peptide-resins or N-protected peptide amides with free amino groups in the side chains were obtained, which were subsequently treated with bis-(4-nitrophenyl)carbonate to form a urea unit. Opioid activities of the peptides were determined in the guinea pig ileum (GPI) and mouse vas deferens (MVD) assays. Several compounds showed high delta opioid agonist potency and high selectivity for delta receptors. The results were compared with those obtained earlier for respective 1-4 deltorphin analogs. The conformations of these peptides have been studied using 2D-NMR in H2O/D2O and molecular dynamics. We observed that the backbone rings had well defined conformations, while the Tyr and Phe side chains and the C-terminal tail had significant conformational freedom. The bioassay data and conformational parameters of these peptides were compared with those of previously described, corresponding 1-4 deltorphin analogs. This comparison permitted an assessment of the role of the C-terminal peptide segment in defining the conformation and receptor interaction of the N-terminal portion and provided insight into the relationship between the putative bioactive conformations and bioactivity.     

Sequencing and model structure of a Naja naja atra protein fragment.

We report the amino acid sequence of a basic protein isolated from the snake venom of Naja naja atra. An automated Edman sequencer was used to determine the 65-residue sequence, aided by electrospray ionization/mass spectrometry. Online reduction and pyridylethylation of the peptide was performed to identify the cysteine residues. Trypsin, chymotrypsin and aspartic digestions were carried out to derive peptide fragments for further sequencing. Fragmented peptides were overlapped to obtain the complete sequence. Molecular mass measurements of the whole protein and its fragments were used as a countercheck for sequence assignment. Further confirmation of the sequence was indicated by sequence homology to other snake venom neurotoxins. A molecular model of the tertiary structure was constructed based on sequence homology, and was refined by global minimization and extensive quality control algorithms. Electrostatic and hydrophobic surface calculations and molecular dynamics simulations were carried out to determine the functional properties of the molecule.     

A study of comparative modelling,simulation and molecular dynamics of CXCR3 receptor with lipid bilayer

The G-coupled receptors seen on the cell surface are composites with a lipid bilayer. The chemokines are kind of G-coupled receptor which majorly involved in the activation and downstream signalling of the cell. In general, many G-coupled receptors lack their 3D structures which become a hurdle in the drug designing process. In this study, comparative modelling of the CXCR3 receptor was carried out, structure evaluation was done using various tools and softwares. Additionally, molecular dynamics and docking were performed to prove the structural quality and architecture. Interestingly, the studies like toggle switch mechanism, lipid dynamics, virtual screening were carried out to find the potent antagonist for the CXCR3 receptor. During virtual screening 14,303 similar molecules were retrieved among them only four compounds have an ability to interact with a crucial amino acid residue of an antagonist. Hence, these screened compounds can serve as a drug candidate for a CXCR3 receptor, but further in vitro and in vivo studies are ought to do to prove its same efficacy.     

LC-MS/MS 检测癫痫患者神经递质类氨基酸

目的:建立液相色谱串联质谱同位素内标法检测神经递质类氨基酸并用于癫痫患者临床评价.方法:选用AAA-C18柱色谱柱,以乙腈水(含有0.01%七氟丁酸、0.1%甲酸)为流动相,采用梯度洗脱进行分离,血浆样品用iTRAQ-115衍生化试剂处理后,加入iTRAQ-114衍生化的氨基酸内标并进样,选用3200QTRAP型质谱仪的多重反应监测(MRM)扫描方式进行检测.疾病组与健康组的统计采用t检验和主成份分析.结果:疾病组和健康组氨基酸测定结果显示:Trp、GABA两组间没有显著性差异(P＞0.05),Arg、Glv、Ser、Tau、Asp、Glu、EtN、两组间有显著性差异(P＜0.05),通过PCA分析显示,疾病组与健康组之间差异明显,Asp、Glu、Ser等是引起差异的主要氨基酸.结论:试验方法灵敏、专属性强,并初步的用于癫痫患者体内氨基酸评价.     

奥利亚罗非鱼胶原蛋白酸解液美拉德反应产物风味成分分析

以奥利亚罗非鱼鱼皮中胶原蛋白酸解液和葡萄糖为主要基质进行美拉德反应,采用氨基酸自动分析仪和GC-MS分析了游离氨基酸组成和主要风味成分。结果表明,酸解后游离氨基酸完全符合胶原蛋白特有的氨基酸组成,且风味氨基酸占59.77%。此外鉴定出19种风味成分,其中包括乙酸乙酯(30.34%)、2,3-二羟基丙醛、柠檬烯、1,1-乙二醇二乙酸酯、己二酸二丁酯、二乙二醇丁醚醋酸酯、苯甲酸乙酯、2-乙酰基吡咯等。