bluuebunny/crossref_metadata_2025_split huggingface dataset:
CONFORMATION OF POLYPEPTIDE CHAINS CONTAINING BOTH L‐AND D‐RESIDUES:
Authors: Prasad B. V. Venkatram , Chandrasekaran R. 
Published: August 2010

Polypeptides with alternating L‐ and D‐amino acid residues can take up stereochemically satisfactory coaxial double‐helical structures, both antiparallel and parallel, which are stabilized by systematic interchain NH O hydrogen bonds. Semiempirical energy calculations over allowed regions of conformational space have yielded the characteristics of these double‐helices.There are four possible types of antiparallel double‐helices ‐ A3, A4, A5 and A6, with n, the number of LD peptide units per turn, around 2.8, 3.6, 4.5 and 5.5 respectively, while for the parallel double‐helices there are two types, P3 and P4, having similar helical parameters as in A3 and A4. The hydrogen‐bonding scheme restricts the pitch in all the models to the narrow range of 10.0 to 11.5 Å. All these helices have large central cores whose radii increase proportionately with n. In this respect, A3 and A4 are suitable models for the structure of gramicidin A.In terms of their relative energies, antiparallel double‐helices are marginally more stable than those with parallel strands. Our results indicate that the energy differences amongst the members in the antiparallel family are not significant and thus provide an explanation for the polymorphism reported for poly(γ‐benzyl‐LD‐glutamate).
HUMAN SOMATOTROPIN:
Authors: Noble Richard L. , Yamashiro Donald , Li Choh Hao 
Published: August 2010

The amino terminal 54 residue peptide fragment of human somatotropin, [Cys(Cam)53]‐HGH‐(I‐54), has been synthesized by the solid‐phase method. The symmetrical anhydride and active ester coupling methods were used exclusively. The synthetic product was purified by gel filtration, isoelectric focusing, and partition chromatography. It was found to be homogeneous by six additional criteria.In complement fixation experiments the synthetic product was immunologically active with antisera to HGH and [Cys(Cam)53]‐HGH‐(I‐134). Antiserum raised against the synthetic product was immunologically active in the homologous assay and with HGH, [Cys(Cam)53]‐HGH‐(I‐134), and [Cys(Cam)53]‐HGH‐(15–125). The synthetic fragment exhibited 53% of the activity of [Cys(Cam)53]‐HGH‐(I‐134) in the rat tibia assay.
EMPIRICAL CALCULATIONS ON CYCLIC DIPEPTIDES
Authors: Genest M. , Ptak M. 
Published: August 2010

Empirical conformational energy calculations were carried out for the dipeptides cyclo‐(L‐Ser‐L‐His) and cyclo‐(L‐Thr‐L‐His). Various DKP structures have been investigated to study side chain conformations through the DKP ring deformations, and prevalent conformers of monosubstituted and disubstituted dipeptides are discussed. The most stable conformations occur when both side chains are folded over a planar DKP ring, the imidazole ring being in the ε‐tautomeric form.Theoretical results are consistent with those obtained from n.m.r. and crystallographic studies.
EMPIRICAL TORSIONAL POTENTIAL FUNCTIONS FROM PROTEIN STRUCTURE DATA Phi‐ and Psi‐Potentials for Non‐glycyl Amino Acid Residues
Authors: KOLASKAR A.S. , PRASHANTH D. 
Published: August 2010

The torsional potential functions Vt(φ) and Vt(ψ) around single bonds N–Cα and Cα‐C, which can be used in conformational studies of oligopeptides, polypeptides and proteins, have been derived, using crystal structure data of 22 globular proteins, fitting the observed distribution in the (φ, ψ)‐plane with the value of Vtot(φ, ψ), using the Boltzmann distribution. The averaged torsional potential functions, obtained from various amino acid residues in l‐configuration, are Vt(φ) = – 1.0 cos (φ + 60°); Vt(ψ) = – 0.5 cos (ψ + 60°) – 1.0 cos (2ψ + 30°) – 0.5 cos (3ψ + 30°).The dipeptide energy maps Vtot(φ, ψ) obtained using these functions, instead of the normally accepted torsional functions, were found to explain various observations, such as the absence of the left‐handed alpha helix and the C7 conformation, and the relatively high density of points near the line ψ = 0°. These functions, derived from observational data on protein structures, will, it is hoped, explain various previously unexplained facts in polypeptide conformation.
SYNTHESIS, CHARACTERIZATION AND FLUORESCENCE STUDIES ON N‐α‐DANSYLALANYLLYSYL TRYPSINO (HIS‐46)‐METHANE
Authors: PENNY GLENN S. , DYCKES DOUGLAS F. , BURLEIGH B. DANIEL 
Published: August 2010

The 1‐dimethylamino‐5‐naphthalene sulfonyl (dansyl) derivative of alanyllsyl chloromethane was synthesized and employed to introduce the fluorescent dansyl moiety specifically into the active site of trypsin via affinity labelling. The potential of dansylalanyllysyl chloromethane lies in its high degree of selectivity and markedly faster rate of enzyme inactivation when compared to previously synthesized, single residue affinity label chromophores. This permits the practical utilization of stoichiometric amounts of the inhibitor to achieve 100% inactivation of trypsin, even at high dilutions.The transfer of energy between the four tryptophan residues of trypsin and the bound dansyl group has been investigated in the fluorescent inhibitor‐enzyme conjugate. From transfer efficiency measurements mean distances of 19.0 Å and 19.3 Å between the point of attachment of the dansyl group and the four tryptophan residues of trypsin have been calculated. These compare well with the mean value of 18.8 Å derived from calculations based on crystallo‐graphic model studies.
ISOLATION AND PHYSICAL CHARACTERIZATION OF BOVINE LENS CRYSTALLINS
Authors: CHIOU SHYH‐HORNG , AZARI P. , HIMMEL MICHAEL E. , SQUIRE PHIL G. 
Published: August 2010

The soluble proteins from bovine lens homogenate were separated on Sepharose CL‐6B (2 times 200 cm) in 0.05 m tris‐NaHSO3 pH 8.2 buffer containing 20 mM EDTA. Five sharp and defined fractions (HMα, α, βH, βL, γ) were obtained. Each crystallin fraction was further purified by rechromatography on the same column. Each protein fraction was pure as judged by ultracentrifugation and SDS‐gel electrophoresis. The molecular weights of the five fractions were 3.04 times 106, 5.83 times 105, 1.58 times 105, 4.59 times 104, 2.14 times 104 as determined from sedimentation coefficient and intrinsic viscosity data by Scheraga‐Mandelkern equation, which was in close agreement with that obtained by gel filtration. The polypeptide composition of crystallins as determined by SDS‐gel electrophoresis revealed one band for high molecular weight α (HMα) and α, three for βH, two for βL and one for γ.The gross CD patterns of crystallins were about the same in the peptide region (200 nm ˜ 250 nm) with a minimum centered at about 217 nm, indicative of α β‐sheet structure in all crystallins. The [0] values at 217 nm ranged from –1700 to –3700 degrees cm2 per decimole. The CD spectra of these crystallins in the aromatic region (250 nm ˜ 300 nm) were different, reflecting the different contributions of aromatic amino acids to the tertiary structure of crystallins.
PRIMARY STRUCTURE OF LOBSTER‐MUSCLE ARGININE KINASE: Amino and Carboxyl‐terminal Structure of the Enzyme and Complete Alignment of the Cyanogen‐Bromide Peptides
Authors: REGNOUF FRANÇOISE , KASSAB RIDHA , DEBUIRE BRIGITTE , RICHARD CLAUDE , HAN KIA‐KI 
Published: August 2010

The acetylation state of the blocked NH2‐terminal end of arginine kinase was characterized by the occurrence of 1 mol acetyl group/mol protein; a 5‐residue segment corresponding to the amino‐terminal portion was isolated from a pronase digest of the enzyme and its amino acid sequence determined as N‐acetyl Ala‐Asx‐Ala‐Ala‐Thr.Arginine kinase is terminated at the carboxyl end by the sequence Lys‐Glu‐MetOH; this particular 3‐residue sequence is repeated three times in the overall structure of the protein and is present in three CNBr fragments. One of these, a peptide of 14 amino acid residues, was identified in the course of this study and its amino acid sequence determined. Its location at the COHO‐terminal end of the enzyme was recognized on the basis of investigations carried out with des‐MetOH‐Glu‐arginine kinase, a specific proteolytic derivative.The alignment of the eight CNBr‐fragments which constitute the arginine kinase molecule was established according to the sequential and compositional properties of seven unique tryptic methionyl peptides isolated from the whole protein. The alignment was confirmed by using BNPS‐skatole fragments of the enzyme as another protein source.
A functioning complex of two cytochrome c fragments with deletion of the (39–58) eicosapeptide*
Authors: WESTERHUIS L.W. , TESSER G.I. , NIVARD R.J.F. 
Published: August 2010

Two major fragments of horse heart cytochrome c involving the sequences (1–38) and (60–104) were found to produce a stable complex. The two fragments were devoid of any cytochrome c activity. The complex exhibited a hardly measurable electron transfer capacity with respect to cytochrome c oxidase and missed the 695 nm absorption band. The introduction of tryptophan in position 59 restored the intrinsic activity of the complex to the level of native cytochrome c. This was concluded from the convergence of the Eady‐Hofstee plots which extrapolate to the same Vmax at high substrate concentrations. The absorption spectrum of the complex in the ferriform contained a clear absorption band at 695 nm (84% of that found with native cytochrome c).The investigation proves the indispensability of tryptophan in position 59 for the transfer of an electron to cytochrome c oxidase and supports the conclusions of Parr et al. about the existence of two consecutive processes in the folding of the two fragments (vide infra).
Intramolecular sulfhydryl‐catalyzed structural alteration of bovine plasma albumin–N‐A isomerization*
Authors: INOUYE HIROSHI , ERA SEIICHI , SAKATA SHIGEKI , KUWATA KAZUO , SOGAMI MASARU 
Published: August 2010

The N‐A isomerization of bovine plasma albumin (BPA) (the intramolecular sulfhydryl‐disulfide exchange reaction) is not a two‐state but a multi‐state reaction as shown in the following equationN ± A1 + mH+ ± A2 + nH+ ±where N and A1 are the N‐ and A(aged)‐forms, respectively. The N‐A isomerization was strongly suppressed by increasing the ionic strength, especially by divalent cations, such as Ca2+. The N‐A isomerization was completely suppressed in the presence of 20 mM sodium caprylate and 40 mM N‐acetyltryptophan. This suppression of the intramolecular sulfhydryl‐disulfide exchange reaction might be due to the reduction of the structural fluctuation of BPA.
Peptide synthesis catalyzed by the Glu/Asp‐specific endopeptidase
Authors: BONGERS JACOB , LIU WEN , LAMBROS THEODORE , BREDDAM KLAUS , CAMPBELL ROBERT M. , FELIX ARTHUR M. , HEIMER EDGAR P. 
Published: August 2010

We recently described a two‐step enzymatic semisynthesis of the superpotent analog of human growth hormone releasing factor, [desNH2Tyr1,D‐Ala2,Ala15]‐GRF(1‐29)‐NH2 (4), from the precursor, [Ala15,29]‐GRF(4‐29)‐OH (1). C‐Terminal amidation of 1 to form [Ala15]‐GRF(4‐29)‐NH2 (2) was achieved by carboxypeptidase‐Y‐catalyzed exchange of Ala29‐OH for Arg‐NH2. The target analog 4 was then obtained by acylation of segment 2 with desNH2Tyr‐D‐Ala‐Asp(OH)‐OR (3) (R = CH3CH2 or 4‐NO2C6H4CH2) catalyzed by the V8 protease. In this paper we report on the use of the recently isolated Glu/Asp‐specific endopeptidase (GSE) from Bacillus licheniformis, which is shown to be an efficient catalyst for the segment condensation of 2 and 3. GSE is more stable than the V8 protease under the conditions employed (20% DMF, pH 8.2, 37 °C). The extent of conversion of 2 into 4 is limited by proteolyses at Asp3‐Ala4 and Asp25‐Ile26. However, this proteolysis is virtually eliminated by use of the appropriate ester leaving group, R.A systematic study of the kinetics of the GSE‐catalyzed segment condensations of 2 and a series of tripeptide esters, desNH2Tyr‐D‐Ala‐Asp(OH)‐OR (3) [R = CH3CH2‐ (3a), CH3‐ (3b), ClCH2CH2‐ (3c), C6H5CH2‐ (3d), 4‐No2C6H4CH2‐ (3e)] revealed that the rate of aminolysis versus proteolysis, and hence the conversion of 2 into 4, increase with increasing specificity (Vmax/Km) of GSE for the tripeptide ester. The specificity varies in the order 3e>3d>3c>3b>3a and appears to depend on an increase in the maximum turnover rate (Vmax) with increasing basicity of R. This work demonstrates the coupling of a small peptide segment containing unnatural amino acids to the N‐terminus of an intermediate‐length polypeptide, without side‐chain protection, by GSE, a potentially less costly and more stable alternative to the V8 protease.
‘Tethered ligand’derived pentapeptide agonists of thrombin receptor: a study of side chain requirements for human platelet activation and GTPase stimulation
Authors: NATARAJAN SESHA , RIEXINGER DOUGLAS , PELUSO MARIANNE , SEILER STEVEN M. 
Published: August 2010

Proteolytic action of α‐thrombin on human thrombin receptor results in cleavage of a portion of the N‐terminus, thereby generating a‘tethered ligand’at the newly exposed N‐terminus, which then activates the receptor in an intramolecular fashion. Agonist peptides incorporating the amino acid sequence of the newly exposed N‐terminal portion of the cleaved receptor cause receptor activation without requiring prior cleavage of the receptor by thrombin. The pentapeptide amide Ser‐Phe‐Leu‐Leu‐Arg‐NH2, which retains the N‐terminal sequence of the‘tethered ligand’of the receptor, has been shown to be the minimum sequence to cause receptor activation. To understand the importance of the side chains of various residues within the pentapeptide amide, we carried out an extensive structure‐activity study of the ability of peptides to stimulate gel‐filtered platelet aggregation. In this study 106 pentapeptide amides were synthesized, utilizing naturally occurring l‐amino acids, unnatural amino acids, D‐amino acids and N‐methyl amino acids for replacements. At position‐1, charged residues (acidic or basic) were not tolerated, and the size and shape of the residue were important. Position‐2 tolerated only aromatic residues. Position‐3 accommodated various residues. A significant finding of this study was that two very different residues, [3‐(2‐naphthyl)]‐l‐alanine and l‐arginine, when substituted for leucine residue at position‐3, resulted in more active agonists. At position‐4 aromatic and aliphatic residues were well tolerated, whereas basic and acidic residues were less tolerated. Position‐5 mimicked position‐3 in its ability to tolerate a wide range of residues. In general, an acidic residue was not preferred in any position. In all positions a ‐Phe‐residue was tolerated. Positions 1 and 3 tolerated ‐Pro‐residue, whereas positions 2, 4 and 5 did not. d‐Amino acid substitution was not tolerated in any position. While N‐methylation of residues at positions‐3 and ‐4 led to poor agonists, at position‐2 it resulted in an inactive analog. These studies define the side chain requirements for the‘tethered ligand’derived pentapeptide agonists of thrombin receptor for human platelet activation.Selected peptides were tested for ability to stimulate platelet membrane GTPase. A good correlation was observed between peptides that stimulate GTPase and those that stimulate platelet aggregation, with the general finding that 3‐10‐fold higher concentrations were required to half maximally activate GTPase when compared with the concentrations needed for activation of platelet aggregation. © Munksgaard 1995.
Synthesis and characterization of the human elastin W4 sequence
Authors: GOWDA D.C. , LUAN C.‐H. , FURNER R.L. , PENG S.Q. , JING N. , HARRIS C.M. , PARKER T.M. , URRY D.W. 
Published: August 2010

Following the nomenclature of Sandberg, the W4 sequence of human elastin, LVPGGPGFGPGVVGVPGAGVPGVGVPGAGIPVVPGAGIPGAGVPGVVSPEG, has been synthesized by solid‐phase methods and characterized by carbon‐13 nuclear magnetic resonance, amino‐acid analysis, mass spectra and elemental analysis. This sequence was then polymerized to greater than 50 kDa as determined by retention in 50 kDa molecular weight cut‐off dialysis tubing. It has been successfully cross‐linked by γ‐irradiation (20 Mrad) to form an elastomeric matrix. designated as X20‐poly(W4). Physical characterizations such as stress/strain, thermoelasticity, acid‐base titration and inverse temperature transition studies have been carried out on this elastomer, which is homologous to the striking, poly(VPGVG), W4 sequence of bovine and porcine elastins. These results are compared with previous results on the polypentapeptide of elastin, (VPGVG)n, and it has been demonstrated that X20‐poly(W4) also is a dominantly entropic elastomer. Finally, the working model for the structure of this human elastin sequence was derived computationally using molecular mechanics and dynamics calculations.Thus the human W4 sequence appears to be structurally and functionally equivalent to the bovine and porcine W4 sequences in spite of the less regular repeating pentamer sequence. © Munksgaard 1995.
Proteinase‐catalyzed peptide synthesis in concentrated solutions of urea and other denaturing agents
Authors: ANISIMOVA VERONIKA V. , FILIPPOVA IRINA YU. , LYSOGORSKAYA ELENA N. , OKSENOIT ELENA S. , KOLOBANOVA SVETLANA V. , STEPANOV VALENTIN M. 
Published: August 2010

Pepsin successfully catalyzed the synthesis of several hydrophobic octa‐ and decapeptides in dimethylformamide‐water solutions containing concentrated urea at pH 4.65. The factors that influence peptide synthesis in the presence of urea aere studied using condensation of the tripeptides Z‐Ala‐Ala‐Phe‐OH and H‐Leu‐Ala‐Ala‐OCH3 as a model. The dependence of Z‐Ala‐Ala‐Phe‐Leu‐Ala‐Ala‐OCH3 yield on pepsin concentration and pH, as well as the behavior of pepsin during peptide synthesis were studied. It was shown that pepsin catalyzed the synthesis of Z‐Ala‐Ala‐Phe‐Leu‐Ala‐Ala‐OCH3 in guanidine hydro‐chloride and sodium dodecyl sulfate solutions. Other proteinases, subtilisin and thermolysin, were applied for the synthesis of p‐nitroanilides of tri‐ and tetrapeptides in urea solutions.Proteinase‐catalyzed peptide synthesis in the presence of denaturing agents might help to overcome the limitations caused by poor solubility of the starting peptide derivatives, although this effect is sometimes counterbalanced by the product solubility. ©Munksgaard 1996.
Photochemical conjugation of peptides to carrier proteins using 1,2,3‐thiadiazole‐4‐carboxylic acid Immunoreactivity of free C‐terminal epitope with specific antibodies
Authors: HANSEN PAUL R. , FLYGE HANNE , HOLM ARNE , LAURITZEN EDGAR , LARSEN BJARNE DUE 
Published: August 2010

A new heterobifunctional cross‐linking reagent, 1,2,3‐thiadiazole‐4‐carboxylic acid, for the photochemical conjugation of peptides to proteins is described. The title compound can be coupled directly to a protected peptide resin during solid‐phase peptide synthesis (SPPS) using standard coupling procedures. The probe is stable to TFA deprotection/cleavage mixtures containing ethanedithiol commonly used in Fmoc‐SPPS. Furthermore, tritium may easily be introduced into the thiadiazole ring by base‐catalyzed hydrogen‐exchange. Upon irradiation at 245‐300 nm, parent 1,2,3‐thiadiazole rapidly eliminates N2, generating very reactive thioketene which reacts with amines to give a thioamide in high yield, even when the photolysis is carried out in hydroxylic solvents.In order to investigate the potential of the title compound as a heterobifunctional cross‐linking reagent a model study with angiotensin II (AII) was conducted. The photoreactive peptide Nα‐4‐carbonyl‐1,2,3‐thiadiazole‐AII (TDA‐AII) was synthesized by Fmoc‐SPPS and conjugated to bovine serum albumin (BSA) by photolysis at 245 and 300 nm. By use of a capture competition ELISA, the C‐terminal Pro‐Phe epitope of photoconjugated AII with the sequence DRVYIHPF was shown to bind specifically to antiAII antibodies (anti‐AII abs), although antibodies against both the C‐ and N‐terminal epitopes were present in the assay. A dipeptide His‐Leu carboxy‐extension form of AII, angiotensin I (AI), only bound to anti‐AII abs at 100‐200 times higher concentrations, showing that the C‐terminal epitope was blocked by the dipeptide. © Munksgaard 1996.
Novel interleukin‐4 and interleukin‐1 receptor antagonist gene variations associated with non‐cardia gastric cancer in Japan: Comprehensive analysis of 207 polymorphisms of 11 cytokine genes
Authors: Seno Hiroshi , Satoh Kiichi , Tsuji Shingo , Shiratsuchi Takayuki , Harada Yosuke , Hamajima Nobuyuki , Sugano Kentaro , Kawano Sunao , Chiba Tsutomu 
Published: August 2010

AbstractBackground and Aim:  Helicobacter pylori (H. pylori)‐induced chronic atrophic gastritis is a high‐risk factor for gastric cancer. Immune responses to H. pylori are involved in gastric mucosal inflammation, and might affect clinical outcome, including the development of gastric cancer. The present study examines the significance of gene polymorphisms of various cytokines in the development of gastric cancer following H. pylori infection.Methods:  One hundred Japanese non‐cardia gastric cancer patients and 93 dyspeptic patients as controls were enrolled in the study (age range 50–75 years). All patients were positive for H. pylori. Genomic DNA was extracted from peripheral whole blood leukocytes, and we comprehensively analyzed 207 single nucleotide polymorphisms (SNP) in 11 cytokine genes; interleukin (IL)‐1α, IL‐1β, IL‐1 receptor antagonist (RN), IL‐4, IL‐4R, IL‐8, IL‐10, IL‐12, TNF‐α, TNF‐β, and IFN‐γ, using either invader assay (163 SNP), direct sequencing (22 SNP), or PCR‐restriction fragment length polymorphism (22 SNP).Results:  Among the 207 SNP examined, the IL‐4 gene diplotypes (984 and 2983 AA/GA) had a significant negative association with gastric cancer development (odds ratio =0.3, 95% confidence interval =0.1–0.9). When we adopted the dyspeptic patients over 66 years of age as the controls, the IL‐1RN gene diplotypes (−1102 and 6110 CG/GA) also had a significant negative association (odds ratio =0.2, 95% confidence interval =0.1–0.7).Conclusion:  A comprehensive analysis of 207 SNP of 11 cytokine genes revealed that variations in IL‐4 and IL‐1RN genes are negatively associated with the risk of developing gastric cancer following H. pylori infection. Distinct host cytokine responses in the gastric mucosa might have a role in H. pylori‐induced carcinogenesis.
Accuracy of the ICare rebound tonometer in glaucomatous eyes with topical ocular hypotensive medication
Authors: Diaz Alberto , Yebra‐Pimentel Eva , Resua Carlos García , Gilino Jorge , Giraldez Mª Jesus 
Published: August 2010

AbstractBackground:  The purpose of this study was to assess the accuracy of the ICare tonometer, using the Perkins applanation tonometer (AT) as the reference, in a sample population being treated with travaprost 0.004% for glaucoma.Material and methods:  Twenty‐eight consecutive patients with open‐angle glaucoma or ocular hypertension who had been receiving travaprost 0.004% to control elevated intraocular pressure (IOP) were included in the study. IOP was measured in the entire sample with ICare and Perkins AT. The difference between the methods was plotted against the mean to compare the tonometers. The hypothesis of zero bias was examined by a paired t‐test. The 95% limits of agreement (LoA) were also calculated.Results:  As previously found in young healthy subjects, ICare showed a tendency to overestimate Perkins IOP measurements by a mean of 3.57 mmHg. The agreement between the two methods is shown by the 95% LoA which was from −9.37 to +2.23 mmHg: 53% of the IOP differences fell within ±3 mmHg.Conclusions:  The performance of the ICare tonometer in glaucomatous patients being treated with travaprost 0.004% to lower the IOP appears to be similar to that of young healthy patients. The tendency of ICare to overestimate the IOP readings should be considered when the instrument is used in the follow‐up of glaucomatous patients.