bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anticariogenic Casein Phosphopeptides
Authors: Reynolds Eric C. 
Published: December 2022

Abstract:
Proteins and peptides containing clusters of phosphoseryl residues have been shown to stabilize amorphous calcium phosphate in solution, and have been implicated in the regulation of biomineralisation processes. Casein phosphopeptides (CPP) containing the cluster sequence -Ser(P)-Ser(P)-Ser(P)-Glu-Glu- have been demonstrated to significantly reduce the level of dental caries (tooth decay) in animal and human experiments and also to repair early stages of decay. Through their multiple phosphoseryl residues the peptides bind to forming nanoclusters of amorphous calcium phosphate (ACP) in metastable solution, preventing their growth to the critical size required for nucleation and phase transformation. Conformational and binding studies have shown that all the phosphoseryl residues are important in interaction with ACP. The CPP localise ACP at the tooth surface providing a reservoir of calcium and phosphate ions thereby helping to maintain a state of supersaturation with respect to tooth enamel. The CPP-ACP, unlike fluoride, can be added to sugar-containing foods as well as oral care products for the control of dental caries.
Recent Applications of Instrumental Biosensors for Protein and Peptide Structure-Function Studies
Authors: Nice Edouard , Catimel Bruno , Domagala Teresa , Nerrie Maureen , Weinstock Janet , White Sara , Abud Helen , Heath Joan 
Published: December 2022

Abstract:
Since the introduction in the early l 990's of a novel biosensor technology that measures changes in refractive index at or near a sensor surface, the technique has been rapidly embraced by the biological research community to measure a wide range of biomolecular interactions. We will review some recent applications of this technology including preparative ligand fishing and cell-based studies, and discuss the relative merits of different instruments for various applications.
Applications of NMR in Drug Design: Structure-Activity Relationships in Disulfide-Rich Peptides
Authors: Craik David J 
Published: December 2022

Abstract:
NMR is a powerful technique for determining structures of biologically active molecules in solution. In recent years.our laboratory has focussed on the structure determination of small disulfide-rich proteins from both plants and animals which are valuable targets in drug design applications. This article will review these structural studies and their implications in drug design.
Synthesis of a New Group of Deltorphin I/II Analogs Modified in the Address Domain with y-Amino Acids, and QSAR Study_ of their δ /µ Opioid Binding
Authors: Heyl Deborah L. , Sanvordekar Medha D. , Dogruyol Guzin , Salamoun Mohamed D. , Rodgers David W. , Renganathan Kutralanathan , Mousigian Carol , Schullery Stephen E. 
Published: December 2022

Abstract:
The δ selectivity of the opioid heptapeptides deltorphin I and II has been attributed to the C-terminal "address" domain, the hydrophobic Val5-Val6 residues apparently playing a topographical role. We now report the synthe­sis, opioid binding affinities, and a QSAR study of a series of peptides in which these valine residues were re­ placed with y-amino acids. Results support a conformation stabilization role for this domain, rather than interaction with a receptor binding pocket.
EPO Mimetic Peptide Fused into PAI-1 Augments its EPO Activity
Authors: Zhong Ma , Le-tian Kuai , Chun-lei Wu , Jing Zhang , Qi-feng Qiu , Ai-wu Zhou , Shi-quan Wang , He-yun Zhang , Qian Song , Shu-ning Liao , Yu Han , Jian-ning Liu 
Published: December 2022

Abstract:
EPO Mimetic Peptide (EMP) encoding sequence was inserted into the gene of PAI-I between P2'-P3', generating a novel gene of PAI-1/EMP (PMP). It was cloned into pETlld expression vector, and a 43kDa protein was expressed in inclusion bodies with an expression level over 30%. The PMP protein was purified by DEAE ion-exchange chromatography to one band in SDS-PAGE (Silver Stained). The EPO activity of PMP was determined by Reticulocyte Counting Assay to be S000IU/mg, 2500 folds that of EMP (as reported).
Effect of Copper Ion on Conformations of Short Alanine-Based Peptides with Single TRP/HIS Stacking Interactions
Authors: Sugimoto Naoki , Zou Jin 
Published: December 2022

Abstract:
cu2+ has an apparent promoting effect on deaggregating β-sheet conformation, conformational
transitions from β-sheet to α-helix, and enhancing α-helix conformation of short alanine-based peptides with single Trp/His (W/H) stacking interactions in different geometrical spacings and positions, respectively.
Crystallization and A Preliminary Crystallographic Analysis of the Catalytic Domain of Chitinase Al from Bacillus Circulans WL-12
Authors: Katouda Haruhiko , Hashimoto Masayuki , Watanabe Takeshi , Matsumoto Takuo , Nonaka Takamasa , Mitsui Yukio 
Published: December 2022

Abstract:
The catalytic domain of chitinase Al from Bacillus circulans WL-12 was crystallized by vapor­ diffusion technique. The crystals belong to the triclinic space group Pl with cell dimensions a = 43.96A, b = 48.62A, c = 54.59A, a =108.90°, f3 = 95.06°, and y= 115.77°, and contain one molecule in the asymmetric unit. High-quality diffraction data were collected at 20°C with radiation from a synchrotron source up to 1.5A resolution.
Crystallization and Preliminary X-ray Crystallographic Studies of Ribonuclease LE from Lycopersicon esculentum
Authors: Nakamura Kazuo T. , Tanaka Nobutada , Arai Jun , lnokuchi Norio , Koyama Takashi , Ohgi Kazuko , Irie Masachika 
Published: December 2022

Abstract:
The ribonuclease LE, a plant ribonuclease from lycopersicon esculentum, has been crystallized by the hanging-drop vapour diffusion method using polyethylene glycol 1,540 as the precipitating agent. The
crystals belong to an orthorhombic space group P2,2,2, with cell dimensions of a = 74.10 A, b = 78.72 A, and c
= 33.00 A. There is one molecule per asymmetric unit. The crystals diffract to at least 2.0 A resolution and
are suitable for X-ray structure analysis at high resolution.
The cysteine-to-histidine substitution in domain of metallothionein enhances its zinc binding ability
Authors: Ru Binggen , Zhou Yanjiao , Zhang Ning , Li Lingyuan 
Published: December 2022

Abstract:
A two-step PCR method was taken to replace the cysteines at position 19, 29 in p domain of Metallothionein with histidines. Then the His19·29-mutant fragment was cloned into the vector pGEX-4T-l and expressed as a fusion protein of glutathione-S-transferase. After cleaved with thrombin and purified, the p domain with the substitution of Cys-to-His was obtained and identified by amino acid composition and molecular weight. The His19·29 mutant can bind with the same amount of zinc or cadmium ions as the p domain but exhibits stronger zinc binding ability and weaker cadmium binding ability.
Expression, purification, crystallization and preliminary x-ray analysis of the augmenter of liver regeneration
Authors: Wu Chia-Kuei , Dailey Tamara A. , Dailey Harry A. , Francavilla Antonio , Starzl Thomas E. , Wang Bi-Cheng , Rose John P. 
Published: December 2022

Abstract:
A novel grow.th factor termed augmenter of liver regeneration (ALR) coptaining an N-terrninal histidine tag has been expressed, purified and crystallized. The crystals diffract to beyond 2 A, belong to space group 141 with a= 99.8A and c = 113.4A, and have four molecules per asymmetric unit. Cadmium proved essential to the crystallization of the protein and the positions of four cadmium atoms have been determined by Bijvoet difference Patterson analysis. A possible role for cadmium stabilization of the his-tagged protein lattice is discussed.
Wolff rearrangement of Na-protected a-aminodiazoketones in presence of substituted phenol as a method for the synthesis of 2,4,5- trichlorophenyl esters of Fmoc-/ Boe-/ Z-P-homoamino acids
Authors: Babu Vommina V. Suresh , Gopi Hosahuciya N. , Ananda Kuppanna 
Published: December 2022

Abstract:
Silver acetate catalyzed decomposition of the Na-protected a­ aminodiazoketones in the presence of 'substituted phenol' and triethylamine at -
1s0c lead to 2,4,S-trichlorophenyl esters of Fmoc-/Boc-/Z-J3-homoamino acids in
good yield and purity. Thus the homologation of a-amino acids to 13-homoamino acids with concomitant active esters formation has been achieved by this method.
Cytotoxicity and membrane perturbation associated with the myristylated n-terminal portion of hiv-1 gag protein
Authors: Macreadie I. G. , Curtain C. C. 
Published: December 2022

Abstract:
The Gag and Nef proteins of human immunodeficiency type l (HIV-1) have conserved N-terminal sequences that appear essential for HIV-1 function. In view of the structural similarities a Gag peptide corresponding to myrGag2_22, was subjected to cytotoxicity tests employing recently developed cell assays. The Gag peptide displays a similar activity to Nef. The role of such sequences may be important in viral membrane association, viral biogenesis and transition of these proteins through the cellular membrane.
The specificity of enteropeptidase relative to the chimeric proteins and trypsinogen processing
Authors: Shibanova Elena , Alexandrov Sergey , Miroshnikov Ariatolii 
Published: December 2022

Abstract:
The limited proteolysis by enteropeptidase of the recombinant chimeric proteins incorporating the linker (Asp)4- Lys was studied. The resistant to the hydrolysis chimeric proteins was shown to be the competitive inhibitors in re­ lation to the effectively splitting chimeric proteins and to the low molecular intermediates of the linker, but not of the trypsinogen processing. The linker was shown to be defined the binding of the protein substrates by enzyme only, rather than the efficiency, determined by the C-terminal component of enzyme specificity.
Human nucleotide excision repair protein xpa: summary of exafs studies on the zn (ii), co (ii) and cd
(ii) associated minimal dna-binding domain
Authors: Kennedy Michael A. , Buchko Garry W. , Hess Nancy J. 
Published: December 2022

Abstract:
The zinc in the metal-binding core of the DNA-binding domain of the nucleotide excision repair protein XPA (M98-F219) can be replaced with cadmium (II) and cobalt (II). Here, we summarize extended X­ ray fine structure spectra collected on each protein in the lyophilized state and in 15% frozen aqueous glycerol solution. Under both conditions the Zn2•, Cd2+,and Co2• are tetrahedrally coordinated to the sulfur atom of four cysteine residues with the Zn-S and Co-S bond lengths nearly identical, at 2.34 A, and the Cd-S bond length at 2.54A.
Equilibrium unfolding of yeast triosephosphate isomerase: a monomeric intermediate in guanidine-hci and two-state behavior in urea
Authors: Vazquez-Contreras Edgar , Zubillaga Rafael A. , Mendoza-Hernandez Guillermo , Costast Miguel , Fernandez-Velascot D. Alejandro 
Published: December 2022

Abstract:
This is the first experimental evidence of an equilibrium intermediate in the unfolding of triosephosphate isomerase (TIM). The reversible unfolding of S. cerevisiae TIM induced by both guanidine­ HCl (Gdn-HCl) and urea, are apparently monophasic when followed by spectroscopic techniques. Kinetic analysis and ANS binding data confirm a two-state transition in urea. nevertheless, in Gdn-HCl they indicate an intermediate. Hydrodynamic properties of the intermediate are consistent with a compact monomer.
Occurrence of an essential amino acid residues in the lytic effect of escherichia coli a -haemolysin
Authors: Bakas Laura 
Published: December 2022

Abstract:
α-Hemolysin (HlyA), an extracellular protein toxin produced by some pathogenic strains of Escherichia coli , is known to disrupt eukaryotic cell membranes. In an attempt to correlate the structure of this toxin with its function, we studied the role of the histidine residues on the toxin activity by their chemical modification with the reagent diethyl pyrocarbonate (DEPC). The results of this study suggest the presence of an essential histidine residue at the Ca2+-binding motif and it.s role in the lytic action of E.coli HlyA.
Analysis of the membrane interactive potential of the escherichia coli pbp6b c-terminus
Authors: Phoenix David A. , Wallace James 
Published: December 2022

Abstract:
Escherichia coli low molecular weight penicillin binding proteins include PBP4,5,6 and recently PBP6b. PBP5 and PBP6 have been shown to possess C-terminal amphiphilic helical anchors. PBP4 has been shown to have the potential to interact at the membrane interface but the protein appears to bind via a different mechanism to PBP5 and PBP6. It has been suggested that since PBP6b has a high homology with PBP6 it also binds via an amphiphilic alpha helix. Here helical wheel, hydrophobic moment and DWIH analysis are used to show that the C-terminus of PBP6b does not resemble the anchor regions of the PBP5 and 6 but may stabilize membrane binding using a mechanism similar to that of PBP4.
Protein photodegradation in the fluorescence unfolding kinetics study of bromelain
Authors: Arroyo-Reyna Alfonso , Tello-Solis Salvador R. 
Published: December 2022

Abstract:
We have detected protein photodegradation in the fluorescence unfolding kinetics experiment of stem bromelain, a cysteine proteinase from the papain family. Thermally induced unfolding has been followed by near and far circular dichroism and tryptophan fluorescence emission. It was found that the fluorescence kinetics involves two phases. This biphasic nature results from ultraviolet induced photolysis oftryptophan.
Conformational changes of human neuronal tau during thermal and guanidine-hcl denatura tion
Authors: Be Rong-Qiao , Luo Jian-Ying , Liu Yang , Bua Qian 
Published: December 2022

Abstract:
Unfolding of human neuronal tau was studied during incubation with guanidine hydrochloride (GuBCI) and under thermal denaturation conditions. The intensity of the intrinsic fluorescence at 305 nm increased markedly in GuBCI solutions. Fluorescence quenching by potassium iodide showed that Tyr residues approached to the interior of the molecule during GuBCI denaturation. The difference ultraviolet absorbance at 215 nm showed a marked increase above 45°C. Light scattering of tau solution
· intensity decreased when temperature increased. Kinetics of the increase in the absorbance was a biphasic procedure. The first order rate of the fast phase was 1.84 x 10-1s-1 and that of the slow phase was
2.68 x 10-2s-1• The difference absorbance of tau was reversible. Kinetics of a decrease in the difference absorbance was a fast procedure during tau refolding. The first order rate of the fast phase was much greater than that of the unfolding procedure. This suggests that tau is not completely at a random conformation at room temperature.
Synthetic glycopeptide and phosphopeptide models of an antibacterial fragment of chromogranin A
Authors: Otvos, Jr. Laszlo , Cudic Mare , Bulet Philippe 
Published: December 2022

Abstract:
In order to fully characterize the activity spectrum and additional biochemical properties of native antimicrobial peptides corresponding to chromogranin A, we synthesized glycosylated, phosphorylated and double modified versions of the reportedly antibacterial 173-194 fragment. While no conformational change was detected, the modifications stabilized the peptide from proteolytic cleavage. All peptides remained inactive against a number of Gram-positive and Gram-negative bacterial strains in the experimental conditions use .
3D-structure of human seminal plasma prostatic inhibin by nonparametric regression
Authors: Jyothi S. , Joshi Rajani R. 
Published: December 2022

Abstract:
Human Seminal Plasma Prostatic Inhibin (HSPI) is a biologically important protein of 94 amino acids isolated from the human prostate glands. No information is yet available on its 3d-structure. Here, we use a nonparametric regression approach to determine the 3d-structure of HSPI. This approach has been validated earlier and is found to be better in accuracy and efficiency than other computational approaches. The structure predicted by us agrees with the properties ofHSPI deciphered experimentally.
Prediction of some spatial structures of proinsulin by hydropathic mass
Authors: HE Rong-Qiao , Liu Yang , Liu Ying 
Published: December 2022

Abstract:
Hydropathic mass (HM) has been used to display the characterization of hydrophilicity and hydrophobicity of proinsulin. The a-helix of the B chain (residues 9-19), which is located at the inner part of the crystalline insulin, possesses a strong positive HM. The proteolytic sites of proinsulin for insulin maturation are located in the most negative HM regions. This suggests that they are exposed to the exterior of the molecule, which contributes to the digestion by proteases during insulin maturing.
Conformation of the α-aminoacrylate intermediate of o-acetylserine sulfhydrylase from salmonella typhimurium as inferred by 31p nmr spectroscopy
Authors: Tai Chia-Hui , Cook Paul F. , Schnackerz Klaus D. 
Published: December 2022

Abstract:
31P NMR chemical shifts of the internal aldimine and the cx.-aminoacrylate intermediate of 0- acetylserine sulfhydrylase were determined and found to be 5.13 and 3.95 ppm, respectively. In addition, the line width decreases upon addition of OAS, suggesting a less restricted rotation around the CS'-0 bond of pyridoxal 5' -phosphate in the cx.-aminoacrylate intermediate The upfield shift of the cx.-aminoacrylate is similar to the behavior of the L-serine external Schiff base and may be interpreted as a loosening of the active site.
Simulation of the highly stable protein: bovine γb-crystallin at room and high temperature
Authors: Goodfellow Julia M. , Purkiss Andrew G. , Slingsby Christine 
Published: December 2022

Abstract:
The behavior of the eye-lens protein bovine γB-crystallin is investigated at both room temperature and at an elevated temperature (at which unfolding would be expected to occur) using molecular dynamics. Even in the high temperature simulation, there is little loss ·of secondary structure. Although only small changes in the tertiary contacts occur, even at high temperature, fluctuations in conformation are much more pronounced at 500K than 300K. These results agree with the experimental observations on the remarkable stability of the eye lens proteins and also indicate where the initial events in unfolding are occurring.
Molecular modeling of arcelin-5c from bean seeds and determination of its solution state
Authors: Cordeiro Artur T. , Gerhardt Isabel R. , de Oliveira-Neto Osmundo B. , Bloch Jr. Carlos , de Sa Maria Fatima Grossi 
Published: December 2022

Abstract:
Phaseo/us arcelin proteins are known to be involved in resistance mechanisms to bruchid pests in plants. The mechanism of action against the larvae is still unclear, but it seems to be related to the oligomeric state and stability of the protein in solution. The solution state of arcelin-5 variants was analyzed by size exclusion chromatography and a molecular model of arcelin-5c was built and compared with the structure of arcelin-1 and phytohemagglutin-L.
Expression and purification of human metallothionein-3 beta domain in e.coli
Authors: Wutt Daqing , Shen Jiong , Ru Binggen 
Published: December 2022

Abstract:
J3-domain of metallothionein-3/growth inhibitory factor(MT-3/GIF) is crucial to the neuronal growth inhibitory activity of MT-3. The MT-3 J3 domain was efficiently expressed as the soluble fusion form with GST protein at a high level which accounted for over 30% total cellular proteins. After the thrombin cleavage and purification, the bioactive recombinant MT-3 J3 domain was recovered with the yield of 6 mg/L of medium.
Crystallization and preliminary crystallographic studies of pekin duck oxyhemoglobin
Authors: Wang Huan-Chen , Zha Zheng , Liang Yu-He , Hua Zi-Qian , Lu Guang-Ying 
Published: December 2022

Abstract:
Pekin duck oxy hemoglobin has been purified and crystallized using PEG 6000 as precipitant. The crystal is of space group P41212 with lattice constants a= b = 81.23, c = 216.3 A. There is one tetramer molecule per asymmetric unit. The crystal diffracts up to 2,8 A resolution and is suitable for X-ray crystallographic studies.
Structural studies of a human malic enzyme
Authors: Tong Liang , Yang Zhiru 
Published: December 2022

Abstract:
Structural studies of the human mitochondrial NAD(Pt-dependent malic enzyme (m-NAD-ME) establish that malic enzymes belong to a new class of oxidative decarboxylases: An open and a closed form of the enzyme have been observed from the crystallographic analysis, with the closed form also revealing the binding modes of the divalent cation and the transition-state analog inhibitor oxalate. The structures show that E255, D256 and D279 are the ligands of the cation, and suggest that Y112 and K183 may be the catalytic residues of the enzyme.
Chemical mechanism of malic enzyme as determined by isotope effects and alternate substrates
Authors: Cleland W. W. 
Published: December 2022

Abstract:
Isotope effect studies have shown that malic enzyme from avian liver or Ascaris suum has a stepwise mechanism with NAD(P) as substrate, but a concerted one with nucleotide substrates with higher redox potentials. It has been possible to calculate intrinsic deuterium and 13C isotope effects and commitments. The enzyme is very
specific, with only erythro-fluoromalate, D- and mesotartrate and L-aspartate with an unprotonated amino group as slow alternate substrates.
Chemical mechanism of 6-phosphogluconate dehydrogenase via kinetic studies and site­ directed mutagenesis
Authors: Cook Paul F. , Zhang Lei 
Published: December 2022

Abstract:
6-Phosphogluconate dehydrogenase catal)jzes the metal ion-independent oxidative decarboxylation of 6- phosphogluconate (6PG). The enzyme catalyzes a reaction in which 6PG is first oxidized at the 3-position, then decarboxylated to the 1,2-enediol of Ru5P , and then tautomerized to give the Ru5P ketone product. In the reaction, Kl83 acts as a general base, general acid, shuttling a proton between the 3-hydroxyl and itself, and E190 acts as a general acid to protonate C1 of the enediol intermediate in the tautomerization step.
6-Phosphogluconate dehydrogenase: Structural symmetry and functional asymmetry
Authors: Dallocchio Franco , Rippa Mario , Hanau Stefania , Cervellati Carlo 
Published: December 2022

Abstract:
6-Phosphogluconate dehydrogenase catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate through an oxidation, a decarboxylation and a tautomerization. The two subunits in the crystals of the dimeric sheep liver enzyme have the same conformation, as the apoenzyme and with the substrate or coenzyme. An hypothesis is now advanced that in solution, during catalysis, the two subunits have a different alternating role and thus a functional asymmetry.
Synthesis of peptide with multiple cysteic acids
Authors: Arendt Anatol , McDowell J. Hugh , Smith W. Clay , Hargrave Paul A. 
Published: December 2022

Abstract:
We have synthesized and purified a 19-amino acid peptide whose sequence is derived from the carboxyl-terminal region of bovine rhodopsin, in which the seven serines and threonines that would normally become phosphorylated have been substituted with cysteic acid. The peptide was synthesized by the Fmoc (DCC/HOBl)' procedure using Fmoc-(S-4-methoxytrityl) Cys {Fmoc-Cys(Mmt)-OH}. The Mmt group was removed and the resin-bound peptide was oxidized with performic acid, which also removed other blocking grou_psand cleaved the peptide from the resin.