bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteolytic mapping of heat shock transcription factor domains
Authors: Zhong Min , Wu Carl 
Published: February 2009

AbstractHeat shock transcription factors (HSFs) of higher eukaryotes respond to physical and cellular stress signals by tri‐merizing, binding to a specific site on DNA, and transactivating genes encoding the heat shock proteins. In this work, limited proteolysis was used as a biochemical probe of the domain organization of Drosophila HSF. Both unshocked monomelic and heat‐shocked trimeric HSF possess an internal protease‐sensitive region located between the aminoterminal and carboxyl‐terminal hydrophobic heptad repeats, suggesting that this is a less structured region compared to those defined for DNA‐binding, trimerization, and transactivation. For a few cleavage sites, the heat‐shocked form of HSF is more accessible to proteases than the unshocked form, providing an additional diagnostic marker for inducible changes in conformation or modification between the latent and activated forms of HSF.
Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction
Authors: Donate Luis E. , Rufino Stephen D. , Canard Luc H.J. , Blundell Tom L. 
Published: February 2009

AbstractLoops are regions of nonrepetitive conformation connecting regular secondary structures. We identified 2,024 loops of one to eight residues in length, with acceptable main‐chain bond lengths and peptide bond angles, from a database of 223 protein and protein‐domain structures. Each loop is characterized by its sequence, main‐chain conformation, and relative disposition of its bounding secondary structures as described by the separation between the tips of their axes and the angle between them. Loops, grouped according to their length and type of their bounding secondary structures, were superposed and clustered into 161 conformational classes, corresponding to 63% of all loops. Of these, 109 (51% of the loops) were populated by at least four nonhomologous loops or four loops sharing a low sequence identity. Another 52 classes, including 12% of the loops, were populated by at least three loops of low sequence similarity from three or fewer nonhomologous groups. Loop class suprafamilies resulting from variations in the termini of secondary structures are discussed in this article. Most previously described loop conformations were found among the classes. New classes included a 2:4 type IV hairpin, a helix‐capping loop, and a loop that mediates dinucleotide‐binding. The relative disposition of bounding secondary structures varies among loop classes, with some classes such as β‐hairpins being very restrictive. For each class, sequence preferences as key residues were identified; those most frequently at these conserved positions than in proteins were GIy, Asp, Pro, Phe, and Cys. Most of these residues are involved in stabilizing loop conformation, often through a positive ø conformation or secondary structure capping. Identification of helix‐capping residues and β‐breakers among the highly conserved positions supported our decision to group loops according to their bounding secondary structures. Several of the identified loop classes were associated with specific functions, and all of the member loops had the same function; key residues were conserved for this purpose, as is the case for the parvalbumin‐like calcium‐binding loops. A significant number, but not all, of the member loops of other loop classes had the same function, as is the case for the helix‐turn‐helix DNA‐binding loops. This article provides a systematic and coherent conformational classification of loops, covering a broad range of lengths and all four combinations of bounding secondary structure types, and supplies a useful basis for modelling of loop conformations where the bounding secondary structures are known or reliably predicted.
Deglycosylation of proteins for crystallization using recombinant fusion protein glycosidases
Authors: Grueninger‐Leitch Fiona , D'Arcy Allan , D'Arcy Brigitte , Chène Christiane 
Published: February 2009

AbstractObtaining high quality protein crystals remains a rate‐limiting step in the determination of three‐dimensional X‐ray structures. A frequently encountered problem in this respect is the high or heterogeneous carbohydrate content of many eukaryotic proteins. A number of reports have demonstrated the use of enzymatic deglycosylation in the crystallization of certain glycoproteins. Although this is an attractive tool, there are some problems that hinder the more widespread use of glycosidases in crystallization. First, commercially available glycosidases are relatively expensive, which virtually prohibits their use on a large scale. Second, the glycosidase must be removed from the glycoprotein of interest following deglycosylation, which is not always straightforward. To circumvent these problems we have cloned the two most generally useful glycosidases, peptide‐N‐glycosidase F and endoglycosidase F1 from Flavobacterium meningosepticum, as fusion proteins with glutathione S‐transferase. The fusion not only allows rapid purification of these enzymes from Escherichia coli cell extracts, but also permits rapid removal from target proteins following deglycosylation. We have used these enzymes to obtain crystals of phytase from Aspergillus ficuum and acid phosphatase from Aspergillus niger and to obtain a new crystal form of recombinant human renin.
The N‐terminal domains of tensin and auxilin are phosphatase homologues
Authors: Haynie Donald T. , Ponting Christopher P. 
Published: February 2009

AbstractTensin, an actin filament capping protein, and auxilin, a component of receptor‐mediated endocytosis, are known to have 350 residue regions of significant sequence similarity near their N‐termini (Schröder et al., 1995, Eur J Biochem 228:297–304). Here we demonstrate that these regions are homologous, not only to each other, but also to the catalytic domain of a putative protein tyrosine phosphatase (PTP) from Saccharomyces cerevisiae and to other PTPs. We propose that the PTP‐like portion of the homology region of tensin and auxilin represents a distinct domain. A detailed sequence comparison indicates that the PTP‐like domain in tensin is unlikely to exhibit phosphatase activity, whereas in auxilin it may possess a different phosphatase specificity from tyrosine phosphatases. It is probable that the PTP‐like domains in tensin and auxilin mediate binding interactions with phosphorylated polypeptides; they may therefore represent members of a distinct class of phosphopeptide recognition domain.
Insights into the local residual entropy of proteins provided by NMR relaxation
Authors: Li Zhigang , Raychaudhuri Soumya , Wand A. Joshua 
Published: February 2009

AbstractA simple model is used to illustrate the relationship between the dynamics measured by NMR relaxation methods and the local residual entropy of proteins. The expected local dynamic behavior of well‐packed extended amino acid side chains are described by employing a one‐dimensional vibrator that encapsulates both the spatial and temporal character of the motion. This model is then related to entropy and to the generalized order parameter of the popular “model‐free” treatment often used in the analysis of NMR relaxation data. Simulations indicate that order parameters observed for the methyl symmetry axes in, for example, human ubiquitin correspond to significant local entropies. These observations have obvious significance for the issue of the physical basis of protein structure, dynamics, and stability.
Interleukin‐6: Structure‐function relationships
Authors: Simpson Richard J. , Hammacher Annet , Smith David K. , Matthews Jacqueline M. , Ward Larry D. 
Published: February 2009

AbstractInterleukin‐6 (IL‐6) is a multifunctional cytokine that plays a central role in host defense due to its wide range of immune and hematopoietic activities and its potent ability to induce the acute phase response. Overexpression of IL‐6 has been implicated in the pathology of a number of diseases including multiple myeloma, rheumatoid arthritis, Castleman's disease, psoriasis, and post‐menopausal osteoporosis. Hence, selective antagonists of IL‐6 action may offer therapeutic benefits. IL‐6 is a member of the family of cytokines that includes interleukin‐11, leukemia inhibitory factor, oncostatin M, cardiotrophin‐1, and ciliary neurotrophic factor. Like the other members of this family, IL‐6 induces growth or differentiation via a receptor‐system that involves a specific receptor and the use of a shared signaling subunit, gp130. Identification of the regions of IL‐6 that are involved in the interactions with the IL‐6 receptor and gp130 is an important first step in the rational manipulation of the effects of this cytokine for therapeutic benefit. In this review, we focus on the sites on IL‐6 which interact with its low‐affinity specific receptor, the IL‐6 receptor, and the high‐affinity converter gp130. A tentative model for the IL‐6 hexameric receptor ligand complex is presented and discussed with respect to the mechanism of action of the other members of the IL‐6 family of cytokines.
Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: Application in predicting the three‐dimensional structure of murine homeodomain Msx‐1
Authors: Li Haicheng , Tejero Roberto , Monleon Daniel , Bassolino‐Klimas Donna , Abate‐Shen Cory , Bruccoleri Robert E. , Montelione Gaetano T. 
Published: February 2009

AbstractWe have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137–168). The accuracy of the method is validated by “predicting” structures of two homeodomain proteins with known three‐dimensional structures, and then applied to predict the three‐dimensional structure of the homeodomain of the murine Msx‐1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by “homology distance constraints,” whereas the conformations of nonhomologous regions of the unknown protein are defined only by the potential energy function. A full energy function (excluding explicit solvent) is employed to ensure that the calculated structures have good conformational energies and are physically reasonable. As in NMR structure determinations, information on the consistency of the structure prediction is obtained by superposition of the resulting family of protein structures. In this paper, our homology modeling algorithm is described and compared with related homology modeling methods using spatial constraints derived from the structures of homologous proteins. The software is then used to predict the DNA‐bound structures of three homeodomain proteins from the X‐ray crystal structure of the engrailed homeodomain protein (Kissinger CR et al., 1990, Cell 63:579–590). The resulting backbone and side‐chain conformations of the modeled yeast Matα2 and D. melanogaster Antennapedia homeodomains are excellent matches to the corresponding published X‐ray crystal (Wolberger C et al., 1991, Cell 67:517–528) and NMR (Billeter M et al., 1993, J Mol Biol 234:1084–1097) structures, respectively. Examination of these structures of Msx‐1 reveals a network of highly conserved surface salt bridges that are proposed to play a role in regulating protein–protein interactions of homeodomains in transcription complexes.
Three‐dimensional structures of glycolate oxidase with bound active‐site inhibitors
Authors: Stenberg Kaj , Lindqvist Ylva 
Published: February 2009

AbstractA key step in plant photorespiration, the oxidation of glycolate to glyoxylate, is carried out by the peroxisomal flavoprotein glycolate oxidase (EC 1.1.3.15). The three‐dimensional structure of this α/β barrel protein has been refined to 2 Å resolution (Lindqvist Y. 1989. J Mol Biol 209:151‐166). FMN dependent glycolate oxidase is a member of the family of α‐hydroxy acid oxidases. Here we describe the crystallization and structure determination of two inhibitor complexes of the enzyme, TKP (3‐Decyl‐2,5‐dioxo‐4‐hydroxy‐3‐pyrroline) and TACA (4‐Carboxy‐5‐(1‐pentyl)hexylsulfanyl‐1,2,3‐triazole). The structure of the TACA complex has been refined to 2.6 Å resolution and the TKP complex, solved with molecular replacement, to 2.2 Å resolution. The Rfree for the TACA and TKP complexes are 24.2 and 25.1%, respectively. The overall structures are very similar to the unliganded holoenzyme, but a closer examination of the active site reveals differences in the positioning of the flavin isoalloxazine ring and a displaced flexible loop in the TKP complex. The two inhibitors differ in binding mode and hydrophobic interactions, and these differences are reflected by the very different Ki values for the inhibitors, 16 nM for TACA and 4.8 μM for TKP. Implications of the structures of these enzyme‐inhibitor complexes for the model for substrate binding and catalysis proposed from the holo‐enzyme structure are discussed.
The role of divalent cations in structure and function of murine adenosine deaminase
Authors: Cooper Bruce F. , Sideraki Vera , Wilson David K. , Dominguez David Y. , Clark Sandra W. , Quiocho Florante A. , Rudolph Frederick B. 
Published: February 2009

AbstractFor murine adenosine deaminase, we have determined that a single zinc or cobalt cofactor bound in a high affinity site is required for catalytic function while metal ions bound at an additional site(s) inhibit the enzyme. A catalytically inactive apoenzyme of murine adenosine deaminase was produced by dialysis in the presence of specific zinc chelators in an acidic buffer. This represents the first production of the apoenzyme and demonstrates a rigorous method for removing the occult cofactor. Restoration to the holoenzyme is achieved with stoichiometric amounts of either Zn2+ or Co2+ yielding at least 95% of initial activity. Far UV CD and fluorescence spectra are the same for both the apo‐ and holoenzyme, providing evidence that removal of the cofactor does not alter secondary or tertiary structure. The substrate binding site remains functional as determined by similar quenching measured by tryptophan fluorescence of apo‐ or holoenzyme upon mixing with the transition state analog, deoxycoformycin. Excess levels of adenosine or N6‐methyladenosine incubated with the apoenzyme prior to the addition of metal prevent restoration, suggesting that the cofactor adds through the substrate binding cleft. The cations Ca2+, Cd2+ Cr2+, Cu+, Cu2+, Mn2+, Fe2+, Fe3+, Pb2+, or Mg2+ did not restore adenosine deaminase activity to the apoenzyme. Mn2+, Cu2+, and Zn2+ were found to be competitive inhibitors of the holoenzyme with respect to substrate and Cd2+ and Co2+ were noncompetitive inhibitors. Weak inhibition (Ki ≥ 1000 μM) was noted for Ca2+, Fe2+, and Fe3+.
Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide‐protein interactions
Authors: Meyer Joachim E. W. , Schulz Georg E. 
Published: February 2009

AbstractThe crystal structure of the maltodextrin‐specific porin from Salmonella typhimurium ligated with a maltotrioside at the pore eyelet is known at 2.4 Å resolution. The three glucose units assume a conformation close to the natural amylose helix. The pore eyelet fits exactly the cross‐section of a maltooligosaccharide chain and thus functions as a constraining orifice. The oligomer permeates the membrane by screwing along the amylose helix through this orifice. Because each glucose glides along the given helix, its interactions can be sampled at any point along the pathway. The interactions are mostly hydrogen bonds, but also contacts to aromatic rings at one side of the pore. We have derived the energy profile of a gliding maltooligosaccharide by following formation and breakage of hydrogen bonds and by assessing the saccharide‐aromatics interactions from a statistical analysis of saccharide binding sites in proteins. The resulting profile indicates smooth permeation despite extensive hydrogen bonding at the orifice.
Kaj Ulrik Linderstrøm‐Lang (1896–1959)
Authors: Schellman John A. , Schellman Charlotte G. 
Published: February 2009

AbstractThe Carlsberg Laboratory in Copenhagen has had a long tradition of outstanding science. At the time covered by this discussion, Kjeldahl, Sørensen, and Linderstrøm–Lang had been consecutive directors of the Chemical Laboratory for 83 years. Lang's inspired leadership began in the 1930s with a number of innovations (study of metabolism in single cells, titrations in non–aqueous solvents, relation of proteolysis to structure) but it was not until the early 1950s that Denmark had sufficiently recovered from the war for the laboratory to enter world science again. During World War II, Lang had been active in the Danish resistance movement.After the war, a number of major advances were being made that would revolutionize the field of protein chemistry (Pauling and Corey's H–bonded structures, Sanger's sequencing techniques, chromatography, Watson and Crick structures, modern instrumentation). The time for the new field of the physical biochemistry of proteins had arrived. Lang, with his broad experience, adventurous spirit, and genius for innovation, created an environment that was ideal for the convergence of these disconnected advances into a uniform science. The emphasis was to be on quantitative measurements on proteins in solution with interpretations based on molecular structures.During an all‐too–brief period of time, Lang's laboratory attracted a large fraction of those who were destined to be the leaders of the next generation of protein chemists. At this time, the Carlsberg Laboratory was probably the most scientifically exciting environment for a protein chemist. The methods developed at that time–hydrogen exchange, limited proteolysis, optical rotatory dispersion, volume changes accompanying protein reactions, automatic titrations– are still all in common use and many of the visitors to the laboratory in that period and their students are still playing major roles in protein research.Lang's other qualities should not be ignored. He was not only a great scientist but also a musician, raconteur, artist, and an exceptionally warm and compassionate human being.
Comparison of high‐resolution structures of the diphtheria toxin repressor in complex with cobalt and zinc at the cation‐anion binding site
Authors: Pohl Ehmke , Qiu Xiayang , Must Lisa M. , Holmes Randall K. , Hol Wim G. J. 
Published: February 2009

AbstractThe diphtheria toxin repressor (DtxR) from Coryne‐bacterium diphtheriae is a divalent‐metal activated repressor of chromosomal genes responsible for siderophore‐mediated iron‐uptake and of a gene on several corynebacteriophages that encodes diphtheria toxin. Even though DtxR is the best characterized iron‐dependent repressor to date, numerous key properties of the protein still remain to be explained. One is the role of the cation‐anion pair discovered in its first metal‐binding site. A second is the reason why zinc exhibits its activating effect only at a concentration 100‐fold higher than other divalent cations.In the presently reported 1.85 Å resolution Co‐DtxR structure at 100K, the sulfate anion in the cation‐anion‐binding site interacts with three side chains that are all conserved in the entire DtxR family, which points to a possible physiological role of the anion.A comparison of the 1.85 Å Cobalt‐DtxR structure at 100K and the 2.4 Å Zinc‐DtxR structure at room temperature revealed no significant differences. Hence, the difference in efficiency of Co2+ and Zn2+ to activate DtxR remains a mystery and might be hidden in the properties of the intriguing second metal‐binding site. Our studies do, however, provide a high resolution view of the cation‐anion‐binding site that has most likely evolved to interact not only with a cation but also with the anion in a very precise manner.
The chemistry and enzymology of the type I signal peptidases
Authors: Dalbey Ross E. , Lively Mark O. , Bron Sierd , Dijl Jan Maarten Van 
Published: February 2009

AbstractThe discovery that proteins exported from the cytoplasm are typically synthesized as larger precursors with cleavable signal peptides has focused interest on the peptidases that remove the signal peptides. Here, we review the membrane‐bound peptidases dedicated to the processing of protein precursors that are found in the plasma membrane of prokaryotes and the endoplasmic reticulum, the mitochondrial inner membrane, and the chloroplast thylakoidal membrane of eukaryotes. These peptidases are termed type I signal (or leader) peptidases. They share the unusual feature of being resistant to the general inhibitors of the four well‐characterized peptidase classes. The eukaryotic and prokaryotic signal peptidases appear to belong to a single peptidase family. This review emphasizes the evolutionary concepts, current knowledge of the catalytic mechanism, and substrate specificity requirements of the signal peptidases.
Structural basis for the negative allostery between Ca2+‐ and Mg2+ ‐binding in the intracellular Ca2+ ‐receptor calbindin D9k
Authors: Andersson Maria , Ivarsson Ianrik , Anders Svensson L. , Malmendal Anders , Linse Sara , Forsén Sture 
Published: February 2009

AbstractThe three‐dimensional structures of the magnesium‐ and manganese‐bound forms of calbindin D9% were determined to 1.6 Å and 1.9 Å resolution, respectively, using X‐ray crystallography. These two structures are nearly identical but deviate significantly from both the calcium bound form and the metal ion‐free (apo) form. The largest structural differences are seen in the C‐terminal EF‐hand, and involve changes in both metal ion coordination and helix packing. The N‐terminal calcium binding site is not occupied by any metal ion in the magnesium and manganese structures, and shows little structural deviation from the apo and calcium bound forms. 1 H‐NMR and UV spectroscopic studies at physiological ion concentrations show that the C‐terminal site of the protein is significantly populated by magnesium at resting cell calcium levels, and that there is a negative allosteric interaction between magnesium and calcium binding. Calcium binding was found to occur with positive cooperativity at physiological magnesium concentration.