bluuebunny/crossref_metadata_2025_split huggingface dataset:
Slipped capital femoral epiphysis
Authors: Billing L. , Bogren H. G. , Henrikson B. , Wallin J. 
Published: February 2005

This particular ailment has many designations in the literature but none is quite adequate. Here we use the terminology slipped capital femoral epiphysis (SCFE). The anatomy of the proximal femur in all mammals reflects their growth and function. The main forces acting on the head are perpendicular to the growth plate. The thick tear‐proof perichondrium‐periosteum on the femoral neck is like a stocking attached to the epiphysis and the trochanter region. Growth in length causes a strong tensile stress in the periosteum, pressing the epiphysis against the metaphysis and thus stabilizing the vulnerable growth plate—the periosteum theory. Several factors may diminish the stability of the growth plate. SCFE begins with fissures, which coalesce to a fracture in the growth plate, invisible on a radiograph. As the slip progresses, an increasing angulation between the epiphysis and the remainder of the femur occurs. Weight and muscular forces displace the epiphysis posteriorly in a flexed hip. A rift in the ventral half of the periosteal stocking occurs at the border to the perichondrium and, after that, a longitudinal rift in the periosteum at the anterior midline of the femoral neck. This rift becomes broader as the epiphysis slips posteriorly, withdrawing the ruptured periosteum. Displacement of the epiphysis is due to a rotational slip and tilt, made possible by a compression fracture in the posterior part of the metaphysis. Parts of the periosteum function as reins steering the slip direction and counteracting the displacement. SCFE may be regarded as a pseudoarthrosis in the growing cartilage of the plate. The periosteum theory extended to a pseudoarthrosis theory has been supported by findings at surgery and on true lateral radiographs of usual and unusual cases of SCFE presented in this opus. On a true lateral view, the displacement can be measured as the slipping angle (SA) based on anatomical and geometrical considerations. SA values from 95 normal hips and from 22 contralateral asymptomatic hips from SCFE patients are presented in a histogram and bar graph. Statistically, SCFE is always bilateral, but in about 1/3 of the asymptomatic, contralateral hips, the physis ossifies and closes with SA below 13°, and surgery is not necessary. It is most important that the position of the femur on the X‐ray table is exactly defined in two dimensions: 1) the angle between the femoral shaft and the tabletop (angle of elevation), 2) the degree of rotation of the femur around its axis. A precisely defined positioning of the femur is a prerequisite for an exact reproducible measurement of the SA on a true lateral view and is also valuable for the evaluation of radiographic “signs”. An aid, the Youth Hip Triangle (YHT), has been designed to facilitate positioning of the femur and measurement of SA. YHT is recommended for routine use in every X‐ray facility. The method is quick, cost effective and makes it possible to diagnose SCFE in the contralateral hip before clinical signs or symptoms have occurred.
Protein aggregation determinants from a simplified model: Cooperative folders resist aggregation
Authors: Clark Louis A. 
Published: February 2005

AbstractTwo‐chain aggregation simulations using minimalist models of proteins G, L, and mutants were used to investigate the fundamentals of protein aggregation. Mutations were selected to break up repeats of hydrophobic beads in the sequence while maintaining native topology and folding ability. Data are collected under conditions in which all chain types have similar folded populations and after equilibrating the separated chains to minimize competition between folding and aggregation. Folding cooperativity stands out as the best single‐chain determinant under these conditions and for these simple models. It can be experimentally measured by the width of the unfolding transition during thermal denaturation and loosely related to population of intermediate‐like states during folding. Additional measures of cooperativity and other properties such as radius of gyration fluctuations and patterning of hydrophobic residues are also examined. Initial contact system states with transition‐state characteristics can be identified and are more expanded than average initial contact states. Two‐chain minimalist model aggregates are considerably less structured than their native states and have minimal domain‐swapping features.
The crystal structure of rabbit phosphoglucose isomerase complexed with D‐sorbitol‐6‐phosphate, an analog of the open chain form of D‐glucose‐6‐phosphate
Authors: Lee Ji Hyun , Jeffery Constance J. 
Published: February 2005

AbstractPhosphoglucose isomerase (PGI) catalyzes the isomerization of D‐glucose‐6‐phosphate (G6P) and D‐fructose‐6‐phosphate (F6P) in glycolysis and gluconeogenesis. Analysis of previously reported X‐ray crystal structures of PGI without ligand, with the cyclic form of F6P, or with inhibitors that mimic the cis‐enediol intermediate led to proposed mechanisms for the ring opening and isomerization steps in the multistep catalytic mechanism. To help complete our model of the overall mechanism, information is needed about the state of PGI between the ring opening and isomerization steps, in other words, a structure of the enzyme complexed with the open form of a substrate or an analog. Here, we report the crystal structure of rabbit PGI complexed with D‐sorbitol‐6‐phosphate (S6P), an analog of the open chain form of G6P, at 2.0 Å resolution. As was seen in the PGI/F6P structure, a helix containing amino acid residues 512–520 is found in the “out” position, which provides sufficient space in the active site for a substrate in its cyclic form and which is probably the location of that helix just after ring opening (or just before ring closure). However, the S6P ligand is in an extended conformation, as was seen previously with ligands that mimic the cis‐enediol intermediate. The extended conformation enables the ligand to interact with Glu357, which transfers a proton during the isomerization step. The PGI/S6P structure represents the conformation of the enzyme and substrate between the ring opening (or ring closing) step and the isomerization step and helps to complete the model for PGI's catalytic mechanism.
Identification of the ligand binding sites on the molecular surface of proteins
Authors: Kinoshita Kengo , Nakamura Haruki 
Published: February 2005

AbstractIdentification of protein biochemical functions based on their three‐dimensional structures is now required in the post–genome‐sequencing era. Ligand binding is one of the major biochemical functions of proteins, and thus the identification of ligands and their binding sites is the starting point for the function identification. Previously we reported our first trial on structure‐based function prediction, based on the similarity searches of molecular surfaces against the functional site database. Here we describe the extension of our first trial by expanding the search database to whole heteroatom binding sites appearing within the Protein Data Bank (PDB) with the new analysis protocol. In addition, we have determined the similarity threshold line, by using 10 structure pairs with solved free and complex structures. Finally, we extensively applied our method to newly determined hypothetical proteins, including some without annotations, and evaluated the performance of our methods.
Analysis of subsecond protein dynamics by amide hydrogen exchange and mass spectrometry using a quenched‐flow setup
Authors: Rist Wolfgang , Rodriguez Fernanda , Jørgensen Thomas J.D. , Mayer Matthias P. 
Published: February 2005

AbstractAmide hydrogen exchange (HX) in combination with mass spectrometry (MS) is a powerful tool to analyze the folding and dynamics of proteins. In the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. Some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform HX at shorter time intervals down to the limit set by the intrinsic chemical exchange rate. We now report the development of the first completely on‐line quenched‐flow setup that allows the performance of HX experiments in the 100‐sec to 30‐sec time scale, on‐line proteolytic digestion using immobilized proteases, rapid desalting, and MS analysis. We show that conformational fluctuations in the range of seconds can be detected and protection factors as small as 10 reproducibly determined. Using this setup we investigated the conformational properties of Escherichia coli heat‐shock transcription factor σ32 free in solution. Our results indicate that the C‐terminal σ4 domain of σ32, which is responsible for the recognition of the −35 region of heat shock promoters, contains more extensive secondary structure than expected when compared with the structure of the homologous σ‐factor σA in complex with the RNA‐polymerase. This setup should be very useful for a more accurate analysis of structural motions in proteins in the subsecond to second time scale relevant to allostery and enzyme function.
Structural features of the focal adhesion kinase–paxillin complex give insight into the dynamics of focal adhesion assembly
Authors: Bertolucci Craig M. , Guibao Cristina D. , Zheng Jie 
Published: February 2005

AbstractThe C‐terminal region of focal adhesion kinase (FAK) consists of a right‐turn, elongated, four‐helix bundle termed the focal adhesion targeting (FAT) domain. The structure of this domain is maintained by hydrophobic interactions, and this domain is also the proposed binding site for the focal adhesion protein paxillin. Paxillin contains five well‐conserved LD motifs, which have been implicated in the binding of many focal adhesion proteins. In this study we determined that LD4 binds specifically to only a single site between the H2 and H3 helices of the FAT domain and that the C‐terminal end of LD4 is oriented toward the H2‐H3 loop. Comparisons of chemical‐shift perturbations in NMR spectra of the FAT domain in complex with the binding region of paxillin and the FAT domain bound to both the LD2 and LD4 motifs allowed us to construct a model of FAK–paxillin binding and suggest a possible mechanism of focal adhesion disassembly.
Polymerization of the SAM domain of MAPKKK Ste11 from the budding yeast: Implications for efficient signaling through the MAPK cascades
Authors: Bhattacharjya Surajit , Xu Ping , Chakrapani Mukundan , Johnston Linda , Ni Feng 
Published: February 2005

AbstractThe sterile α‐motif (SAM) is a protein module ∼70 residues long and mainly involved in the protein–protein interactions of cell signaling and transcriptional repression. The SAM domain of the yeast MAPKKK Ste11 has a well‐folded dimeric structure in solution. Interestingly, the well‐folded dimer of the Ste11 SAM undergoes a time‐dependent self‐assembly upon lowering of the pH, leading to the formation of high molecular weight oligomers. The oligomeric structures rapidly disassemble to the well‐folded dimer upon reversal of the pH to close to neutral conditions. Circular dichroism (CD) and atomic force microscopy (AFM) experiments demonstrate that the oligomeric structure formed at pH 5.0 appears to be highly helical and has architecture akin to proto‐fibrils. Residue‐specific kinetics of pH‐triggered oligomerization obtained from real‐time 15N‐1H HSQC experiments indicate that the dimer‐oligomer transition appears to involve all residues of the well‐folded dimeric structure of the Ste11 SAM. Very interestingly, the interactions of the Ste11 and Ste50 SAM domains also lead to the formation of non‐homogeneous hetero‐complexes with significant populations of high molecular weight aggregates. AFM imaging shows that the Ste11‐Ste50 hetero‐polymeric aggregates assume the shapes of circular nano‐particles with dimensions of 50–60 nano‐meters (nm), in contrast to the proto‐fibrils formed by the Ste11 SAM domain alone. Such intrinsic propensity for dimer to oligomer transition of the Ste50‐binding SAM domain of Ste11 may endow the MAPKKK Ste11 with unique functional properties required for efficient and high fidelity signal transduction in the budding yeast.
An efficient strategy for high‐throughput expression screening of recombinant integral membrane proteins
Authors: Eshaghi Said , Hedrén Marie , Nasser Marina Ignatushchenko Abdel , Hammarberg Tove , Thornell Anders , Nordlund Pär 
Published: February 2005

AbstractThe recombinant expression of integral membrane proteins is considered a major challenge, and together with the crystallization step, the major hurdle toward routine structure determination of membrane proteins. Basic methodologies for high‐throughput (HTP) expression optimization of soluble proteins have recently emerged, providing statistically significant success rates for producing such proteins. Experimental procedures for handling integral membrane proteins are generally more challenging, and there have been no previous comprehensive reports of HTP technology for membrane protein production.Here, we present a generic and integrated parallel HTP strategy for cloning and expression screening of membrane proteins in their detergent solubilized form. Based on this strategy, we provide overall success rates for membrane protein production in Escherichia coli, as well as initial benchmarking statistics of parameters such as expression vectors, strains, and solubilizing detergents. The technologies were applied to 49 E. coli integral membrane proteins with human homologs and revealed that 71% of these proteins could be produced at sufficient levels to allow milligram amounts of protein to be relatively easily purified, which is a significantly higher success rate than anticipated. We attribute the high success rate to the quality and robustness of the methodology used, and to introducing multiple parameters such as different vectors, strains, and detergents. The presented strategy demonstrates the usefulness of HTP technologies for membrane protein production, and the feasibility of large‐scale programs for elucidation of structure and function of bacterial integral membrane proteins.
All three Ca2+‐binding loops of photoproteins bind calcium ions: The crystal structures of calcium‐loaded apo‐aequorin and apo‐obelin
Authors: Deng Lu , Vysotski Eugene S. , Markova Svetlana V. , Liu Zhi‐Jie , Lee John , Rose John , Wang Bi‐Cheng 
Published: February 2005

AbstractThe crystal structures of calcium‐loaded apoaequorin and apo‐obelin have been determined at resolutions 1.7 Å and 2.2 Å, respectively. A calcium ion is observed in each of the three EF‐hand loops that have the canonical calcium‐binding sequence, and each is coordinated in the characteristic pentagonal bipyramidal configuration. The calcium‐loaded apo‐proteins retain the same compact scaffold and overall fold as the unreacted photoproteins containing the bound substrate, 2‐hydroperoxycoelenterazine, and also the same as the Ca2+‐discharged obelin bound with the product, coelenteramide. Nevertheless, there are easily discerned shifts in both helix and loop regions, and the shifts are not the same between the two proteins. It is suggested that these subtle shifts are the basis of the ability of these photoproteins to sense Ca2+ concentration transients and to produce their bioluminescence response on the millisecond timescale. A mechanism of intrastructural transmission of the calcium signal is proposed.
The orientations of cytochrome c in the highly dynamic complex with cytochrome b5 visualized by NMR and docking using HADDOCK
Authors: Volkov Alexander N. , Ferrari Davide , Worrall Jonathan A.R. , Bonvin Alexandre M.J.J. , Ubbink Marcellus 
Published: February 2005

AbstractThe interaction of bovine microsomal ferricytochrome b5 with yeast iso‐1‐ferri and ferrocytochrome c has been investigated using heteronuclear NMR techniques. Chemical‐shift perturbations for 1H and 15N nuclei of both cytochromes, arising from the interactions with the unlabeled partner proteins, were used for mapping the interacting surfaces on both proteins. The similarity of the binding shifts observed for oxidized and reduced cytochrome c indicates that the complex formation is not influenced by the oxidation state of the cytochrome c. Protein–protein docking simulations have been performed for the binary cytochrome b5–cytochrome c and ternary (cytochrome b5)–(cytochrome c)2 complexes using a novel HADDOCK approach. The docking procedure, which makes use of the experimental data to drive the docking, identified a range of orientations assumed by the proteins in the complex. It is demonstrated that cytochrome c uses a confined surface patch for interaction with a much more extensive surface area of cytochrome b5. Taken together, the experimental data suggest the presence of a dynamic ensemble of conformations assumed by the proteins in the complex.
Crystal structure of the pyridoxal‐5′‐phosphate‐dependent serine dehydratase from human liver
Authors: Sun Lei , Bartlam Mark , Liu Yiwei , Pang Hai , Rao Zihe 
Published: February 2005

AbstractL‐serine dehydratase (SDH), a member of the β‐family of pyridoxal phosphate‐dependent (PLP) enzymes, catalyzes the deamination of L‐serine and L‐threonine to yield pyruvate or 2‐oxobutyrate. The crystal structure of L‐serine dehydratase from human liver (hSDH) has been solved at 2.5 Å‐resolution by molecular replacement. The structure is a homodimer and reveals a fold typical for β‐family PLP‐dependent enzymes. Each monomer serves as an active unit and is subdivided into two distinct domains: a small domain and a PLP‐binding domain that covalently anchors the cofactor. Both domains show the typical open α/β architecture of PLP enzymes. Comparison with the rSDH‐(PLP‐OMS) holo‐enzyme reveals a large structural difference in active sites caused by the artifical O‐methylserine. Furthermore, the activity of hSDH‐PLP was assayed and it proved to show catalytic activity. That suggests that the structure of hSDH‐PLP is the first structure of the active natural holo‐SDH.
β2‐Microglobulin isoforms display an heterogeneous affinity for type I collagen
Authors: Giorgetti Sofia , Rossi Antonio , Mangione Palma , Raimondi Sara , Marini Sara , Stoppini Monica , Corazza Alessandra , Viglino Paolo , Esposito Gennaro , Cetta Giuseppe , Merlini Giampaolo , Bellotti Vittorio 
Published: February 2005

AbstractIt has been claimed that β2‐microglobulin (β2‐m) interacts with type I and type II collagen, and this property has been linked to the tissue specificity of the β2‐m amyloid deposits that target the osteo‐articular system. The binding parameters of the interaction between collagen and β2‐m were determined by band shift electrophoresis and surface plasma resonance by using bovine collagen of type I and type II and various isoforms of β2‐m. Wild‐type β2‐m binds collagen type I with a Kd of 4.1 × 10−4 M and type II with 2.3 × 10−3 M. By the BIAcore system we monitored the binding properties of the conformers of the slow phase of folding of β2‐m. The folding intermediates during the slow phase of folding do not display any significant difference with respect to the binding properties of the fully folded molecule. The affinity of β2‐m truncated at the third N‐terminal residue does not differ from that reported for the wild‐type protein. Increased affinity for collagen type I is found in the case of N‐terminal truncated species lacking of six residues. The Kd of this species is 3.4 × 10 −5 M at pH 7.4 and its affinity increases to 4.9 × 10−6 M at pH 6.4. Fluctuations of the affinity caused by β2‐m truncation and pH change can cause modifications of protein concentration in the solvent that surrounds the collagen, and could contribute to generate locally a critical protein concentration able to prime the protein aggregation.
Protein folding: Defining a “standard” set of experimental conditions and a preliminary kinetic data set of two‐state proteins
Authors: Maxwell Karen L. , Wildes David , Zarrine‐Afsar Arash , De Los Rios Miguel A. , Brown Andrew G. , Friel Claire T. , Hedberg Linda , Horng Jia‐Cherng , Bona Diane , Miller Erik J. , Vallée‐Bélisle Alexis , Main Ewan R.G. , Bemporad Francesco , Qiu Linlin , Teilum Kaare , Vu Ngoc‐Diep , Edwards Aled M. , Ruczinski Ingo , Poulsen Flemming M. , Kragelund Birthe B. , Michnick Stephen W. , Chiti Fabrizio , Bai Yawen , Hagen Stephen J. , Serrano Luis , Oliveberg Mikael , Raleigh Daniel P. , Wittung‐Stafshede Pernilla , Radford Sheena E. , Jackson Sophie E. , Sosnick Tobin R. , Marqusee Susan , Davidson Alan R. , Plaxco Kevin W. 
Published: February 2005

AbstractRecent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. Our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. These difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the difficulty of obtaining correct and complete sequence and structural details for the characterized constructs. The lack of a single approach to data analysis and error estimation, or even of a common set of units and reporting standards, further hinders comparative studies of folding. In an effort to overcome these problems, we define here a “consensus” set of experimental conditions (25°C at pH 7.0, 50 mM buffer), data analysis methods, and data reporting standards that we hope will provide a benchmark for experimental studies. We take the first step in this initiative by describing the folding kinetics of 30 apparently two‐state proteins or protein domains under the consensus conditions. The goal of our efforts is to set uniform standards for the experimental community and to initiate an accumulating, self‐consistent data set that will aid ongoing efforts to understand the folding process.
Crystal structure of a predicted phosphoribosyltransferase (TT1426) from Thermus thermophilus HB8 at 2.01 Å resolution
Authors: Kukimoto‐Niino Mutsuko , Shibata Rie , Murayama Kazutaka , Hamana Hiroaki , Nishimoto Madoka , Bessho Yoshitaka , Terada Takaho , Shirouzu Mikako , Kuramitsu Seiki , Yokoyama Shigeyuki 
Published: February 2005

AbstractTT1426, from Thermus thermophilus HB8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (PRTase) domain, as revealed by a Pfam database search. The 2.01 Å crystal structure of TT1426 has been determined by the multiwavelength anomalous dispersion (MAD) method. TT1426 comprises a core domain consisting of a central five‐stranded β sheet surrounded by four α‐helices, and a subdomain in the C terminus. The core domain structure resembles those of the type I PRTase family proteins, although a significant structural difference exists in an inserted 43‐residue region. The C‐terminal subdomain corresponds to the “hood,” which contains a substrate‐binding site in the type I PRTases. The hood structure of TT1426 differs from those of the other type I PRTases, suggesting the possibility that TT1426 binds an unknown substrate. The structure‐based sequence alignment provides clues about the amino acid residues involved in catalysis and substrate binding.