temporary banners

 



 

Journal Issue - Volume 15 Issue 7 (July 2006)

Abstract Studies that compare proteins from thermophilic and mesophilic organisms can provide insights into ability of thermophiles to function at their high habitat temperatures and may provide clues that enable us to better define the forces that stabilize all proteins. Most of the comparative studies have focused on thermal stability and show, as expected, that thermophilic proteins have higher Tm values than their mesophilic...

Abstract We present the Coordinate Internal Representation of Solvation Energy (CIRSE) for computing the solvation energy of protein configurations in terms of pairwise interactions between their atoms with analytic derivatives. Currently, CIRSE is trained to a Poisson/surface‐area benchmark, but CIRSE is not meant to fit this benchmark exclusively. CIRSE predicts the overall solvation energy of protein structures from 331 NMR...

Abstract Several members of the ATP‐binding cassette (ABC) transporter superfamily, including P‐glycoprotein and the half‐transporter ABCG2, can confer multidrug resistance to cancer cells in culture by functioning as ATP‐dependent efflux pumps. ABCG2 variants harboring a mutation at arginine 482 have been cloned from several drug‐resistant cell lines, and these variants differ in their substrate transport phenotype. In this study,...

Abstract The folding of naturally occurring, single‐domain proteins is usually well described as a simple, single‐exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this implies, and the rapid kinetics it engenders, arises due to the extraordinary thermodynamic cooperativity of protein folding. Studying Miyazawa‐Jernigan lattice polymers, we find that, even...

Abstract Lens α‐crystallin is an oligomeric protein with a molecular mass of 500–1000 kDa and a polydispersed assembly. It consists of two types of subunits, αA and αB, each with a molecular mass of 20 kDa. The subunits also form homo‐oligomers in some other tissues and in vitro. Their quaternary structures, which are dynamic and characterized by subunit exchange, have been studied by many techniques, including fluorescence...

Abstract Epoxide hydrolases catalyze the conversion of epoxides to diols. The known functions of such enzymes include detoxification of xenobiotics, drug metabolism, synthesis of signaling compounds, and intermediary metabolism. In plants, epoxide hydrolases are thought to participate in general defense systems. In the present study, we report the first structure of a plant epoxide hydrolase, one of the four homologous enzymes found...

Abstract Simplified Gō models, where only native contacts interact favorably, have proven useful to characterize some aspects of the folding of small proteins. The success of these models is limited by the fact that all residues interact in the same way so that the folding features of a protein are determined only by the geometry of its native conformation. We present an extended version of a Cα‐based Gō model where different...

Abstract Reliable prediction of model accuracy is an important unsolved problem in protein structure modeling. To address this problem, we studied 24 individual assessment scores, including physics‐based energy functions, statistical potentials, and machine learning–based scoring functions. Individual scores were also used to construct ∼85,000 composite scoring functions using support vector machine (SVM) regression. The scores were...

Abstract The β1,3‐glucuronosyltransferases are responsible for the completion of the protein–glycosaminoglycan linkage region of proteoglycans and of the HNK1 epitope of glycoproteins and glycolipids by transferring glucuronic acid from UDP‐α‐D‐glucuronic acid (UDP‐GlcA) onto a terminal galactose residue. Here, we develop phylogenetic and mutational approaches to identify critical residues involved in UDP‐GlcA binding and enzyme...

Abstract The mechanisms by which G‐protein‐coupled receptors (GPCRs) activate G‐proteins are not well understood due to the lack of atomic structures of GPCRs in an active form or in GPCR/G‐protein complexes. For study of GPCR/G‐protein interactions, we have generated a series of chimeras by replacing the third cytoplasmic loop of a scaffold protein bacteriorhodopsin (bR) with various lengths of cytoplasmic loop 3 of bovine...

Abstract Strontium is used in the treatment of osteoporosis as a ranelate compound, and in the treatment of painful scattered bone metastases as isotope. At very high doses and in certain conditions, it can lead to osteomalacia characterized by impairment of bone mineralization. The osteomalacia symptoms resemble those of hypophosphatasia, a rare inherited disorder associated with mutations in the gene encoding for...

Abstract The class A PBP1b from Streptococcus pneumoniae is responsible for glycosyltransferase and transpeptidase (TP) reactions, forming the peptidoglycan of the bacterial cell wall. The enzyme has been produced in a stable, soluble form and undergoes time‐dependent proteolysis to leave an intact TP domain. Crystals of this TP domain were obtained, diffracting to 2.2 Å resolution, and the structure was solved by using molecular ...

Abstract Light‐chain amyloidosis (AL) is characterized by immunoglobulin light‐chain fragments aggregating into amyloid fibrils that deposit extracellularly in vital organs such as the kidney, the heart, and the liver, resulting in tissue degeneration and organ failure, leading to death. Cardiac involvement is found in 50% of AL patients and presents the most severe cases with a life expectancy of less than a year after diagnosis....

Abstract One of the goals of structural genomics is to obtain a structural representative of almost every fold in nature. A recent estimate suggests that 70%–80% of soluble protein domains identified in the first 1000 genome sequences should be covered by about 25,000 structures—a reasonably achievable goal. As no current estimates exist for the number of membrane protein families, however, it is not possible to know whether family...

Abstract We report here the crystal structure of a trehalose‐6‐phosphate phosphatase–related protein (T6PP) from Thermoplasma acidophilum, TA1209, determined by the dual‐wavelength anomalous diffraction (DAD) method. T6PP is a member of the haloacid dehalogenase (HAD) superfamily with significant sequence homology with trehalose‐6‐phosphate phosphatase, phosphoserine phosphatase, P‐type ATPases and other members of the family. T6PP possesses a...

Page:   1 2 Next