temporary banners

 



 

Journal Issue - Volume 13 Issue 7 (July 2004)

Abstract Combinatorial libraries of de novo amino acid sequences can provide a rich source of diversity for the discovery of novel proteins with interesting and important activities. Randomly generated sequences, however, rarely fold into well‐ordered proteinlike structures. To enhance the quality of a library, features of rational design must be used to focus sequence diversity into those regions of sequence space that are most...

Abstract The crystal structure of rat α‐parvalbumin has been determined at 1.05 Å resolution, using synchrotron data collected at Advanced Photon Source beamline 19‐ID. After refinement with SHELX, employing anisotropic displacement parameters and riding hydrogen atoms, R = 0.132 and Rfree = 0.162. The average coordinate estimated standard deviations are 0.021 Å and 0.038 Å for backbone atoms and side‐chain atoms, respectively....

Abstract It is well known that the sequence of amino acids in proteins code for its tertiary structure. It is also known that there exists a relationship between sequence and the quaternary structure of proteins. The question addressed here is whether the nature of quaternary association can be predicted from the sequence, similar to the three‐dimensional structure prediction from the sequence. The class of proteins called legume...

Abstract Proteins are minimally frustrated polymers. However, for realistic protein models, nonnative interactions must be taken into account. In this paper, we analyze the effect of nonnative interactions on the folding rate and on the folding free energy barrier. We present an analytic theory to account for the modification on the free energy landscape upon introduction of nonnative contacts, added as a perturbation to the strong...

Abstract The crystal structure of IκBα in complex with the transcription factor, nuclear factor κ‐B (NF‐κB) shows six ankyrin repeats, which are all ordered. Electron density was not observed for most of the residues within the PEST sequence, although it is required for high‐affinity binding. To characterize the folded state of IκBα (67–317) when it is not in complex with NF‐κB, we have carried out circular dichroism (CD)...

Abstract GroEL can solubilize membrane proteins by binding them in its hydrophobic cavity when detergent is removed by dialysis. The best‐studied example is bacteriorhodopsin, which can bind in the GroEL chaperonin at two molecules per tetradecamer. Applying this approach to the holin and antiholin proteins of phage λ, we find that both proteins are solubilized by GroEL, in an ATP‐sensitive mode, but to vastly different extents. The...

Abstract Classification of the amounts and types of lower order structural elements in proteins is a prerequisite to effective comparisons between protein folds. In an effort to provide an additional vehicle for fold comparison, we present an alternative classification scheme whereby protein folds are represented in statistical thermodynamic terms in such a way as to illuminate the energetic building blocks within protein...

Abstract The removal of N‐terminal translation initiator Met by methionine aminopeptidase (MetAP) is often crucial for the function and stability of proteins. On the basis of crystal structure and sequence alignment of MetAPs, we have engineered Escherichia coli MetAP by the mutation of three residues, Y168G, M206T, Q233G, in the substrate‐binding pocket. Our engineered MetAPs are able to remove the Met from bulky or acidic penultimate...

Abstract Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5′‐nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges. The mutant proteins have been expressed, purified, and crystallized, to structurally characterize the designed...

Abstract The near‐UV absorption spectra of barnase double‐point mutants are calculated using a combination of molecular dynamics and ab initio techniques. The atoms of the fluorescent probes are placed in a cloud of point charges, generated by molecular dynamics simulations. Ab initio calculations (CASPT2) are performed on these systems. Three molecular dynamics packages are compared—Amber5.0, CHARMM‐c27b1, and GROMOS96—using indole...

Abstract The structures of membrane transporters are still mostly unsolved. Only recently, the first two high‐resolution structures of transporters of the major facilitator superfamily (MFS) were published. Despite the low sequence similarity of the two proteins involved, lactose permease and glycerol‐3‐phosphate transporter, the reported structures are highly similar. This leads to the hypothesis that all members of the MFS share a...

Abstract We have recently developed a flexible protein structure alignment program (FATCAT) that identifies structural similarity, at the same time accounting for flexibility of protein structures. One of the most important applications of a structure alignment method is to aid in functional annotations by identifying similar structures in large structural databases. However, none of the flexible structure alignment methods were...

Abstract The reactivation efficiency in the refolding of denatured luciferase in the presence and the absence of monoclonal antibodies (mAbs) has been studied. Luciferase could be partially reactivated when the protein was denatured in high concentrations of guanidium chloride (GdmCl; >4.5 M) and the refolding was carried out in very low protein concentrations. The refolding yield was, however, significantly lower when it was...

Abstract The metastable serpin architecture is perturbed by extremes of temperature, pH, or changes in primary sequence resulting in the formation of inactive, polymeric conformations. Polymerization of a number of human serpins in vivo leads to diseases such as emphysema, thrombosis, and dementia, and in these cases mutations are present within the gene encoding the aggregating protein. Here we show that aggregation of the human...

Abstract Similarity of protein structures has been analyzed using three‐dimensional Delaunay triangulation patterns derived from the backbone representation. It has been found that structurally related proteins have a common spatial invariant part, a set of tetrahedrons, mathematically described as a common spatial subgraph volume of the three‐dimensional contact graph derived from Delaunay tessellation (DT). Based on this property...

Page:   1 2 Next