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Journal Issue - Volume 16 Issue 7 (July 2007)

Abstract Proteins adopt complex folds in nature that typically avoid conformations that are knotted or “threaded” through closed loops. Is this the result of fundamental barriers to folding, or have proteins simply evolved to avoid threaded conformations? Organic synthesis has been used in supramolecular chemistry to install topological links in small molecules. By following these principles, we now show that it is possible to...

Abstract High‐throughput screening of protein–protein and protein–peptide interactions is of high interest both for biotechnological and pharmacological applications. Here, we propose the use of the noncoded amino acids o‐nitrotyrosine and p‐iodophenylalanine as spectroscopic probes in combination with circular dichroism and fluorescence quenching techniques (i.e., collisional quenching and resonance energy transfer) as a means to determine the...

Abstract Molecular density information (as measured by electron microscopic reconstructions or crystallographic density maps) can be a powerful source of information for molecular modeling. Molecular density constrains models by specifying where atoms should and should not be. Low‐resolution density information can often be obtained relatively quickly, and there is a need for methods that use it effectively. We have previously...

Abstract In bacteria, the dehydration of 2‐methylcitrate to yield 2‐methylaconitate in the 2‐methylcitric acid cycle is catalyzed by a cofactor‐less (PrpD) enzyme or by an aconitase‐like (AcnD) enzyme. Bacteria that use AcnD also require the function of the PrpF protein, whose function was previously unknown. To gain insights into the function of PrpF, the three‐dimensional crystal structure of the PrpF protein from the bacterium...

Abstract YqfO of Bacillus cereus is a member of the widespread Nif3 family of proteins, which has been highlighted as an important target for structural genomics. The N‐ and C‐terminal domains are conserved across the family and contain a dimetal‐binding motif in a putative active site. YqfO contains an insert in the middle of the protein, present in a minority of bacterial family members. The structure of YqfO was determined at a...

Abstract We introduce a new algorithm, IRECS (Iterative REduction of Conformational Space), for identifying ensembles of most probable side‐chain conformations for homology modeling. On the basis of a given rotamer library, IRECS ranks all side‐chain rotamers of a protein according to the probability with which each side chain adopts the respective rotamer conformation. This ranking enables the user to select small rotamer sets that...

Abstract The tumor suppressor protein pp32 is highly overexpressed in many cancers of the breast and prostate, and has also been implicated in the neurodegenerative disease spinocerebellar ataxias type 1 (SCA1). Pp32 is a multifunctional protein that is involved in the regulation of transcription, apoptosis, phosphorylation, and cell cycle progression, the latter through its association with the hyperphosphorylated form of the...

Abstract Certain proteins of unicellular organisms are translated as precursor polypeptides containing inteins (intervening proteins), which are domains capable of performing protein splicing. These domains, in conjunction with a single residue following the intein, catalyze their own excision from the surrounding protein (extein) in a multistep reaction involving the cleavage of two intein–extein peptide bonds and the formation of...

Abstract In apo and holoCaM, almost half of the hydrogen bonds (H‐bonds) at the protein backbone expected from the corresponding NMR or X‐ray structures were not detected by h3JNC′ couplings. The paucity of the h3JNC′ couplings was considered in terms of dynamic features of these structures. We examined a set of seven proteins and found that protein‐backbone H‐bonds form two groups according to the h3JNC′ couplings measured in solution. H‐bonds...

Abstract Escherichia coli YfcE belongs to a conserved protein family within the calcineurin‐like phosphoesterase superfamily (Pfam00149) that is widely distributed in bacteria and archaea. Superfamily members are metallophosphatases that include monoesterases and diesterases involved in a variety of cellular functions. YfcE exhibited catalytic activity against bis‐p‐nitrophenyl phosphate, a general substrate for phosphodiesterases, and had an...

Abstract Detailed knowledge of how networks of surface salt bridges contribute to protein thermal stability is essential not only to understand protein structure and function but also to design thermostable proteins for industrial applications. Experimental studies investigating thermodynamic stability through measurements of free energy associated with mutational alterations in proteins provide only macroscopic evidence regarding...

Abstract Crystal structures of two orthologs of the regulatory subunit of acetohydroxyacid synthase III (AHAS, EC 2.2.1.6) from Thermotoga maritima (TM0549) and Nitrosomonas europea (NE1324) were determined by single‐wavelength anomalous diffraction methods with the use of selenomethionine derivatives at 2.3 Å and 2.5 Å, respectively. TM0549 and NE1324 share the same fold, and in both proteins the polypeptide chain contains two separate domains...

Abstract PhyA from Selenomonas ruminantium (PhyAsr), is a bacterial protein tyrosine phosphatase (PTP)‐like inositol polyphosphate phosphatase (IPPase) that is distantly related to known PTPs. PhyAsr has a second substrate binding site referred to as a standby site and the P‐loop (HCX5R) has been observed in both open (inactive) and closed (active) conformations. Site‐directed mutagenesis and kinetic and structural studies indicate PhyAsr...

Abstract Glucose‐1‐phosphate uridylyltransferase, or UGPase, catalyzes the production of UDP‐glucose from glucose‐1‐phosphate and UTP. Because of the biological role of UDP‐glucose in glycogen synthesis and in the formation of glycolipids, glycoproteins, and proteoglycans, the enzyme is widespread in nature. Recently this laboratory reported the three‐dimensional structure of UGPase from Escherichia coli. While the initial X‐ray...

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