temporary banners

 



 

Journal Issue - Volume 7 Issue 12 (December 1998)

Abstract X‐ray crystal structures of carbonic anhydrase II (CAII) complexed with sulfonamide inhibitors illuminate the structural determinants of high affinity binding in the nanomolar regime. The primary binding interaction is the coordination of a primary sulfonamide group to the active site zinc ion. Secondary interactions fine‐tune tight binding in regions of the active site cavity >5 Å away from zinc, and this work...

Abstract The structure of a nonspecific lipid transfer protein from barley (ns‐LTPbarley) in complex with palmitate has been determined by NMR spectroscopy. The structure has been compared to the structure of ns‐LTPbarley in the absence of palmitate, to the structure of ns‐LTPbarley in complex with palmitoyl coenzyme A, to the structure ofns‐LTPmaize in its free form, and to the maize protein complexed with palmitate. Binding of palmitate only affects the structure of...

Abstract A new method is presented for identifying distantly related homologous proteins that are unrecognizable by conventional sequence comparison methods. The method combines information about functionally conserved sequence patterns with information about structure context. This information is encoded in stochastic discrete state‐space models (DSMs) that comprise a new family of hidden Markov models. The new models are called...

Abstract The crystal structure of the Escherichia coli trehalose repressor (TreR) in a complex with its inducer trehalose‐6‐phosphate was determined by the method of multiple isomorphous replacement (MIR) at 2.5 Å resolution, followed by the structure determination of TreR in a complex with its noninducer trehalose at 3.1 Å resolution. The model consists of residues 61 to 315 comprising the effector binding domain, which forms a dimer ...

Abstract A number of recent studies called attention to the presence of kinetically important residues underlying the formation and stabilization of folding nuclei in proteins, and to the possible existence of a correlation between conserved residues and those participating in the folding nuclei. Here, we use the Gaussian network model (GNM), which recently proved useful in describing the dynamic characteristics of proteins for...

Abstract In the 35‐residue pulmonary surfactant‐associated lipopolypeptide C (SP‐C), the stability of the valyl‐rich α‐helix comprising residues 9–34 has been monitored by circular dichroism, nuclear magnetic resonance, and Fourier transform infrared spectroscopy in both a mixed organic solvent and in phospholipid micelles. The α‐helical form of SP‐C observed in freshly prepared solutions in a mixed solvent of CHCl3/CH3OH/0.1 M HCl...

Abstract NADPH: ferredoxin reductase (AvFPR) is involved in the response to oxidative stress in Azotobacter vinelandii. The crystal structure of AvFPR has been determined at 2.0 Å resolution. The polypeptide fold is homologous with six other oxidoreductases whose structures have been solved including Escherichia coli flavodoxin reductase (EcFldR) and spinach, and Anabaena ferredoxin:NADP+ reductases (FNR). AvFPR is overall most homologous to EcFldR. The...

Abstract Stringent specificity and complementarity between the receptor, a periplasmic phosphate‐binding protein (PBP) with a two‐domain structure, and the completely buried and dehydrated phosphate are achieved by hydrogen bonding or dipolar interactions. We recently found that the surface charge potential of the cleft between the two domains that contains the anion binding site is intensely electronegative. This novel finding...

Abstract The crystal structures of two complexes of dethiobiotin synthetase, enzyme‐diaminopelargonic acid‐MgADP‐AlF3 and enzyme‐dethiobiotin‐MgADP‐Pi, respectively, have been determined to 1.8 Å resolution. In dethiobiotin synthetase, AlF3 together with carbamylated diaminopelargonic acid mimics the phosphorylated reaction intermediate rather than the transition state complex for phosphoryl transfer. Observed differences in the binding of substrate,...

Abstract The interaction of the wheat antibacterial peptide α‐thionin with large unilamellar vesicles has been investigated by means of fluorescence spectroscopy. Binding of the peptide to the vesicles is followed by the release of vesicle contents, vesicle aggregation, and lipid mixing. Vesicle fusion, i.e., mixing of the aqueous contents, was not observed. Peptide binding is governed by electrostatic interactions and shows no...

Abstract Whether knowledge‐based intra‐molecular inter‐residue potentials are valid to represent inter‐molecular interactions taking place at protein‐protein interfaces has been questioned in several studies. Differences in the chain connectivity effect and in residue packing geometry between interfaces and single chain monomers have been pointed out as possible sources of distinct energetics for the two cases. In the present study,...

Abstract The binding of partially‐folded mitochondrial malate dehydrogenase (mMDH) to GroEL was assessed by steady and nanosecond emission spectroscopy. Partially‐folded intermediates of mMDH show significant residual secondary structure when examined by CD spectroscopy in the far UV. They bind the extrinsic fluorescent probe ANS and the protein‐ANS complexes display a rotational correlation time of 19 ns. Similar rotational...

Abstract Elongation‐factor‐3 (EF‐3) is an essential factor of the fungal protein synthesis machinery. In this communication the structure of EF‐3 from Saccharomyces cerevisiae is characterized by differential scanning calorimetry (DSC), ultra‐centrifugation, and limited tryptic digestion. DSC shows a major transition at a relatively low temperature of 39 °C, and a minor transition at 58 °C. Ultracentrifugation shows that EF‐3 is a...

Abstract To better understand the structural basis for the binding of proteinase‐transformed human α2‐macroglobulin (α2M) to its receptor, we have used three‐dimensional multinuclear NMR spectroscopy to determine the secondary structure of the receptor binding domain (RBD) of human α2M. Assignment of the backbone NMR resonances of RBD was made using 13C/15N and 15N‐enriched RBD expressed in Escherichia coli. The secondary structure of RBD was determined...

Abstract The self‐organizing tree algorithm (SOTA) was recently introduced to construct phylogenetic trees from biological sequences, based on the principles of Kohonen's self‐organizing maps and on Fritzke's growing cell structures. SOTA is designed in such a way that the generation of new nodes can be stopped when the sequences assigned to a node are already above a certain similarity threshold. In this way a phylogenetic tree...

Page:   1 2 Next