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Journal Issue - Volume 6 Issue 6 (June 1997)

Abstract The discovery that proteins exported from the cytoplasm are typically synthesized as larger precursors with cleavable signal peptides has focused interest on the peptidases that remove the signal peptides. Here, we review the membrane‐bound peptidases dedicated to the processing of protein precursors that are found in the plasma membrane of prokaryotes and the endoplasmic reticulum, the mitochondrial inner membrane, and the...

Abstract The three‐dimensional structures of the magnesium‐ and manganese‐bound forms of calbindin D9% were determined to 1.6 Å and 1.9 Å resolution, respectively, using X‐ray crystallography. These two structures are nearly identical but deviate significantly from both the calcium bound form and the metal ion‐free (apo) form. The largest structural differences are seen in the C‐terminal EF‐hand, and involve changes in both metal ion...

Abstract DsbA is a protein‐folding catalyst from the periplasm of Escherichia coli that interacts with newly translocated polypeptide substrate and catalyzes the formation of disulfide bonds in these secreted proteins. The precise nature of the interaction between DsbA and unfolded substrate is not known. Here, we give a detailed analysis of the DsbA crystal structure, now refined to 1.7 Å, and present a proposal for its interaction with...

Abstract The streptavidin‐biotin complex provides the basis for many important biotechnological applications and is an interesting model system for studying high‐affinity protein‐ligand interactions. We report here crystallographic studies elucidating the conformation of the flexible binding loop of streptavidin (residues 45 to 52) in the unbound and bound forms. The crystal structures of unbound streptavidin have been determined in...

Abstract We have previously reported the development and evaluation of a computational program to assist in the design of hydrophobic cores of proteins. In an effort to investigate the role of core packing in protein structure, we have used this program, referred to as Repacking of Cores (ROC), to design several variants of the protein ubiquitin. Nine ubiquitin variants containing from three to eight hydrophobic core mutations were...

Abstract A new multidimensional scoring approach for identifying and distinguishing trimeric and dimeric coiled coils is implemented in the MultiCoil program. The program extends the two‐stranded coiled‐coil prediction program PairCoil to the identification of three‐stranded coiled coils. The computations are based upon data gathered from a three‐stranded coiled‐coil database comprising 6,319 amino acid residues, as well as from the...

Abstract The three‐dimensional optimization of the electrostatic interactions between the charged amino acid residues and the peptide partial charges was studied by Monte‐Carlo simulations on a set of 127 nonhomologous protein structures with known atomic coordinates. It was shown that this type of interaction is very well optimized for all proteins in the data set, which suggests that they are a valuable driving force, at least for...

Abstract Villin 14T is the amino terminal actin monomer binding domain from the actin‐severing and bundling protein villin. Its structure has been determined in solution using heteronuclear multidimensional nuclear magnetic resonance (NMR) spectroscopy (Markus MA, Nakayama T, Matsudaira P, Wagner G. 1994. Solution structure of villin 14T, a domain conserved among actin‐severing proteins. Protein Science 3:70‐81). An additional...

Abstract Compactness has been used to locate discontinuous structural units containing one or more polypeptide chains in proteins of known structure. Rather than exhaustively calculating the compactness of all possible units, our procedure uses a screening algorithm to find discontinuous regions that are potentially compact. Precise calculations of compactness are restricted only to units in these regions. With our procedure,...

Abstract The structure of toxic shock syndrome toxin‐1 (TSST‐1), the causative agent in toxic shock syndrome, has been determined in three crystal forms. The three structural models have been refined to R‐factors of 0.154, 0.150, and 0.198 at resolutions of 2.05 Å, 2.90 Å, and 2.75 Å, respectively. One crystal form of TSST‐1 contains a zinc ion bound between two symmetry‐related molecules. Although not required for biological activity, zinc...

Abstract We performed a series of experiments using alanine‐scanning mutagenesis to locate side chains within human granulocyte colony‐stimulating factor (G‐CSF) that are involved in human G‐CSF receptor binding. We constructed a panel of 28 alanine mutants that examined all surface exposed residues on helices A and D, as well as all charged residues on the surface of G‐CSF. The G‐CSF mutants were expressed in a transiently...

Abstract γδ Resolvase is a site‐specific DNA recombinase (Mr 20.5 kDa) in Escherichia coli that shares homology with a family of bacterial resolvases and invertases. We have characterized the secondary and tertiary structural behavior of the cloned DNA binding domain (DBD) and a dimerization defective mutant in solution. Low‐salt conditions were found to destabilize the tertiary structure of the DBD dramatically, with concomitant changes in the...

Abstract The tendency of HIV‐1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three‐dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340‐345) and for X‐ray crystallography (Lee et al., 1996, Cell 85:931‐942). Methods used to determine the Nef structure by NMR at pH 8...

Abstract The helix content of a series of peptides containing single substitutions of the 20 natural amino acids in a new designed host sequence, succinyl‐YSEEEEKAKKAXAEEAEKKKK‐NH2, has been determined using CD spectroscopy. This host is related to one previously studied, in which triple amino acid substitutions were introduced into a background of Glu‐Lys blocks completely lacking alanine. The resulting free energies show that only ...

Abstract Using a dimeric bZIP protein, we have designed a leucine zipper that becomes more stable after a serine in the e position is phosphorylated by protein kinase A (δδGP = ‐1.4 kcal mol−1 dimer−1 or ‐0.7 kcal mol−1 residue−1). Mutagenesis studies indicate that three arginines form a network of inter‐helical (i, i' + 5; i, i' + 2) and intra‐helical (i, i + 4) attractive interactions with the phosphorylated serine. When the arginines are replaced with...

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