temporary banners

 



 

Journal Issue - Volume 12 Issue 2 (February 2003)

Abstract Long insertions into a loop of a folded host protein are expected to have destabilizing effects because of the entropic cost associated with loop closure unless the inserted sequence adopts a folded structure with amino‐ and carboxy‐termini in close proximity. A loop entropy reduction screen based on this concept was used in an attempt to retrieve folded sequences from random sequence libraries. A library of long random...

Abstract The effect of pressure on the heme environment structure of sperm whale and horse heart metcyanomyoglobins was investigated up to 300 MPa by high‐pressure 1H NMR spectroscopy. Pressure‐induced changes in the distances between the observed protons and the heme iron atom were estimated from changes in the dipolar shift due to the paramagnetic effect on the protons. The changes showed that the heme peripheral structure as a...

Abstract The tight junction tetraspan protein claudin‐4 creates a charge‐selective pore in the paracellular pathway across epithelia. The structure of the pore is unknown, but is presumed to result from transcellular adhesive contacts between claudin's extracellular loops. Here we report the expression of claudin‐4 by baculovirus infection of Sf9 cells and describe the biochemical analysis suggesting it has a hexameric quaternary...

Abstract Pulsed‐field gradient (PFG) diffusion NMR spectroscopy studies were conducted with several helix‐loop‐helix regulatory Ca2+‐binding proteins to characterize the conformational changes associated with Ca2+‐saturation and/or binding targets. The calmodulin (CaM) system was used as a basis for evaluation, with similar hydrodynamic radii (Rh) obtained for apo‐ and Ca2+‐CaM, consistent with previously reported Rh data. In addition, conformational...

Abstract The turn‐forming ability of a series of three‐residue sequences was investigated by substituting them into a well‐characterized β‐hairpin peptide. The starting scaffold, bhpW, is a disulfide‐cyclized 10‐residue peptide that folds into a stable β‐hairpin with two antiparallel strands connected by a two‐residue reverse turn. Substitution of the central two residues with the three‐residue test sequences leads to less stable...

Abstract Unlike the heme cd1‐based nitrite reductase enzymes, the molecular mechanism of copper‐containing nitrite reductases remains controversial. A key source of controversy is the productive binding mode of nitrite in the active site. To identify and characterize the molecular determinants associated with nitrite binding, we applied a combinatorial mutagenesis approach to generate a small library of six variants at position 257...

Abstract The apoptosis‐associated Par‐4 protein has been implicated in cancers of the prostate, colon, and kidney, and in Alzheimer's and Huntington's diseases, among other neurodegenerative disorders. Previously, we have shown that a peptide from the Par‐4 C‐terminus, which is responsible for Par‐4 self‐association as well as interaction with all currently identified effector molecules, is natively unfolded at neutral pH, but forms...

Abstract Animal toxins are small proteins built on the basis of a few disulfide bonded frameworks. Because of their high variability in sequence and biologic function, these proteins are now used as templates for protein engineering. Here we report the extensive characterization of the structure and dynamics of two toxin folds, the “three‐finger” fold and the short α/β scorpion fold found in snake and scorpion venoms, respectively....

Abstract As recently described, the deliberate removal of the proposed electron transfer pathway from cytochrome c peroxidase resulted in the formation of an extended ligand‐binding channel. The engineered channel formed a template for the removed peptide segment, suggesting that synthetic surrogates might be introduced to replace the native electron transfer pathway. This approach could be united with the recent development of...

Abstract PsiCSI is a highly accurate and automated method of assigning secondary structure from NMR data, which is a useful intermediate step in the determination of tertiary structures. The method combines information from chemical shifts and protein sequence using three layers of neural networks. Training and testing was performed on a suite of 92 proteins (9437 residues) with known secondary and tertiary structure. Using a...

Abstract The activation domain of human procarboxypeptidase A2, ADA2h, is an 81‐residue globular domain released during the proteolytic activation of the proenzyme. The role of this and other similar domains as assistants of the correct folding of the enzyme is not fully understood. The folding pathway of ADA2h was characterized previously, and it was also observed that under certain conditions it may convert into amyloid fibrils in...

Abstract The Yeast MATa1 and MATα2 are homeodomain proteins that bind DNA cooperatively to repress transcription of cell type specific genes. The DNA affinity and specificity of MATa1 in the absence of MATα2, however, is very low. MATa1 is converted to a higher affinity DNA‐binding protein by its interaction with the C‐terminal tail of MATα2. To understand why MATa1 binds DNA weakly by itself, and how the MATα2 tail affects the affinity of...

Abstract The calculation of the physical properties of a protein from its X‐ray structure is of importance in virtually every aspect of modern biology. Although computational algorithms have been developed for calculating everything from the dynamics of a protein to its binding specificity, only limited information is available on the ability of these methods to give accurate results when used with a particular X‐ray structure. We...

Abstract Coenzyme A (CoA) is an essential cofactor used in a wide variety of biochemical pathways. The final step in the biosynthesis of CoA is catalyzed by dephosphocoenzyme A kinase (DPCK, E.C. 2.7.1.24). Here we report the crystal structure of DPCK from Escherichia coli at 1.8 Å resolution. This enzyme forms a tightly packed trimer in its crystal state, in contrast to its observed monomeric structure in solution and to the...

Abstract Membrane proteins and water‐soluble proteins share a similar core. This similarity suggests that it should be possible to water‐solubilize membrane proteins by mutating only their lipid‐exposed residues. We have developed computational tools to design water‐soluble variants of helical membrane proteins, using the pentameric phospholamban (PLB) as our test case. To water‐solublize PLB, the membrane‐exposed positions were...

Page:   1 2 Next