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Journal Issue - Volume 13 Issue 5 (May 2004)

Abstract For apparently two‐state proteins, we found that the size (number of folded residues) of a transition state is mostly encoded by the topology, defined by total contact distance (TCD) of the native state, and correlates with its folding rate. This is demonstrated by using a simple procedure to reduce the native structures of the 41 two‐state proteins with native TCD as a constraint, and is further supported by analyzing the...

Abstract The kinetics of disulfide‐coupled folding and unfolding of four circularly permuted forms of bovine pancreatic trypsin inhibitor (BPTI) were studied and compared with previously published results for both wild‐type BPTI and a cyclized form. Each of the permuted proteins was found to be less stable than either the wild‐type or circular proteins, by 3–8 kcal/mole. These stability differences were used to estimate effective...

Abstract Animal toxins block voltage‐dependent potassium channels (Kv) either by occluding the conduction pore (pore blockers) or by modifying the channel gating properties (gating modifiers). Gating modifiers of Kv channels bind to four equivalent extracellular sites near the S3 and S4 segments, close to the voltage sensor. Phrixotoxins are gating modifiers that bind preferentially to the closed state of the channel and fold into...

Abstract Xyl1 from Streptomyces sp. S38 belongs to the low molecular mass family 11 of endo‐β‐1,4‐xylanases. Its three‐dimensional structure has been solved at 2.0 Å and its optimum temperature and pH for enzymatic activity are 60°C and 6.0, respectively. Aspergillus kawachii xylanase XynC belongs to the same family but is an acidophilic enzyme with an optimum pH of 2.0. Structural comparison of Xyl1 and XynC showed differences in residues...

Abstract Phosphorylation of phenylalanine hydroxylase (PAH) at Ser16 by cAMP‐dependent protein kinase increases the basal activity of the enzyme and its resistance to tryptic proteolysis. The modeled structures of the full‐length phosphorylated and unphosphorylated enzyme were subjected to molecular dynamics simulations, and we analyzed the energy of charge–charge interactions for individual ionizable residues in the final...

Abstract Intestinal fatty acid‐binding protein (I‐FABP) has a clam‐shaped structure that may serve as a scaffold for the design of artificial enzymes and drug carriers. In an attempt to optimize the scaffold for increased access to the interior‐binding cavity, several helix‐less variants of I‐FABP have been engineered. The solution‐state NMR structure of the first generation helix‐less variant, known as Δ17‐SG, revealed a...

Abstract The regulators of complement activation (RCA) are critical to health and disease because their role is to ensure that a complement‐mediated immune response to infection is proportionate and targeted. Each protein contains an uninterrupted array of from four to 30 examples of the very widely occurring complement control protein (CCP, or sushi) module. The CCP modules mediate specific protein–protein and protein–carbohydrate...

Abstract Several proteins and peptides that can convert from α‐helical to β‐sheet conformation and form amyloid fibrils, including the amyloid β‐peptide (Aβ) and the prion protein, contain a discordant α‐helix that is composed of residues that strongly favor β‐strand formation. In their native states, 37 of 38 discordant helices are now found to interact with other protein segments or with lipid membranes, but Aβ apparently lacks...

Abstract The crystal structure of fosfomycin resistance protein FosA from transposon Tn2921 has been established at a resolution of 2.5 Å. The protein crystallized without bound Mn(II) and K+, ions crucial for efficient catalysis, providing a structure of the apo enzyme. The protein maintains the three‐dimensional domain‐swapped arrangement of the paired βαβββ‐motifs observed in the genomically encoded homologous enzyme from Pseudomonas aeruginosa...

Abstract The influence of the deletion of the tetra peptide segment α23–26 of the B‐helix of the α‐chain of hemoglobin‐A on its assembly, structure, and functional properties has been investigated. The hemoglobin with the deletion, ss‐Hemoglobin‐Einstein, is readily assembled from semisynthetic α1–141 des23–26 globin and human βA‐chain. The deletion of α23–26 modulates the O2 affinity of hemoglobin in a buffer/allosteric effector specific fashion, but has...

Abstract Headpiece (HP) is a 76‐residue F‐actin‐binding module at the C terminus of many cytoskeletal proteins. Its 35‐residue C‐terminal subdomain is one of the smallest known motifs capable of autonomously adopting a stable, folded structure in the absence of any disulfide bridges, metal ligands, or unnatural amino acids. We report the three‐dimensional solution structures of the C‐terminal headpiece subdomains of human villin...

Abstract Raman microscopy was used to follow conformational changes in single protein crystals. Crystals of native insulin and of the 5S and 12S subunits of the enzyme transcarboxylase showed a mixture of Raman marker bands signifying α‐helix, β‐sheet and nonordered secondary structure. However, by reducing the S–S bonds in the insulin crystal, or by lowering the pH for the 5S crystal, or by soaking substrates into the 12S crystal,...

Abstract We identified in Salmonella enterica serovar Typhi a cluster of four genes encoding a deoxyribokinase (DeoK), a putative permease (DeoP), a repressor (DeoQ), and an open reading frame encoding a 337 amino acid residues protein of unknown function. We show that the latter protein, called DeoM, is a hexamer whose synthesis is increased by a factor over 5 after induction with deoxyribose. The CD spectrum of the purified...

Abstract To further understand oligomeric protein assembly, the folding and unfolding kinetics of the H3–H4 histone tetramer have been examined. The tetramer is the central protein component of the core nucleosome, which is the basic unit of DNA compaction into chromatin in the eukaryotic nucleus. This report provides the first kinetic folding studies of a protein containing the histone fold dimerization motif, a motif observed in...

Abstract Small monomeric proteins often fold in apparent two‐state processes with folding speeds dictated by their native‐state topology. Here we test, for the first time, the influence of monomer topology on the folding speed of an oligomeric protein: the heptameric cochaperonin protein 10 (cpn10), which in the native state has seven β‐barrel subunits noncovalently assembled through β‐strand pairing. Cpn10 is a particularly useful...

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