temporary banners

 



 

Journal Issue - Volume 9 Issue 3 (2000)

Abstract Well‐resolved ion signals of intact large protein assemblies, with molecular masses extending above one million Dalton, have been detected and mass analyzed using electrospray ionization mass spectrometry, with an uncertainty in mass of <0.2%. the mass spectral data seem to reflect known solution‐phase behavior of the studied protein assembly and have therefore been directly used to probe the protein assembly topology...

Abstract The Ure2 protein from Saccharomyces cerevisiae has been proposed to undergo a prion‐like autocatalytic conformational change, which leads to inactivation of the protein, thereby generating the [URE3] phenotype. The first 65 amino acids, which are dispensable for the cellular function of Ure2p in nitrogen metabolism, are necessary and sufficient for [URE3] (Masison & Wickner, 1995), leading to designation of this domain as the Ure2...

Abstract This paper presents an analytically tractable model that captures the most elementary aspect of the protein folding problem, namely that both the energy and the entropy decrease as a protein folds. In this model, the system diffuses within a sphere in the presence of an attractive spherically symmetric potential. The native state is represented by a small sphere in the center, and the remaining space is identified with...

Abstract In a general approach to the understanding of protein adaptation to high temperature, molecular models of the closely related mesophilic Streptomyces sp. S38 Xyl1 and thermophilic Thermomonospora fusca TfxA family 11 xylanases were built and compared with the three‐dimensional (3D) structures of homologous enzymes. Some of the structural features identified as potential contributors to the higher thermostability of TfxA were introduced...

Abstract The chaperonin HSP60 (GroEL) proteins are essential in eubacterial genomes and in eukaryotic organelles. Functional regions inferred from mutation studies and the Escherichia coli GroEL 3D crystal complexes are evaluated in a multiple alignment across 43 diverse HSP60 sequences, centering on ATP/ADP and Mg2+ binding sites, on residues interacting with substrate, on GroES contact positions, on interface regions between monomers ...

Abstract A combination of epitope excision, epitope extraction, and differential chemical modification followed by mass spectrometric peptide mapping was used for the characterization of a discontinuous epitope that is recognized by the mouse anti‐HIV‐p24 monoclonal antibody 5E2.A3. In epitope excision, the protein is first bound to an immobilized antibody and then digested with proteolytic enzymes. In epitope extraction, the...

Abstract A single water molecule (w135), buried within the structure of rat intestinal fatty acid binding protein (I‐FABP), is investigated by NMR, molecular dynamics simulations, and analysis of known crystal structures. An ordered water molecule was found in structurally analogous position in 24 crystal structures of nine different members of the family of fatty acid binding proteins. There is a remarkable conservation of the...

Abstract Transmembrane helices are the most readily predictable secondary structure components of proteins. They can be predicted to a high degree of accuracy in a variety of ways. Many of these methods compare new sequence data with the sequence characteristics of known transmembrane domains. However, the known transmembrane sequences are not necessarily representative of a particular organism. We attempt to demonstrate that...

Abstract NMR spectroscopy was used to search for mechanistically significant differences in the local mobility of the main‐chain amides of Bacillus circulans xylanase (BCX) in its native and catalytically competent covalent glycosyl‐enzyme intermediate states. 15N T1, T2, and 15N{1H} NOE values were measured for ∼120 out of 178 peptide groups in both the apo form of the protein and in BCX covalently modified at position Glu78 with a...

Abstract The oxidative refolding of ribonuclease A has been investigated in several experimental conditions using a variety of redox systems. All these studies agree that the formation of disulfide bonds during the process occurs through a nonrandom mechanism with a preferential coupling of certain cysteine residues. We have previously demonstrated that in the presence of glutathione the refolding process occurs through the...

  • Cytochrome c folds through a smooth funnel

  • Markandeswar Panda, Maria G. Benavides‐Garcia, Michael M. Pierce, Barry T. Nall
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1110/ps.9.3.536 (p 536-543)

Abstract A dominant feature of folding of cytochrome c is the presence of nonnative His‐heme kinetic traps, which either pre‐exist in the unfolded protein or are formed soon after initiation of folding. The kinetically trapped species can constitute the majority of folding species, and their breakdown limits the rate of folding to the native state. A temperature jump (T‐jump) relaxation technique has been used to compare the...

Abstract The X‐ray structure of chitinase from the fungal pathogen Coccidioides immitis has been solved to 2.2 Å resolution. Like other members of the class 18 hydrolase family, this 427 residue protein is an eight‐stranded β/α‐barrel. Although lacking an N‐terminal chitin anchoring domain, the enzyme closely resembles the chitinase from Serratia marcescens. Among the conserved features are three cis peptide bonds, all involving conserved...

Abstract The refolding kinetics of a single‐chain Fv (scFv) fragment, derived from a stabilized mutant of the phosphorylcholine binding antibody McPC603, was investigated by H/D exchange and ESI‐MS and compared with the folding kinetics of its constituting domains VH and VL. Both VH and VL adopt essentially native‐like exchange protection within the dead time of the manual‐mixing H/D exchange experiment (10 s) and in the case of VL,...

Abstract The effects of 1,1,1,3,3,3‐hexafluoro‐isopropanol (HFIP) on the conformation of cytochrome c (cyt c) at pH 1.9 were studied using a combination of spectroscopic and physical methods. Analysis varying the HFIP concentration showed that a compact denatured conformation (MHF) accumulates in a low concentration range of HFIP in the middle of structural transition from the highly unstructured acid‐denatured state to the highly helical...

Abstract The issue of specificity in tyrosine kinase intracellular signaling mediated by src homology 2 (SH2) domains has great importance in the understanding how individual signals maintain their mutual exclusivity and affect downstream responses. Several proteins contain tandem SH2 domains that, on interacting with their ligand, provide a higher level of specificity than can be afforded by the interaction of a single SH2 domain....

Page:   1 2 Next