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Journal Issue - Volume 8 Issue 6 (1999)

  • Editor' note

  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1110/ps.8.6.1165 (p 1165-1165)

Abstract This paper surveys the emerging role of statistical mechanics and polymer theory in protein folding. In the polymer perspective, the folding code is more a solvation code than a code of local ØΨ propensities. The polymer perspective resolves two classic puzzles: (1) the Blind Watchmaker' Paradox that biological proteins could not have originated from random sequences, and (2) Levinthal' Paradox that the folded state of a...

Abstract Folding funnels have been the focus of considerable attention during the last few years. These have mostly been discussed in the general context of the theory of protein folding. Here we extend the utility of the concept of folding funnels, relating them to biological mechanisms and function. In particular, here we describe the shape of the funnels in light of protein synthesis and folding; flexibility, conformational...

Abstract Elicitins, produced by most of the phytopathogenic fungi of the genus Phytophthora, provoke in tobacco both remote leaf necrosis and the induction of a resistance against subsequent attack by various microorganisms. Despite the recent description of the three‐dimensional crystal structure of cryptogein (CRY), the molecular basis of the interactions between Phytophthora and plants largely remains unknown. The X‐ray crystal structure,...

Abstract Two equilibrium intermediates have previously been observed in the urea denaturation of the α subunit of tryptophan synthase (αTS) from Escherichia coli, an eight‐stranded β/α barrel protein. In the current study, a series of amino‐terminal fragments were characterized to probe the elementary folding units that may be in part responsible for this complex behavior. Stop‐codon mutagenesis was used to produce eight fragments...

Abstract We carry out a systematic analysis of the correlation between similarity of protein three‐dimensional structures and their evolutionary relationships. The structural similarity is quantitatively identified by an all‐against‐all comparison of the spatial arrangement of secondary structural elements in nonredundant 967 representative proteins, and the evolutionary relationship is judged according to the definition of...

Abstract The first crystal structure of an inorganic pyrophosphatase (S‐PPase) from an archaebacterium, the thermophile Sulfolobus acidocaldarius, has been solved by molecular replacement and refined to an R‐factor of 19.7% at 2.7 Å. S‐PPase is a D3 homohexameric protein with one Mg2+ per active site in a position similar to, but not identical with, the first activating metal in mesophilic pyrophosphatases (PPase). In mesophilic PPases, Asp65, Asp70, and...

Abstract Cytochrome cH is the electron donor to the oxidase in methylotrophic bacteria. Its amino acid sequence suggests that it is a typical Class I cytochrome c, but some features of the sequence indicated that its structure might be of special interest. The structure of oxidized cytochrome cH has been solved to 2.0 Å resolution by X‐ray diffraction. It has the classical tertiary structure of the Class 1 cytochromes c but bears a...

Abstract Principles of protein thermostability have been studied by comparing structures of thermostable proteins with mesophilic counterparts that have a high degree of sequence identity. Two tetrameric NADP(H)‐dependent alcohol dehydrogenases, one from Clostridium beijerinckii (CBADH) and the other from Thermoanaerobacter brockii (TBADH), having exceptionally high (75%) sequence identity, differ by 30° in their melting temperatures. The crystal...

Abstract The X‐ray structure of the complex formed between yeast 5‐aminolaevulinic acid dehydratase (ALAD) and the inhibitor laevulinic acid has been determined at 2.15 Å resolution. The inhibitor binds by forming a Schiff base link with one of the two invariant lysines at the catalytic center: Lys263. It is known that this lysine forms a Schiff base link with substrate bound at the enzyme' so‐called P‐site. The carboxyl group of...

Abstract Extended retro (reversed) peptide sequences have not previously been accommodated within functional proteins. Here, we show that the entire transmembrane portion of the β‐barrel of the pore‐forming protein α‐hemolysin can be formed by retrosequences comprising a total of 175 amino acid residues, 25 contributed by the central sequence of each subunit of the heptameric pore. The properties of wild‐type and retro heptamers in...

Abstract A sequence motif that is Similar to Ubiquitin (SUb) has been identified in the Saccharomyces cerevisiae ubiquitin‐specific protease Ubp6. SUb is conserved in all known Ubp6 homologues from a spectrum of eukaryotic species and is also present in a group of hypothetical proteins of unknown function (Unk1–3) present in sequence databases. An N‐terminal deletion mutant of Ubp6 that lacks SUb is still capable of cleaving α‐linked ubiquitin...

Abstract The Escherichia coli tryptophan repressor protein (TR) represses the transcription of several genes in response to the concentration of tryptophan in the environment. In the co‐crystal structure of TR bound to a DNA fragment containing its target very few direct contacts between TR and the DNA were observed. In contrast, a number of solvent mediated contacts were apparent. NMR solution structures, however, did not resolve...

Abstract The refolding of barstar, the intracellular inhibitor of barnase, is dominated by the slow formation of a cis peptidyl prolyl bond in the native protein. The triple mutant C40/82A P27A in which two cysteine residues and one trans proline were replaced by alanine was used as model system to investigate the kinetics and structural consequences of the trans/cis interconversion of Pro48. One‐ and two‐dimensional real‐time NMR spectroscopy was used to...

Abstract BBA1 is a designed protein that has only 23 residues. It is the smallest protein without disulfide bridges that has a well‐defined tertiary structure in solution. We have performed unfolding molecular dynamics simulations on BBA1 and some of its mutants at 300, 330, 360, and 400 K to study their kinetic stability as well as the unfolding mechanism of BBA1. It was shown that the unfolding simulations can provide insights...

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