The p53 protein is a transcription factor, the function of which is abrogated by oncogenic mutations which affect a flexible domain in the central portion of p53, altering its reactivity with conformation-specific antibodies. Here we show that both conformation and sequence-specific DNA binding of p53 translated in vitro can be modulated by metal chelators and oxidizing agents. Oxidation disrup...

The response of the calmodulin (CaM) protein as a function of calcium ion removal, ionic strength, and temperature at physiological pH condition was investigated using classical molecular dynamics simulations. Changing the ionic strength and temperature came out to be two of the possible routes for observing a conformation change in the protein. This behavior is similar to the conformation chan...

Instead of conformation states of single residues, refined conformation states of quintuplets are proposed to reflect conformation correlation. Simple hidden Markov models combined with sliding window scores are used to predict the secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies within a narrow range, we can ignore the dura...

Protein conformation problem, one of the hard and important problems, is to identify conformation rules which transform sequences to their tertiary structures, called conformations. Our aim of this work is to give a concrete theoretical foundation for graph-theoretic approach for the protein conformation problem in the framework of a probabilistic learning model. We propose the conformation pro...

introduction: omp31 is animmunodominant and protective antigen conserved in brucella species and a good candidate for vaccine design. material & methods: the present study aimed at in silico design of the truncated omp31 (tomp31) using bioinformatic tools and to express the selected form in escherichia coli (e. coli) results and conclusion: various bioinformatically calculated scores for the mo...

Circular dichroism spectra of the arabinogalactan-protein from suspension-cultured Lolium multiflorum (ryegrass) endosperm cells demonstrate the presence of polyproline II conformation in the protein moiety of the proteoglycan. Subject to a number of theoretical and practical constraints of the method, it can be estimated that at least 30% of the protein component is in this conformation.

In protein dynamics, allosteric regulation is a mechanism in which chemical interaction at an allosteric site, which is to say a site other than the catalytically active protein site, affects the conformation and subsequent function of the protein. Allosteric control is a fundamental control mechanism in cells, especially with regards to enzymes. We use mechanical forces applied to allosteric s...

The PDZ domains are modular that recognise short linear C-terminal sequences in proteins organise the formation of complex multi-component assemblies. We have crystallised third domain neuronal postsynaptic density-95 protein (PSD95-PDZ3) at mildly acidic pH conditions and obtained up to four polymorphs. Thus, below 4.0, into prism-shaped crystals belonged trigonal space group P3112. In contras...

Recently, the L1 capsid protein of canine oral papillomavirus (COPV) has been used as an effective systemic vaccine that prevents viral infections of the oral mucosa. The efficacy of this vaccine is critically dependent upon native L1 conformation and, when purified from Sf9 insect cells, the L1 protein not only displays type-specific, conformation-dependent epitopes but it also assembles spont...