The cooperative formation of a higher-order complex between transcription factors NFAT and Fos-Jun is accompanied by conformational changes in both DNA and protein. This allows formation of an extended interface between the proteins, while conserving recognition of the core DNA binding sequences.

Protein flexibility and rigidity can be analyzed using constraint theory, which views proteins as 3D networks of constraints involving covalent bonds and also including hydrophobic interactions and hydrogen bonds. This article describes an algorithm, ROCK (Rigidity Optimized Conformational Kinetics), which generates new conformations for these complex networks with many interlocked rings while ...

Window profiles of amino acids in protein sequences are used to describe the amino acid environment. The relative entropy or Kullback-Leibler distance derived from these profiles is used as a measure of dissimilarity for comparison of amino acids and secondary structure conformations. Distance matrices of amino acid pairs at different conformations are obtained, which display a non-negligible d...

All staggered and eclipsed conformations of 1,2-ethanediol, 2-aminoethanol, and 1,2-ethanediamine have been studied by the semiempirical CNDO/2 method with optimization of structural parameters. The conformations of the -OH and -NH2 functional groups have been also investigated. The results obtained are compared with available experimental and theoretical data. The energy of particular conforma...

Summary Apical hook formation protects fragile tissues of the hypocotyl in soil during seedling emergence. A new study reveals a positive feedback loop between asymmetric distribution hormone auxin and cell wall pectin conformations underpinning elongation tissue bending.

This study generates ensembles of decoy or test structures for eight small proteins with a variety of different folds. Between 35,000 and 200,000 decoys were generated for each protein using our four-state off-lattice model together with a novel relaxation method. These give compact self-avoiding conformations each constrained to have native secondary structure. Ensembles of these decoy conform...

Many proteins contain flexible structures such as loops and hinged domains. A simple root mean square deviation (RMSD) alignment of two different conformations of the same protein can be skewed by the difference between the mobile regions. To overcome this problem, we have developed a novel method to overlay two protein conformations by their atomic coordinates using a Gaussian-weighted RMSD (w...

Protein loop structure modeling is regarded as a mini protein folding problem with significant scientific importance. Efficiently sampling the loop conformation space is a key step to computationally obtain accurate loop structure models. Due to the large size of the conformation space and the complication of the scoring functions describing protein energy, it is difficult to obtain broad, dive...

Aβ folding and assembly are believed to be seminal pathogenic events in Alzheimer’s disease. We study Aβ(1-42) folding by discrete molecular dynamics using a four-bead protein model with hydrogen bonds and amino acid-specific interactions. Interactions account for hydrophobic/hydrophilic effect that mimic the solvent as well as electrostatic effects. We study monomer conformations on a wide tem...