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Effect of intracellular loop 3 on intrinsic dynamics of human β2-adrenergic receptor
Springer Science and Business Media LLC - Tập 13 - Trang 1-17 - 2013
To understand the effect of the long intracellular loop 3 (ICL3) on the intrinsic dynamics of human β2-adrenergic receptor, molecular dynamics (MD) simulations were performed on two different models, both of which were based on the inactive crystal structure in complex with carazolol (after removal of carazolol and T4-lysozyme). In the so-called loop model, the ICL3 region that is missing in avail...... hiện toàn bộ
Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE – binding linear epitopes of allergens
Springer Science and Business Media LLC - Tập 2 - Trang 1-11 - 2002
Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. A strategy is proposed, in which the positive outcomes of the sequence comparison with a minimal length of six amino acid...... hiện toàn bộ
Discriminating the native structure from decoys using scoring functions based on the residue packing in globular proteins
Springer Science and Business Media LLC - Tập 9 Số 1 - Trang 76 - 2009
Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures
Springer Science and Business Media LLC - Tập 10 - Trang 1-13 - 2010
Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to lo...... hiện toàn bộ
A role of proton transfer in peroxidase-catalyzed process elucidated by substrates docking calculations
Springer Science and Business Media LLC - Tập 1 - Trang 1-6 - 2001
Previous kinetic investigations of fungal-peroxidase catalyzed oxidation of N-aryl hydroxamic acids (AHAs) and N-aryl-N- hydroxy urethanes (AHUs) revealed that the rate of reaction was independent of the formal redox potential of substrates. Moreover, the oxidation rate was 3–5 orders of magnitude less than for oxidation of physiological phenol substrates, though the redox potential was similar. T...... hiện toàn bộ
The crystal structure of superoxide dismutase from Plasmodium falciparum
Springer Science and Business Media LLC - Tập 6 - Trang 1-10 - 2006
Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as...... hiện toàn bộ
Deciphering the shape and deformation of secondary structures through local conformation analysis
Springer Science and Business Media LLC - Tập 11 - Trang 1-17 - 2011
Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon co...... hiện toàn bộ
Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification
Springer Science and Business Media LLC - Tập 6 - Trang 1-12 - 2006
Recently a new class of methods for fast protein structure comparison has emerged. We call the methods in this class projection methods as they rely on a mapping of protein structure into a high-dimensional vector space. Once the mapping is done, the structure comparison is reduced to distance computation between corresponding vectors. As structural similarity is approximated by distance between p...... hiện toàn bộ
Elastic network model of allosteric regulation in protein kinase PDK1
Springer Science and Business Media LLC - Tập 10 - Trang 1-9 - 2010
Structural switches upon binding of phosphorylated moieties underpin many signalling networks. The ligand activation is a form of allosteric modulation of the protein, where the binding site is remote from the structural change in the protein. Recently this structural switch has been elegantly demonstrated with the crystallisation of the activated form of 3-phosphoinositide-dependent protein kinas...... hiện toàn bộ
The binding site for neohesperidin dihydrochalcone at the human sweet taste receptor
Springer Science and Business Media LLC - Tập 7 - Trang 1-12 - 2007
Differences in sweet taste perception among species depend on structural variations of the sweet taste receptor. The commercially used isovanillyl sweetener neohesperidin dihydrochalcone activates the human but not the rat sweet receptor TAS1R2+TAS1R3. Analysis of interspecies combinations and chimeras of rat and human TAS1R2+TAS1R3 suggested that the heptahelical domain of human TAS1R3 is crucial...... hiện toàn bộ
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