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An engineered variant of T4 Lysozyme serves as a model for studying induced remote conformational changes in a full protein context. The design involves a duplicated surface helix, flanked by two loops, that switches between two different conformations spanning about 20 å. Molecular dynamics simulations of the engineered protein, up to 1 μs, rule out α-helix to β-sheet transitions within the duplicated helix as suggested by others. These simulations highlight how the use of different force fields can lead to radical differences in the structure of the protein. In addition, Markov state modeling and transition path theory were employed to map a 6.6 μs simulation for possible early intermediate states and to provide insights into the onset of the switching motion. The putative intermediates involve the folding of one helical turn in the C-terminal loop through energy driven, sequential rearrangement of nearby salt bridges around the key residue Arg63. These results provide a first step towards understanding the energetics and dynamics of a rather complicated intra-protein motion. This article is protected by copyright. All rights reserved.
This article was published in the following journal.
Name: Protein science : a publication of the Protein Society
Alzheimer's disease is associated with the abnormal self-assembly of amyloid-β (Aβ) peptide into toxic oligomers and fibrils. Recent experiments reported that Aβ16-22, containing the central hydrop...
Two experimental studies reported the spontaneous formation of amorphous and crystalline structures of C60 molecules intercalated between graphene and a surface. The findings observed included interes...
The With-No-Lysine (WNK) kinase is considered to be a master regulator for various cation-chloride cotransporters involved in maintaining cell-volume and ion homeostasis. Here, we have investigated th...
Recent crystallography studies have shown that the binding site oxyanion hole plays an important role in inhibitor binding, but can exist in two conformations (active/inactive). We have undertaken mol...
Mutation is considered an important factor in the accumulation of Amyloid-β (Aβ), which is a hallmark of Alzheimer's disease (AD). A2V Aβ40 shows a higher aggregation tendency, however, the existin...
The aim of this study is to assess the effectiveness in preventing exacerbation of 52 weeks lysozyme administration in patients with COPD.
The CHAMP (Chemotherapy, Host response And Molecular dynamics in Periampullary cancer) study is a prospective, single-arm observational study that started Sept 1 2018. Patients diagnosed w...
Randomized, double-blind, placebo controlled trial of daily lactoferrin and lysozyme supplementation in improving environmental enteric dysfunction in Malawian children
This study evaluates the significance of differences in serum angiotensin converting enzyme and lysozyme levels of patients with ocular involvement of other autoimmune inflammatory and inf...
The purpose of this study is to determine if the "Re-Engineered Discharge" will decrease rehospitalization rates and adverse events of patients leaving Boston Medical Center.
A zinc finger motif of approximately 30 amino acids with the general sequence X2-Cys-X2,4-Cys-X12-His-X3,4,5-His that forms a simple beta sheet-beta sheet-alpha helix fold stabilized by zinc ions. It recognizes and binds to a variety of eukaryotic DNA sequences and is very common among sequence-specific DNA BINDING PROTEINS and TRANSCRIPTION FACTORS.
The first DNA-binding protein motif to be recognized. Helix-turn-helix motifs were originally identified in bacterial proteins but have since been found in hundreds of DNA-BINDING PROTEINS from both eukaryotes and prokaryotes. They are constructed from two alpha helices connected by a short extended chain of amino acids, which constitute the "turn." The two helices are held at a fixed angle, primarily through interactions between the two helices. (From Alberts et al., Molecular Biology of the Cell, 3d ed, p408-9)
A computer simulation developed to study the motion of molecules over a period of time.
The branch of medicine concerned with the application of NANOTECHNOLOGY to the prevention and treatment of disease. It involves the monitoring, repair, construction, and control of human biological systems at the molecular level, using engineered nanodevices and NANOSTRUCTURES. (From Freitas Jr., Nanomedicine, vol 1, 1999).
A subfamily of HELIX-TURN-HELIX DNA-binding proteins that contain a variable length loop adjacent to the HTH motif. The loop connects two anti-parallel strands and forms a wing when bound to DNA.
Within medicine, nutrition (the study of food and the effect of its components on the body) has many different roles. Appropriate nutrition can help prevent certain diseases, or treat others. In critically ill patients, artificial feeding by tubes need t...