Search results for "folding"

Protein knot server: detection of knots in protein structures

2007

KNOTS (http://knots.mit.edu) is a web server that detects knots in protein structures. Several protein structures have been reported to contain intricate knots. The physiological role of knots and their effect on folding and evolution is an area of active research. The user submits a PDB id or uploads a 3D protein structure in PDB or mmCIF format. The current implementation of the server uses the Alexander polynomial to detect knots. The results of the analysis that are presented to the user are the location of the knot in the structure, the type of the knot and an interactive visualization of the knot. The results can also be downloaded and viewed offline. The server also maintains a regul…

Collective properties of hydration: long range and specificity of hydrophobic interactions

1997

We report results of molecular dynamics (MD) simulations of composite model solutes in explicit molecular water solvent, eliciting novel aspects of the recently demonstrated, strong many-body character of hydration. Our solutes consist of identical apolar (hydrophobic) elements in fixed configurations. Results show that the many-body character of PMF is sufficiently strong to cause 1) a remarkable extension of the range of hydrophobic interactions between pairs of solute elements, up to distances large enough to rule out pairwise interactions of any type, and 2) a SIF that drives one of the hydrophobic solute elements toward the solvent rather than away from it. These findings complement re…

Crystal Structure of Perakine Reductase, Founding Member of a Novel Aldo-Keto Reductase (AKR) Subfamily That Undergoes Unique Conformational Changes …

2012

Perakine reductase (PR) catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. Sequence alignment shows that PR is the founder of the new AKR13D subfamily and is designated AKR13D1. The x-ray structure of methylated His(6)-PR was solved to 2.31 Å. However, the active site of PR was blocked by the connected parts of the neighbor symmetric molecule in the crystal. To break the interactions and obtain the enzyme-ligand complexes, the A213W mutant was generated. The atomic structure of His(6)-PR-A213W complex with NADPH was determined at 1.77 Å. Overal…

The effect of genetic robustness on evolvability in digital organisms

2008

Abstract Background Recent work has revealed that many biological systems keep functioning in the face of mutations and therefore can be considered genetically robust. However, several issues related to robustness remain poorly understood, such as its implications for evolvability (the ability to produce adaptive evolutionary innovations). Results Here, we use the Avida digital evolution platform to explore the effects of genetic robustness on evolvability. First, we obtained digital organisms with varying levels of robustness by evolving them under combinations of mutation rates and population sizes previously shown to select for different levels of robustness. Then, we assessed the abilit…

Self-healing silk from the sea: role of helical hierarchical structure inPinna nobilisbyssus mechanics

2019

11 pages; International audience; The byssus fibers of Mytilus mussel species have become an important role model in bioinspired materials research due to their impressive properties (e.g. high toughness, self-healing); however, Mytilids represent only a small subset of all byssus-producing bivalves. Recent studies have revealed that byssus from other species possess completely different protein composition and hierarchical structure. In this regard, Pinna nobilis byssus is especially interesting due to its very different morphology, function and its historical use for weaving lightweight golden fabrics, known as sea silk. P. nobilis byssus was recently discovered to be comprised of globula…

C-terminal amino acids are essential for human heat shock protein 70 dimerization

2014

The human inducible heat shock protein 70 (hHsp70), which is involved in several major pathologies, including neurodegenerative disorders and cancer, is a key molecular chaperone and contributes to the proper protein folding and maintenance of a large number of protein structures. Despite its role in disease, the current structural knowledge of hHsp70 is almost exclusively based on its Escherichia coli homolog, DnaK, even though these two proteins only share ~50 % amino acid identity. For the first time, we describe a complete heterologous production and purification strategy that allowed us to obtain a large amount of soluble, full-length, and non-tagged hHsp70. The protein displayed both …

Guidance Provided by Teacher and Simulation for Inquiry-Based Learning: a Case Study

2016

Current research indicates that inquiry-based learning should be guided in order to achieve optimal learning outcomes. The need for guidance is even greater when simulations are used because of their high information content and the difficulty of extracting information from them. Previous research on guidance for learning with simulations has concentrated on guidance provided by the simulation. Little research has been done on the role of the teacher in guiding learners with inquiry-based activities using simulations. This descriptive study focuses on guidance provided during small group investigations; pre-service teachers (n = 8) guided third and fifth graders using a particular simulatio…

Chaperoning the <em>Mononegavirales</em>: Current Knowledge and Future Directions

2018

The order Mononegavirales harbors numerous viruses of significant relevance for human health, including both established and emerging infections. Currently, vaccines are only available for a small subset of these viruses and antiviral therapies remain limited. Being obligate cellular parasites, viruses must utilize the cellular machinery for their replication and spread. Therefore, targeting cellular pathways used by viruses can provide novel therapeutic approaches. One of the key challenges confronted by both hosts and viruses alike is the successful folding and maturation of proteins. In cells, this task is faced by cellular molecular chaperones, a group of conserved and abundant proteins…

Paintings as Solid Affective Scaffolds

2019

Scaffolding for motivation by parents, and child homework motivations and emotions: Effects of a training programme

2018

Background and aims Based on the principles of scaffolding for motivation and on the assumptions of self-determination theory, two studies aimed to assess the role played by perceived parental autonomy-supportive scaffolding on child homework autonomous motivation, self-efficacy, affect, and engagement. Samples and results The results of Study 1, which involved 122 parents and their children, showed that the higher the parental autonomous motivation, the more their children perceived them as autonomy-supportive while scaffolding for motivation, and hence developed autonomous motivation, self-efficacy, and engagement in homework. In Study 2, 37 parents were involved in a four-session trainin…