Search results for "structure analysi"
showing 10 items of 66 documents
The Protein Structure Context of PolyQ Regions.
2016
Proteins containing glutamine repeats (polyQ) are known to be structurally unstable. Abnormal expansion of polyQ in some proteins exceeding a certain threshold leads to neurodegenerative disease, a symptom of which are protein aggregates. This has led to extensive research of the structure of polyQ stretches. However, the accumulation of contradictory results suggests that protein context might be of importance. Here we aimed to evaluate the structural context of polyQ regions in proteins by analysing the secondary structure of polyQ proteins and their homologs. The results revealed that the secondary structure in polyQ vicinity is predominantly random coil or helix. Importantly, the region…
Evidence for Water-Tuned Structural Differences in Proteins: An Approach Emphasizing Variations in Local Hydrophilicity
2012
We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands' points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have re…
Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes
2015
In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝn space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝn space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragme…
Small-angle X-ray scattering reveals compact domain-domain interactions in the N-terminal region of filamin C
2014
Filamins are multi-domain, actin cross-linking, and scaffolding proteins. In addition to the actin cross-linking function, filamins have a role in mechanosensor signaling. The mechanosensor function is mediated by domain-domain interaction in the C-terminal region of filamins. Recently, we have shown that there is a three-domain interaction module in the Nterminal region of filamins, where the neighboring domains stabilize the structure of the middle domain and thereby regulate its interaction with ligands. In this study, we have used small-angle X-ray scattering as a tool to screen for potential domain-domain interactions in the N-terminal region. We found evidence of four domain-domain in…
Crystallization and Preliminary Analysis of Crystals of the 24-Meric Hemocyanin of the Emperor Scorpion (Pandinus imperator)
2011
Hemocyanins are giant oxygen transport proteins found in the hemolymph of several invertebrate phyla. They constitute giant multimeric molecules whose size range up to that of cell organelles such as ribosomes or even small viruses. Oxygen is reversibly bound by hemocyanins at binuclear copper centers. Subunit interactions within the multisubunit hemocyanin complex lead to diverse allosteric effects such as the highest cooperativity for oxygen binding found in nature. Crystal structures of a native hemocyanin oligomer larger than a hexameric substructure have not been published until now. We report for the first time growth and preliminary analysis of crystals of the 24-meric hemocyanin (M(…
The Role of Side-Arms for Supramolecular Affinity Materials Based on 9,9′-Spirobifluorenes
2017
An eightfold functionalized D2d-symmetric 9,9' spirobifluorene was condensed with a collection of diketones with elaborated structural features to form three-dimensional supramolecular architectures with active surfaces. Gas sorption measurements by quartz crystal microbalances revealed remarkable indications about the molecular interactions for the application as affinity materials for the detection of volatile organic compounds. Single-crystal X-ray structure analysis further gave insight by packing motifs and for potential host-guest interactions.
A Stevedore's protein knot.
2009
Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered α-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified …
RepeatsDB
2015
Database of annotated tandem repeat protein structures.
Cloud and Fog Effects and Their Parameterisation in Regional Air Quality Models
1997
For the special purpose of cloud chemistry a tool ASOCC was developed which is able to generate a differential equation system from a given set of chemical kinetics equations. Sensitivity and structure analysis have been performed to evaluate the great number of investigated reactions in the liquid phase and to derive a condensed mechanism for use in regional chemistry-transport models.
A Validation Study of Classroom Assessment Scoring System–Secondary in the Finnish School Context
2017
This study examined the reliability and validity of the Classroom Assessment Scoring System–Secondary (CLASS-S) in Finnish classrooms. Trained observers coded classroom interactions based on video recordings of 46 Grade 6 classrooms (450 cycles). Concurrent associations were investigated with respect to teacher self-ratings (e.g., efficacy beliefs and teaching-related stress). Confirmatory factor analysis showed that the hypothesized three-factor structure of the original CLASS-S (Emotional Support, Organizational Support, and Instructional Support), with some modifications, provided a better fit for the data compared with one- and two-factor structures. Structural validity was demonstrate…