Extracting hydrogen-bond signature patterns from protein structure data.
Classification of protein sequences and structures into families is a fundamental task in biology, and it is often... more Classification of protein sequences and structures into families is a fundamental task in biology, and it is often used as a basis for designing experiments for gaining further knowledge. Some relationships between proteins are detected by the similarities in their sequences, and many more by the similarities in their structures. Despite this, there are a number of examples of functionally similar molecules without any recognisable sequence or structure similarities, and there are also a number of protein molecules that share common structural scaffolds but exhibit different functions. Newer methods of comparing molecules are required in order to detect similarities and dissimilarities in protein molecules. In this article, it is proposed that the precise 3-dimensional disposition of key residues in a protein molecule is what matters for its function, or what conveys the "meaning" for a biological system, but not what means it uses to achieve this. The concept of comparing two molecules through their intramolecular interaction networks is explored, since these networks dictate the disposition of amino acids in a protein structure. First, signature patterns, or fingerprints, of interaction networks in pre-classified protein structural families are computed using an approach to find structural equivalences and consensus hydrogen bonds. Five examples from different structural classes are illustrated. These patterns are then used to search the entire Protein Data Bank, an approach through which new, unexpected similarities have been found. The potential for finding relationships through this approach is highlighted. The use of hydrogen-bond fingerprints as a new metric for measuring similarities in protein structures is also described
DownloadInfluence of Glycation of Wheat Albumins and Globulins on Their Immunoreactivity and Physicochemical Properties
published in "Polish Journal of Food and Nutrition Sciences" (2010, 60(4) pp335-340), co-authored (first author)
Glycation (non-enzymatic glycosylation) is a spontaneous reaction that occurs during food processing, storage and... more
Glycation (non-enzymatic glycosylation) is a spontaneous reaction that occurs during food processing, storage and preparation of food, which can have a significant influence on physiochemical and biological properties of food proteins. Glycation has been used mostly for improvement of functional properties of proteins although there is increasing concern of possible changes in biologic properties of glycation products.
The influence of dry-heat glycation with glucose on immunoreactive properties of wheat salt-soluble proteins has been studied. It has been shown that glycation caused differences in electrophoretic patterns (both 1D and 2D), as well as in Western-immunoblotting with rabbit IgG and human IgE. A significant increase in immunoreactivity has been observed, as well as a decrease in free amino group. Thermostable, immunoreactive and susceptible for glycation protein band with molecular weight of approximately 13 kDa (by SDS-PAGE) has been selected for the N-terminal sequence analysis and determined to be an alpha-amylase inhibitor.
Dry heat glycation is a very potent but nondestructive method of protein glycation, that leads to high degree of substitution and changes in both physicochemical and biological (immunological) properties of food proteins.
ProCoS: Protein composition server
published in Bioinformation', 2010
ProCoS is a free online tool for computing different combinations of peptide compositions. It is developed as an... more
ProCoS is a free online tool for computing different combinations of peptide compositions. It is developed as an applet and a server with a capability to
handle multiple FASTA sequences. The generalized algorithm for computing poly-amino acid composition forms the core of ProCoS. It produces output
in different formats for easy visualization of results. It also allows composition analysis of sequences in full or in specific parts. Thus, ProCoS is userfriendly,
flexible and unique.
The proteomes of Sydney rock oysters vary spatially according to exposure to acid sulfate runoff
Amaral V, Thompson EL, Bishop MJ, Raftos DA, 2012 Mar Freshwat Res 63: 361-369. doi:10.1071/MF11213 [featured in the cover of the issue]
Runoff from acid sulfate soils (ASS) has large negative environmental and economic impacts on estuarine ecosystems.... more Runoff from acid sulfate soils (ASS) has large negative environmental and economic impacts on estuarine ecosystems. Oysters display reduced abundance, growth rate and shell thickness when exposed to ASS runoff, yet the molecular underpinnings of their responses have not been explored. We hypothesized that the proteomes of wild Sydney rock oysters, Saccostrea glomerata, would differ between populations that are recurrently exposed to and that are unaffected by runoff from ASS. We used two-dimensional electrophoresis to compare protein abundances in the gills of S. glomerata collected from two sites close to (acidified) and two sites away from (reference) major ASS outflow drains in a south-east Australian estuary. Approximately 5 % of the proteome was differentially expressed between oysters from acidified and reference sites, with 5 protein spots more abundant and one less abundant at the sites close to drains. Another protein spot was present only in oysters from reference sites. This study has provided the first screening of spatial variation in the protein expression of S. glomerata with respect to discharge from ASS. Altered protein expression may underpin short-term inducible responses to ASS runoff, or genetic resistance acquired through recurrent exposure of populations to the stressor.
Modification of Hydroaffinity of Silicone/Hydrophobic Acrylic Surfaces of Medical Implant Devices and laparoscopic lenses to control condensation mechanisms during and after surgery using Visco-Elastic Colloids and Blood Proteins
This manuscript for this abstract is in preparation and is
to be submitted 12/11/11. It was successfully presented as an oral contribution by Ross B. Bennett-Kennett, ASU '14, at the 58th American Vacuum Society (AVS) Fall International Symposium, Oct 31st-Nov 4th, Nashville, in the Bio-Materials Division.
BIOMATERIAL INTERFACES DIVISION
ROOM: 108 - SESSION BI-THM - Thursday, November 3rd, 2011, 11:20 am
BIOMEDICAL MATERIALS MODERATOR:
S.L. MCARTHUR, SWINBURNE UNIVERSITY OF TECHNOLOGY, AUSTRALIA
N. Herbots, ASU / SiO2 NanoTech, R.J. Culbertson, Q.Xing, D.A. Sell, A.M. Murphy, R.B. Bennett-Kennett*, S.D. Whaley,... more
N. Herbots, ASU / SiO2 NanoTech, R.J. Culbertson, Q.Xing, D.A. Sell, A.M. Murphy, R.B. Bennett-Kennett*, S.D. Whaley, ASU, Drs. C.H. Sell, MD & H.M. Kwong, Arizona Vitro-Retinal Consultants , T. Kutz, A.S. Benitez, B.J. Wilkens, ASU.
Silicone inter-occular lenses and laparoscopic lenses can fog during surgery. This work solves the problem by modifying water affinity of silicone and acrylic, as well as silica lenses via a bio-identical visco-elastic colloidal emulsion, VitreOx™ [1-5] with a 100% success rate in the lab. Ten surgical trials yielded success rate of 80% with failure inferred to be due to blood proteins.
The protein that prevents coagulation, heparin, during surgery, is investigated. Heparin behaves identically to H2O on hydrophobic surfaces. It does not prevent fogging nor interfere with our anti-fogging emulsion.
Fibrinogen is also investigated because it causes coagulation. Fibrinogen applied to IOL's in various dilutions does prevent fogging. Our research shows that the blood proteins studied as well as whole do not modify the hydro-affinity of the surfaces we treated nor their condensation behavior.
We presently combine the bio-identical visco-elastic colloidal emulsion we have developed with blood proteins to modify tissue growth and cell accumulation on implant surfaces.
[1] U. S. Patent Pending, Filed 11/9/10
[2] PhD Dissertation, Q. Xing, ASU (2011).
[3] N. Herbots, Q. Xing, et al. Nucl. Instr. & Meth. B, IBMM 17 (2010), www.sciencedirect.com/science/article/pii/S0168583X11001170
* Presenter at the AVS