2007 Week 19: Related Articles

ENTIRE CATALOG OF FERRET PROTEINS TO DATE

Knots, Origami, & Water

"Knot" To Be Undone, Researchers Discover Unusual Protein Structure
Researchers funded by the National Institute of General Medical Sciences have determined the structure of a protein with a surprising feature in it: a knot. This is the first time a knot has been found in a protein from the most ancient type of single-celled organism, an archaebacterium, and one of only a few times a knot has been seen in any protein structure.
"It's a surprising and different structure," said NIGMS' John Norvell, Ph.D., director of the Protein Structure Initiative. Protein folding theory previously held that forming a knot was beyond the ability of a protein. Joachimiak suggests that the newly discovered knot may stabilize the amino acid subunits of the protein.

MIT Finds Most Complex Protein Knot Ever Seen
Knots are rare in proteins - less than 1 percent of all proteins have any knots, and most are fairly simple. The researchers analyzed 32,853 proteins, using a computational technique never before applied to proteins at this scale.
Of those that had knots, all were enzymes. Most had a simple three-crossing, or trefoil knot, a few had four crossings, and the most complicated, a five-crossing knot, was initially found in only one protein - ubiquitin hydrolase.
The complicated knot found in ubiquitin hydrolase may prevent it from getting sucked into the proteasome as it works, Mirny said. The researchers hypothesize that proteins with complex knots can't be pulled into the proteasome as easily, and the knots may make it harder for the protein to unfold, which is necessary for degradation.
The same knot is found in ubiquitin hydrolase in humans and in yeast, supporting the theory that there is a connection between the knot and the protein's function. This also seems to suggest that the knot has been "highly preserved throughout evolution," Virnau said.

Since their initial screening, the researchers have discovered five-crossing knots in two other proteins - a brain protein whose overexpression and mutations are linked with cancer and Parkinson's disease, and a protein involved in the HIV replication cycle. They have also found examples of proteins that are closely related and structurally similar except for the presence or absence of a knot.

Origami Helps Scientists Solve Problems
"Origami helps in the study of mathematics and science in many ways," says Martin Kruskal, a mathematician at Rutgers University, "Using origami anyone can become a scientific experimenter with no fuss." Kruskal found that origami is simpler to develop than most scientific theories and a lot easier to apply.

'DNA Origami': Caltech Scientist Creates New Method For Folding Strands Of Dna To Make Microscopic Structures
In a new development in nanotechnology, a researcher at the California Institute of Technology has devised a way of weaving DNA strands into any desired two-dimensional shape or figure, which he calls "DNA origami."
"The construction of custom DNA origami is so simple that the method should make it much easier for scientists from diverse fields to create and study the complex nanostructures they might want," Rothemund explains.
Although Rothemund has hitherto worked on two-dimensional shapes and structures, he says that 3-D assemblies should be no problem. In fact, researchers at other institutions are already using his method to attempt the building of 3-D cages. One biomedical application that Rothemund says could come of this particular effort is the construction of cages that would sequester enzymes until they were ready for use in turning other proteins on or off.

Unexpected Similarities Between Raindrops And Proteins
Raindrops and proteins seem to have a lot in common. This has been shown in a new study by scientists at Umeå University in Sweden. The principle behind the formation of raindrops is very similar to how proteins fold. This knowledge is vital to our understanding of neurodegenerative diseases like ALS.


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2007 week 01: Articles in Proteins

ENTIRE CATALOG OF FERRET PROTEINS TO DATE


Locating missing water molecules in protein cavities by the three-dimensional reference interaction site model theory of molecular solvation

Water molecules confined in protein cavities are of great importance in understanding the protein structure and functions. However, it is a nontrivial task to locate such water molecules in protein by the ordinary molecular simulation and modeling techniques as well as experimental methods. The present study proves that the three-dimensional reference interaction site model (3D-RISM) theory, a recently developed statistical-mechanical theory of molecular solvation, has an outstanding advantage in locating such water molecules. In this paper, we demonstrate that the 3D-RISM theory is able to reproduce the structure and the number of water molecules in cavities of hen egg-white lysozyme observed commonly in the X-ray structures of different resolutions and conditions. Furthermore, we show that the theory successfully identified a water molecule in a cavity, the existence of which has been ambiguous even from the X-ray results. In contrast, we confirmed that molecular dynamics simulation is helpless at present to find such water molecules because the results substantially depend on the initial coordinates of water molecules. Possible applications of the theory to problems in the fields of biochemistry and biophysics are also discussed. Proteins 2007. © 2006 Wiley-Liss, Inc.

Protein-RNA interactions: Structural analysis and functional classes

A data set of 89 protein-RNA complexes has been extracted from the Protein Data Bank, and the nucleic acid recognition sites characterized through direct contacts, accessible surface area, and secondary structure motifs.
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However, the analysis of hydrogen bond and van der Waal contacts showed that in general proteins complexed with messenger RNA, transfer RNA and viral RNA have more base specific contacts and less backbone contacts than expected, while proteins complexed with ribosomal RNA have less base-specific contacts than the expected. Hence, whilst the types of amino acids involved in the interfaces are similar, the distribution of specific contacts is dependent upon the functional class of the RNA bound. Proteins 2007. © 2006 Wiley-Liss, Inc.

valuating protein structures determined by structural genomics consortia

Structural genomics projects are providing large quantities of new 3D structural data for proteins. To monitor the quality of these data, we have developed the protein structure validation software suite (PSVS), for assessment of protein structures generated by NMR or X-ray crystallographic methods. PSVS is broadly applicable for structure quality assessment in structural biology projects.
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PSVS is particularly useful in assessing protein structures determined by NMR methods, but is also valuable for assessing X-ray crystal structures or homology models. Using these tools, we assessed protein structures generated by the Northeast Structural Genomics Consortium and other international structural genomics projects, over a 5-year period. Protein structures produced from structural genomics projects exhibit quality score distributions similar to those of structures produced in traditional structural biology projects during the same time period. However, while some NMR structures have structure quality scores similar to those seen in higher-resolution X-ray crystal structures, the majority of NMR structures have lower scores. Potential reasons for this "structure quality score gap" between NMR and X-ray crystal structures are discussed. Proteins 2007. © 2006 Wiley-Liss, Inc.

Achieving 80% ten-fold cross-validated accuracy for secondary structure prediction by large-scale training

An integrated system of neural networks, called SPINE, is established and optimized for predicting structural properties of proteins. SPINE is applied to three-state secondary-structure and residue-solvent-accessibility (RSA) prediction in this paper. The integrated neural networks are carefully trained with a large dataset of 2640 chains, sequence profiles generated from multiple sequence alignment, representative amino acid properties, a slow learning rate, overfitting protection, and an optimized sliding-widow size. Proteins 2007. © 2006 Wiley-Liss, Inc.

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