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Topic: Protein design

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	One- and two-body decomposable Poisson-Boltzmann methods for protein design calculations -- Marshall et al. 14 (5): ...
		in the context of the folded protein versus the electrostatic
		The key distinctions between the two methods are as follows: The exact calculation uses the protein backbone and all of the side chains in the protein to define the dielectric boundary, while in the one-body method, the dielectric boundary is defined by the backbone and a single side chain only.
		The key distinctions between the exact, one-body, and two-body methods are as follows: The exact calculation uses the protein backbone and all of the side chains in the protein to define the dielectric boundary, and a single calculation is used to determine the folded-state solvation energy.
	www.proteinscience.org /cgi/content/full/14/5/1293 (5573 words)

	Hecht Lab Research (Site not responding. Last check: 2007-10-13)
		The designed proteins were expressed from a library of synthetic genes and several were purified and characterized.
		Each protein in the library has a distinct 63 amino acid sequence, yet they all share an identical binary pattern of polar and nonpolar residues, which was designed to favor the formation of six stranded amphiphilic beta-strands.
		Moreover, since the designed pattern is compatible with a wide variety of different sequences, it may be possible to fabricate beta-sheet monolayers using combinations of side chains that are explicitly designed for particular applications of novel biomaterials.
	www.princeton.edu /~hecht/research.html (4506 words)

	Food Product Design: Applications -- Protein Power: Functionality and Versatility
		This increase in whey protein viscosity with heating is used to thicken foods such as soups, sauces and yogurt, with the added advantage that the formula stays thin and flows easily until heated.
		Anti-freeze proteins, which scientists have found in polar fish and in cold-tolerant insects and plants, are being studied for their potential applications in foods.
		Anti-freeze proteins thus could be useful for lowering the temperature of the initial onset of freezing, as well as for preventing the growth of large ice crystals on recrystallization during frozen storage.
	www.foodproductdesign.com /archive/1993/0993ap2.html (2808 words)

	ScienceDaily: Researchers Design And Build First Artificial Protein
		In their design and construction effort, the scientists chose a version of a globular protein of a type called an alpha/beta conformation that was not found in nature.
		Protein microarray -- A protein microarray is a piece of glass on which different molecules of protein have been affixed at separate locations in an ordered manner thus forming a microscopic array.
		Protein -- Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together between the carboxyl atom of one amino acid and the amine nitrogen of another.
	www.sciencedaily.com /releases/2003/11/031121071356.htm (2291 words)

	Research Overview
		Over the past several years, we have used our computational protein design method to stabilize dramatically several small proteins by redesigning every residue of their sequences, to redesign protein backbone conformation, to convert a monomeric protein to a strand-swapped dimer, and to thermostabilize an enzyme.
		The design of a new globular protein fold and the close correspondence of the crystal structure to the design model have broad implications for protein design and protein-structure prediction and open the door to the exploration of the large regions of the protein universe not yet observed in nature.
		The picture of protein folding that motivates our approach to ab initio protein tertiary structure prediction is that sequence-dependent local interactions bias segments of the chain to sample distinct sets of local structures, and that nonlocal interactions select the lowest free-energy tertiary structures from the many conformations compatible with these local biases.
	boinc.bakerlab.org /rosetta/rah_research.php (2184 words)

	Rosetta Design -- Documentation
		The result is that in some cases you may observe a large cluster of hydrophobic residues on the surface of a protein, or a cluster of polars in the core.
		Design of a novel globular protein fold with atomic-level accuracy.
		Accurate computer-based design of a new backbone conformation in the second turn of protein L. Kuhlman B, et al.
	rosettadesign.med.unc.edu /documentation.html (831 words)

	DrexlerNanotechnology81PNAS
		The detailed design of many specific devices to render them describable by dynamical equations would be a task of another order (consider designing a clock from scratch) and appears unnecessary to the establishment of the feasibility of certain general capabilities.
		Still, the synthetic abilities of protein machines will be limited by their need for a moderate temperature aqueous environment (although applied forces can sometimes replace or exceed thermal agitation as a source of activation energy and reaction sites and reactive groups can be protected from the surrounding water, as in some enzymatic active sites).
		Further, even if protein design were to prove intractible (because of difficulties in predicting conformations), this would in no way preclude developing an alternative polymer system with predictable coiling and using it as a basis for further development.
	www.imm.org /PNAS.html (4296 words)

	DARPA Defense Sciences Office - Protein Design Processes (Site not responding. Last check: 2007-10-13)
		Small proteins are composed of approximately 300 amino acids, and hence the sequence, and possibly the structure space, of naturally occurring proteins is vast.
		To achieve this goal, significant advances must be made in the understanding of several problems including the relationship of sequence to physical structure to biological function and the definition of reusable components of proteins leading to the equivalent of a periodic table for proteins.
		The Protein Design Processes (PDP) Program changes the paradigm by beginning with an understanding of the binding and chemical reaction that is to be expressed; designing an active site that is compatible with the initial, transition, and final state chemistry; and then embedding the resulting structure in a scaffold.
	www.darpa.mil /dso/thrust/biosci/pdp.htm (293 words)

	Food Product Design: Protein Possibilities
		High-lysine protein has been extracted from yellow peas to produce pea flour and pea protein isolate; this is recommended for use as a stabilizer for water-in-oil emulsions.
		Protein denaturation and the resultant decrease in solubility can lower the emulsification properties, although a mild heat treatment that exposes additional hydrophobic areas in certain proteins can increase the emulsifying properties.
		The quality of protein in food sources is classified according to the protein's digestibility and bioavailability, and is based on the type and variety of amino acids present.
	www.foodproductdesign.com /archive/1997/1097AP.html (3751 words)

	BioMed Central \| Full text \| A maximum likelihood framework for protein design
		Seen from this new point of view, the design problem raises new questions: natural proteins are the result of a complex evolutionary process, involving an intricate interplay between mutation and selection, and this probably entails many constraints directly related to the native conformation, but nevertheless not equivalent to the mere requirement of structural stability.
		The evolutionary approach to protein design is particularly relevant to phylogenetic studies, where one of the current motivations is to develop the so-called structurally constrained models of protein evolution, i.e.
		To compare natural protein sequences with those predicted by the optimized potentials, marginal, leave-one-out and empirical profiles (see methods) were generated for the 60 proteins used in the design specificity experiment described above; the profiles obtained for the best and the worst scoring structures are provided as supplementary materials [see Additional file 7].
	www.biomedcentral.com /1471-2105/7/326 (7444 words)

	Protein Design by Combinatorial Protein Microarrays
		We are developing protein array systems in which one thousand arrays, each containing one thousand different protein sequences are interrogated, thus allowing the relative stabilities of one million proteins to be measured and compared.
		We are using this knowledge to address the protein folding problem via directed self assembly of libraries of short peptide sequences in order to identify those assemblies of peptides that constitute the optimally stable sequences of higher order protein structures.
		Protein arrays are prepared as nanoliter spots on conventional (3 x 1 inch) glass microscope slides functionalized with aldehyde groups.
	www.uvm.edu /~mcase/microarrays.htm (679 words)

	Projects
		How proteins self-assemble into their native state (responsible for biological function) has been a much studied problem for over a decade.
		By designing new sequences that could form these specific protein structures, we're setting the stage to attack a number of significant contemporary issues in structural biology, genetics, and medicine.
		Try to unravel a fundamental issue in the "protein folding problem" (which itself lies at the heart of a huge amount of modern biomedical research): the fact that thousands of different sequences can all form the same three-dimensional structure.
	www.stanford.edu /group/pandegroup/projects.html (767 words)

	Accelrys: QUANTA—Protein Health and Protein Modeling
		Protein Design is a versatile application for modeling and analyzing protein structures.
		The Protein Utilities palette, which contains visual tools and structure checks, is a means for accessing the Protein Health utility that is described below.
		The Protein Health utility helps to identify features in a protein structure that are uncommon or incorrect and therefore warrant closer examination, such as the wrong chirality of Ca atoms, main chain conformations that fall outside accepted regions on the Ramachandran map, or side chain conformations that do not correspond to regularly observed rotamers.
	www.accelrys.com /products/quanta/protein_model_health.html (277 words)

	HHMI News: Researchers Design and Build First Artificial Protein
		The ability to specify and design artificial proteins also opens the way for researchers to engineer artificial protein enzymes for use as medicines or industrial catalysts, said the study's lead author, Howard Hughes Medical Institute investigator David Baker at the University of Washington.
		Understanding and predicting the rules that govern this complex folding process—involving the folding of the main backbone and the packing of the molecular side chains of the amino acids—is one of the central problems of biology.
		Their computational design approach was iterative, in that they specified a starting backbone conformation and identified the lowest energy amino acid sequence for this conformation using the RosettaDesign program they had developed previously.
	www.hhmi.org /news/baker3.html (1199 words)

	[No title]
		With an improved understanding of the molecular structures and interactions of proteins, drug designers are enabled to develop new treatments that target specific human, animal, and plant diseases.
		Most plant foods contain protein and in fact it would be very difficult to design a vegetarian diet that is short on protein.
		The two proteins added today are phosphodiesterase IV (PDE-4) and peroxisome proliferator-activated receptor delta (PPAR delta), both are active targets of structure based drug design.
	www.lycos.com /info/protein--protein-design.html (454 words)

	Protein Design Labs' Future [Fool.com] February 25, 2005 (Site not responding. Last check: 2007-10-13)
		A month ago, Protein Design Labs announced that it was acquiring privately held ESP Pharma.
		Protein Design Labs' management commented that this will accelerate the company's transition to becoming cash flow positive to 2006, instead of later this decade.
		Protein Design Labs has always been great about communicating details of its drug programs in the past, and I expect the same level of disclosure on the new programs.
	www.fool.com /investing/high-growth/2005/02/25/protein-design-labs-future.aspx (468 words)

	Hellinga, Ph.D.
		This approach starts with a protein of known structure, and uses design algorithms to predict the set of mutations necessary to alter or introduce ligand binding or enzyme activity in that structure.
		These designs are then produced by oligo-nucleotide-directed mutagenesis (typically 10-20 mutations) and heterologous protein expression.
		De Lorimier, RM, Tian, Y and Hellinga, HW (2006) Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins.
	www.biochem.duke.edu /Hellinga/hellinga.html (778 words)

	David Baker
		He is applying this knowledge to the prediction and design of macromolecular structures and interactions.
		A highlight was the redesign of the folding pathway of protein G, a small protein containing two β hairpins separated by an α helix.
		A particularly notable result is that the orientation dependence of the hydrogen bond in quantum chemistry calculations on formamide dimers is remarkably similar to that seen in side-chain–side-chain hydrogen bonds in protein structures but different from that in current molecular mechanics force fields, which neglect the covalent character of the hydrogen bond.
	www.hhmi.org /research/investigators/bakerd.html (1985 words)

	C&EN: TODAY'S HEADLINES - NEW PROTEIN FOLD MADE TO ORDER
		The new protein, called Top7, is the first globular protein with a new fold that was designed from scratch and validated by determination of its 2.5-Å-resolution X-ray crystal structure.
		Globular proteins are roughly spherical structures with multiple long-range interactions--contacts between amino acids far removed from each other in the protein's sequence.
		Biochemistry professor Anna Tramontano of the University of Rome "La Sapienza," who specializes in protein structure prediction and analysis, says she would ideally like to have seen one thing that was missing in the Baker paper: some element of functionality in the protein, such as the ability to bind a metal or catalyze a reaction.
	pubs.acs.org /cen/topstory/8147/8147notw6.html (667 words)

	Thoroughly sampling sequence space: Large-scale protein design of structural ensembles -- Larson et al. 11 (12): 2804 ...
		The distribution of sequence entropies for the designed sequences is plotted in fl, with the sequence entropy from the allowed rotamers in gray.
		Dahiyat, B.I. In silico design for protein stabilization.
		Desjarlais, J.R. and Handel, T.M. De novo design of the hydrophobic cores of proteins.
	www.proteinscience.org /cgi/content/full/11/12/2804 (5532 words)

	[No title] (Site not responding. Last check: 2007-10-13)
		Other protein design problems that are equivalent to or exceed the challenges posed here and that share the same critical features cited above would also be of interest to DARPA.
		Therefore, successful proposals will have to clearly identify the fundamental scientific and technical issues now faced by the protein design community and describe innovative and interdisciplinary approaches to overcoming current scientific and technical barriers that limit rapid protein design.
		Current approaches to protein design (Journal of Structural Biology 134:269, 2001) primarily involve either top-down approaches via the modification of known protein frameworks (Nature 423:185, 2003) or are limited to the design of protein scaffolds with hydrophobic cores and fixed backbones (Science 282:1462, 1998; Science 302:1364; 2003).
	www.darpa.mil /baa/baa04-12mod7.htm (1383 words)

	SignOnSanDiego.com > News > Business > Biotechnology -- Protein Design's asthma drug results boosts shares
		CHICAGO – Protein Design Labs Inc. said Monday its experimental asthma drug helped patients breathe better in the latest human study of the compound, boosting shares by as much as 12 percent.
		The drug improved patients' ability to move air out of the lungs significantly better than a placebo in a 114-person study of the compound, called daclizumab, the company said.
		Protein Design Labs specializes in developing antibodies to treat disease, a promising new area of research.
	www.signonsandiego.com /news/business/biotech/20040315-0732-health-proteindesign-stocks.html (279 words)

	Protein Design: Automated protein discovery and synthesis
		We will train the networks with natural proteins whose 3D structure and amino acid sequence is known.
		To check the protein's 3D structure, we need to have a model of actual physical world in the computer model.
		If the protein produced is successful in carrying out our desired unction, then it is fit else it is not.
	www.paraschopra.com /articles/protein-design/protein-design.php (522 words)

	Rowland Groups - Protein Folding and Protein Design Laboratory
		The primary interest of our group is the study of protein folding as a means to uderstanding the relationships among sequence, structure, stability and folding kinetics and as a way to further our ability to accomplish de novo protein design.
		Our approach has been to design, de novo, a helical hairpin peptide, alpha-t-alpha, to use as a model system for folding intermediates at the level of secondary structure association and as a test bed for de novo protein design.
		Most of the reseach in our group focuses on studying the physical properties of our model system, on redesigning alpha-t-alpha to investigate specific questions related to protien design or on cloning and expression of the molecule.
	www.rowland.org /organization/past_research/folding/folding.html (150 words)

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