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Topic: Protein engineering

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	Protein Engineering
		Protein engineering, that is creating proteins sequences whose specific functions are determined by their three dimensional shape, holds the key to tailoring protein catalysts and rational drug design.
		While gene sequences are converted to protein sequences by ribosomes, the process of correctly converting sequences to folding patterns is not well understood.
		The sequence of amino acids in a protein regulates the folding of the protein chain, with the folding pattern dependent on interactions among the amino acid's side chains.
	istf.ucf.edu /Tools/NCTs/Living_Systems/Protein_Engineering (264 words)

	Protein engineering - Wikipedia, the free encyclopedia
		Protein engineering is the application of science, mathematics, and economics to the process of developing useful or valuable proteins.
		However, there is a major drawback in that detailed structural knowledge of a protein is often unavailable, and even when it is available, it can be extremely difficult to predict the effects of various mutations.
		This is where random mutagenesis is applied to a protein, and a selection regime is used to pick out variants that have the desired qualities.
	en.wikipedia.org /wiki/Protein_engineering (486 words)

	Chimera (protein) - Wikipedia, the free encyclopedia
		A Chimera (or chimeric protein) is a human-engineered or in vivo mutated protein that is encoded by a nucleotide sequence made by a splicing together of two or more complete or partial genes or cDNA.
		Chimeric proteins can be manufactured with toxins or anti-bodies attached to them in order to study disease development.
		Mostly, these chimeras are generated by overlap extension PCR or by ligating two pieces of cDNA and are then cloned into a plasmid, that is able to express the chimeric gene in a cellular environment.
	en.wikipedia.org /wiki/Chimera_(protein) (174 words)

	Protein engineering glossary (Site not responding. Last check: 2007-11-02)
		In proteins hydrogen bonds involving the main chain oxygen and amide are critical in forming the secondary structures.
		Protein: A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene coding for the protein.
		Proteins are required for the structure, function, and regulation of the body’s cells, tissues, and organs, and each protein has unique functions.
	xray.bmc.uu.se /~kenth/bioinfo/glossary.html (7983 words)

	Protein Folding and Protein Structure Prediction
		Proteins accomplish their task by three-dimensional tertiary and quaternary interactions between various substrates such as DNA and RNA, and other proteins.
		Since it was discovered that proteins are capable of folding into their unique functional 3D structures without any additional genetic mechanisms, over 25 years of effort has been expended into the prediction of 3D structure from sequence.
		Structural analyses on demand of proteins for further mutagenesis, substrate and inhibitor design, and enhanced function and stability is also possible, as is analysis of basic functional behaviour on demand using time-tested methods such as molecular dynamics simulations.
	www.iscb.org /ismb2000/tutorials/samudrala.html (1093 words)

	SCOTT BANTA
		With different combinations of the 20 common amino acids (and some modifications of these amino acids), proteins have evolved with a staggering array of functions and capabilities including: the specific binding of ligands, catalysis of complex chemical reactions, functionality in extreme environments, transportation of valuable molecules, and the exhibition of diverse structural and material properties.
		Originally, protein engineering evolved as a powerful method for the investigation and verification of hypotheses during the study of protein functions.
		Proteins are generally optimized to function in their native environments.
	www.columbia.edu /~sb2373/protein.html (426 words)

	Danith H. Ly -> Research -> Protein Engineering (Site not responding. Last check: 2007-11-02)
		Protein uses surface morphology as a recognition element for binding (through a multitude of H-bonding, van der Waals, electrostatics, and covalent interactions).
		Although the kinetic and thermodynamic parameters governing the binding properties of some of these proteins have been fairly understood, it is still problematic to design proteins that would fold and assemble in a prescribed manner.
		The ability to tailored-design proteins with simple recognition code is essential to deciphering the cellular network, in which any protein can be directed to bind to protein target of interest.
	www.chem.cmu.edu /groups/ly/research/protein.html (244 words)

	Analytical - Protein engineering
		Side-chain modifications or unusual amino acids can be used, and protein folding is performed routinely with control of the disulfide pattern.
		This is performed through solid phase peptide synthesis, recombinant protein expression systems using controlled growth media or semi-synthesis.
		In addition to solid phase peptide synthesis and refolding, we also use liquid phase chemistry to specifically modify or label free amino acids or polypeptidic structures.
	www.atheris.com /prot_eng.htm (285 words)

	Thayer School - Research in Therapeutic Protein Engineering
		Engineering fungal expression systems that produce therapeutic proteins with human-like structures could serve to effectively alleviate this manufacturing bottleneck.
		Fungal-based protein expression systems offer inherent advantages over conventional mammalian cell culture systems in that they do not promote human pathogens, do not rely on any animal-derived growth factors or media components which could harbor infectious agents, and are able to produce properly folded proteins at an industrial scale.
		Some human proteins naturally lack glycosylation (attachment of specific complex carbohydrate structures to the protein) and can therefore be produced by a simple bacterial host.
	engineering.dartmouth.edu /thayer/research/protein.html (328 words)

	B I O T E C H N O L O G Y - PROTEIN ENGINEERING
		Proteins have diverse functions, and can be transport molecules (haemoglobin, the oxygen carrier in the blood), receptors for specific molecules on cell surfaces, enzymes (biocatalysts), antibodies, structural proteins (i.e.
		Protein engineering entails the chemical or genetic alteration of a protein in order to alter its function in a predictable manner and requires the interaction of physicists, chemists, biochemists, molecular biologists, and computer scientists.
		Protein engineering can be utilized to facilitate protein design for the production of protein and peptide mimics (e.g., neuropeptidase inhibitors), for enzyme inhibitors which are effective as pharmaceuticals, and for vaccine development (synthesis of oligopeptides that can induce a positive immune response).
	www.odofin.com /english/protein.htm (356 words)

	Directed Mutagenesis and Protein Engineering
		The enzyme subtilisin is a protease (a protein-digesting protein) produced by bacteria, and has a broad specificity for proteins that commonly soil clothing.
		It was found that substitution of methionine by alanine was the best in terms of activity and stability, and now many laundry detergents contain cloned, genetically engineered subtilisin.
		Generally, it is unknown which of these combinations is what one is looking for, as it is difficult to predict on the basis of a primary sequence what the three-dimensional structure of a protein (and of the active site) will be in detail.
	photoscience.la.asu.edu /photosyn/courses/BIO_343/lecture/protein.html (772 words)

	DrexlerNanotechnology81PNAS
		In attempting this, protein chemists can search for a minimum-energy chain conformation (in hope that the protein assumes not a local but a global minimum-energy conformation) (6) or can attempt to follow the chain-folding mechanism to find the final conformation (7).
		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).
		Protein engineers, exploiting their freedom of design, can work with sequences artificially selected for superior predictability and stability of folding.
	www.imm.org /PNAS.html (4296 words)

	Foresight Update 6 Page 3
		Protein engineering is a new field; separate meetings, journals, and books devoted to the topic have only appeared during the last two to three years.
		You use computer graphics to display the three dimensional structure, which has been experimentally determined for the protein that you are studying, or, failing that, of a protein that is sufficiently closely related to serve as a model.
		Enzymology, a branch of classical biochemistry, leads to the idea that a protein's function follows from its three-dimensional, or "tertiary," structure, and further, that its three-dimensional structure follows from the linear sequence of amino acid residues that comprises its "primary" structure.
	www.foresight.org /Updates/Update06/Update06.3.html (3386 words)

	Nano Mechanism to Control Protein May Lead to New Protein Engineering
		Proteins are switched on and off in living cells by a mechanism called allosteric control; proteins are regulated by other molecules that bind to their surface, inducing a change of conformation, or distortion in the shape, of the protein, making the protein either active or inactive, Zocchi explained.
		The MBP protein binds and transports a sugar.
		Zocchi's co-authors, in addition to Choi, are L. Jeanne Perry, director of UCLA's Protein Expression Technology Center in the Institute for Genomics and Proteomics and adjunct associate professor of molecular, cell and developmental biology; former UCLA undergraduate Stephen Canale; and staff researchers Yim Wu and Sum Chan.
	www.physorg.com /news3074.html (712 words)

	BOSTON UNIVERSITY \| DEPARTMENT OF BIOMEDICAL ENGINEERING
		Protein Legos - We believe that favorable packing arrangements between alpha helices and beta strands are finite.
		We call such arrangements "protein legos" and predict them to be the fundamental units of protein structure.
		Protein Engineering - This is the wet-lab component of our lab.
	www.bu.edu /dbin/bme/research/labs/protein_eng.php (222 words)

	Pharmaceutical proteins glossary
		Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties.
		All new proteins in the cell have a tag on them, telling whether the protein is to be sent out of the cell or to a special part in the cell.
		Proteins provide the critical link between genes and disease, and as such are the key to understanding of basic biological processes including disease pathology, diagnosis, and treatment.
	www.genomicglossaries.com /content/proteins_glossary.asp (3523 words)

	Microbial Cell Factories \| Full text \| Insertional protein engineering for analytical molecular sensing
		In this context, insertional protein engineering offers the possibility to develop new devices, efficiently responding to ligand interaction by dramatic conformational changes, in which the specificity and magnitude of the sensing response can be adjusted up to a convenient level for specific analyte species.
		In this context, the convenient insertional engineering of the carboxy terminus of p53, containing such a regulatory element, has resulted in a set of p53 variants that are activated upon its removal mediated by either the lethal factor (LF) or the human immunodeficiency virus (HIV) protease [28].
		Feliu JX, Villaverde A: Engineering of solvent-exposed loops in Escherichia coli beta-galactosidase.
	www.microbialcellfactories.com /content/5/1/15 (4011 words)

	CHI's PepTalk 2006 (Site not responding. Last check: 2007-11-02)
		Protein engineering can be defined as the use of genetic and chemical techniques to change the structure and function of a protein, thus producing a novel product with specific, desired, properties.
		A major challenge in the development of effective protein therapeutics is to minimize any adverse side effects that may be caused by multiple interactions among families of related receptors and corresponding ligands, such as occur in the FGF and TNF receptor/ligand families.
		In its native form, this protein binds to two related cytokine ligands, with one of these interactions responsible for the therapeutic effects in reducing bone loss, and the other interaction interfering in apoptotic mechanisms such that tumor growth may be enhanced.
	www.chi-peptalk.com /pttn2006.asp (1943 words)

	Oxford Journals \| Life Sciences \| PEDS
		In January 2004, the journal Protein Engineering was relaunched as Protein Engineering, Design and Selection, or PEDS.
		PEDS publishes research papers and review articles relevant to the engineering, design and selection of proteins for use in biotechnology and therapy, and for understanding fundamental properties of activity, stability, folding, misfolding and disease.
		The journal has new editors, a new editorial structure, and a new reviewing system to make it a community journal run by protein scientists for their own discipline.
	peds.oxfordjournals.org (107 words)

	Determining the substrate specificity of protein kinases
		Protein kinases are a family of enzymes that catalyze the transfer of a gamma phosphate from nucleotide triphosphates (usually ATP) to tyrosine, serine, or threonine amino acid residues of substrate proteins.
		Obviously, protein kinases are a very important class of enzymes and a great deal of research has been done in an effort to understand these proteins.
		Identifying the substrates of protein kinases is an important goal, as it will contribute greatly to the understanding of complex cellular processes controlled by kinase signaling and will also undoubtedly uncover novel drug targets [1-13].
	www.udel.edu /chem/bahnson/chem645/websites/Brohawn (2694 words)

	ScienceDaily: Nano Mechanism To Control Protein May Lead To New Protein Engineering
		Novel Protein Is Both Ion Channel And Enzyme (January 19, 2001) -- Researchers have discovered a new protein component of cell-signaling pathways that does double dutyacting as both an ion channel that controls calcium entry into cells and as an enzyme that...
		Novel Mechanism Of Protein Processing Found (September 12, 2006) -- Colinearity of DNA and protein sequences is thought to be a fundamental feature of the universal genetic code.
		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/2005/02/050222112801.htm (1841 words)

	:: MIT ChE :: Research - Biological Engineering
		Chemical engineering thermodynamics, transport, and chemical kinetics, so useful for manufacturing processes, are fruitful tools for exploring biological systems, as well.
		Biological engineering research may be directed at molecular level processes, the cell, tissues, the organism, and large-scale manufacturing in biotech processes.
		It may be applied to producing specialized proteins, genetic modification of cells, transport of nutrients and wastes in tissue, therapeutic methods of drug delivery, tissue repair and generation, purification of product molecules, and control strategies for complex bio-production plants.
	web.mit.edu /cheme/research/biological.html (285 words)

	ScienceDaily: Physicists Report Advance Toward Nanotechy Approach To Protein Engineering
		In the new research, the group succeeded in activating the enzyme PKA through the same principle, by using the molecular spring to induce the change in conformation that, in the cell, is induced by the natural activator of PKA (the signaling molecule cAMP).
		Nano Mechanism To Control Protein May Lead To New Protein Engineering (February 23, 2005) -- UCLA scientists have created a mechanism at the nanoscale to externally control the function and action of a protein.
		Heat shock protein -- Heat shock proteins (HSP) are a group of proteins the expression of which is increased when the cells are exposed to elevated...
	www.sciencedaily.com /releases/2006/06/060610225705.htm (2084 words)

	Headlines@Hopkins: Johns Hopkins University News Releases
		Using a lab technique called domain insertion, Johns Hopkins researchers have joined two proteins in a way that creates a molecular "switch." The result, the researchers say, is a microscopic protein partnership in which one member controls the activity of the other.
		Through such survival tests, the researchers ultimately were able to find two fusion proteins in which not only were both proteins still active, but in which the presence of maltose actually caused the beta-lactamase partner to step up its attack on an antibiotic.
		Ostermeier also suggested that one part of a fusion protein might react to the presence of a biological warfare agent, signaling its partner to set off a bright green flourescent glow that could alert soldiers and others to the danger.
	www.jhu.edu /news_info/news/home03/mar03/molecule.html (827 words)

	Protein Engineering and Biocatalysis - ChBE- SCS - UIUC (Site not responding. Last check: 2007-11-02)
		In contrast, we may use a combinatorial, semi-rational approach for protein engineering termed directed evolution.
		He is now using his expertise for directed evolution of new genes, proteins, enzymatic pathways, and whole genomes for biomedical and biotechnological applications.
		Pack is applying similar methods for engineering of viral gene delivery vectors for human gene therapy and for evolving enzymes and proteins in mammalian systems for therapeutic applications.
	www.chemeng.uiuc.edu /Research/ProtEng.html (235 words)

	Research team borrows metal tool for protein engineering - MIT News Office
		Each protein's function depends on its unique three-dimensional structure, which, in turn, rests on the molecule's specific linear chain, or sequence, of 20 different amino acids.
		Beginning with an existing protein structure does reduce the number of possible ways to rearrange the amino acids, but the numbers are still mind-boggling.
		MIT engineers mine with computers - A computational technique used to predict everything from books that a given customer might like to the function of an unknown protein is now being applied by MIT engineers and colleagues to the search for new materials.
	web.mit.edu /newsoffice/2005/protein.html (885 words)

	Wiley::Protein Engineering: Principles and Practice
		Protein Engineering: Principles and Practice provides a basic framework for understanding both proteins and protein engineering.
		The book begins by introducing the main concepts of protein engineering, including: understanding protein conformation, comprehending the relationship between protein composition and structure, and potential methods for predicting a protein's conformation.
		Of primary interest to protein scientists-both students and researchers, in academia as well as industry-Protein Engineering is also extremely useful to chemical engineers, protein chemists, biochemists, and pharmaceutical chemists.
	www.wiley.com /WileyCDA/WileyTitle/productCd-0471103543.html (295 words)

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