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Topic: Tertiary structure protein

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	Tertiary Protein
		The tertiary structure is the final specific geometric shape that a protein assumes.
		In the prion protein, tyr 128 is hydrogen bonded to asp 178, which cause one part of the chain to be bonding with a part some distance away.
		The example on the left is from the prion protein with the salt bridge of glutamic acid 200 and lysine 204.
	www.elmhurst.edu /~chm/vchembook/567tertprotein.html (510 words)

	Protein structure prediction - Wikipedia, the free encyclopedia
		Protein structure prediction is one of the most significant technologies pursued by computational structural biology and theoretical chemistry.
		The output of experimentally determined protein structures, typically by time-consuming and relatively expensive X-ray crystallography or NMR spectroscopy, is lagging far behind the output of protein sequences.
		Given the amino acid sequence of an unknown structure and the solved structure of a homologous protein, each amino acid in the solved structure is mutated, computationally, into the corresponding amino acid from the unknown structure.
	en.wikipedia.org /wiki/Protein_structure_prediction (708 words)

	Tertiary structure - Wikipedia, the free encyclopedia
		In biochemistry, the tertiary structure of a protein is its overall shape.
		All protein molecules are simple unbranched chains of amino acids, but it is by coiling into a specific three-dimensional shape that they are able to perform their biological function.
		The tertiary structure that a protein assumes to carry out its physiological role inside a cell is known as the native state or sometimes the native conformation.
	en.wikipedia.org /wiki/Tertiary_structure (161 words)

	Tertiary Structure
		Davies) represent the tertiary structure of the antigen-binding portion of an antibody molecule.
		Where the entire protein or parts of a protein are exposed to water (e.g., in blood or the cytosol), hydrophilic R groups — including R groups with sugars attached [Link] — are found at the surface; hydrophobic R groups are buried in the interior.
		A mutation in the gene encoding a protein is a frequent cause of altered tertiary structure.
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/T/TertiaryStructure.html (800 words)

	Proteins (Site not responding. Last check: 2007-10-20)
		The primary structure of a segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain(s), without regard to spatial arrangement (apart from configuration at the alpha-carbon atom).
		The tertiary structure of a protein molecule, or of a subunit of a protein molecule, is the arrangement of all its atoms in space, without regard to its relationship with neighbouring molecules or subunits (IUPAC-IUB, 1970).
		The degree to which the three-dimensional structure of a protein may differ from the native state may vary from a change in a single noncovalent bond or side-chain orientation to the case where almost no atom exist in the same spatial relationship to others except for the constraints of the primary structure.
	www.friedli.com /herbs/phytochem/proteins.html (11287 words)

	Lecture 7: Protein Structure 2 (Site not responding. Last check: 2007-10-20)
		A key feature of protein structure is that the stability depends on the simultaneous presence of all of the noncovalent interactions of the native state.
		During protein folding, the transition from the countless unfolded states to a single native state is accompanied by the burial of solvated nonpolar side chains (and polar peptide units) into the nonsolvated core of the protein.
		The "hydophobic effect" or "hydophobic interaction" in protein structure is derived from the combined properties of H-bonds in water and van der Waals forces applied to amino acid residues with nonpolar side chains.
	info.bio.cmu.edu /Courses/03231/LecF03/Lec07/lec07.html (1114 words)

	Protein @ iCookClub.com
		A protein (from the Greek protas meaning "of primary importance") is a complex, high-molecular-mass, organic compound that consists of amino acids joined by peptide bonds.
		Proteins are essential to the structure and function of all living cells and viruses.
		Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structural motifs to one another; primarily formed by hydrophobic interactions, but hydrogen bonds, ionic interactions, and disulfide bonds are usually involved too.
	reference.icookclub.com /protein.html (625 words)

	Comments on the Difficulty of Protein Tertiary Structure Prediction
		When attempting to understand this lack of success, several things should be kept in mind: x-ray and NMR structures may not represent the native, active conformation of the protein, the protein likely has multiple variant conformations, and the active conformation of the protein may not be at the global potential energy minimum.
		While the determination of tertiary structure through NMR spectroscopy does not require the luck and patience of crystallization of proteins, it shares with this method the placement of the protein into an alien solution for the structure determination.
		Furthermore, the structures produced by x-ray diffraction and NMR spectroscopy are inherently limited in their usefulness due to the methods used in preparing the protein for data collection which prevent the protein from being in its native conformation at the time of data collection.
	bioinfo.mbb.yale.edu /mbb452a/projects/Samuel-C-Stubblefield.html (975 words)

	MLNNg: Protein Structure Prediction
		Even if the number of proteins whose primary sequence is known counts in the number of millions, only few thousands of them have been crystallized and their 3D structure deposited in the Protein Data Bank Unfortunately, neither alternative approaches based on nuclear magnetic resonance cannot be applied at the genomic scale.
		Reliable predictors of the secondary structure of a protein are fundamental to study its folding and functions.
		In this way, the task of predicting the tertiary structure of a protein is splitted in two steps: initially a reliable predictor of secondary structure must be realized (here), then a predictor for the coarse-grained contact map can be used to identify contacts between the segments.
	www.dsi.unifi.it /neural/ProteinStructure/proteomics.html (1415 words)

	Protein Structure Prediction Project (Site not responding. Last check: 2007-10-20)
		It is a remarkable fact that almost all naturally occuring proteins fold into a unique three-dimensional structure, the so-called native state, that is stabilized by only a small free energy of folding of the order of a few 10 kcal/mol.
		Since the cost of experimental techniques for protein structure determination, mostly x-ray crystallography and increasingly NMR, is much higher than the cost of protein sequencing, the number of structure resolved proteins is much smaller than the number of sequenced proteins.
		Both the elucidation of the protein folding mechanism as well as the urgent biomedical need to structurally resolve the sequences proteins as quickly as possible, make it highly desirable to develop theoretical tools that can aid in protein structure prediction on the basis of the amino acid sequence alone.
	iwrwww1.fzk.de /biostruct/PSP/intro.htm (322 words)

	4 Tertiary Protein Structure and folds
		Tertiary structure describes the folding of the polypeptide chain to assemble the different secondary structure elements in a particular arrangement.
		But bear in mind that there are very many protein sequences of which the three dimensional structures are not known for certain, so that the term "motif" strictly applies to primary rather than supersecondary or tertiary structure in these cases.
		This constitutes the structure of the small (63 residue) RNA-binding protein Rop, which is found in certain plasmids (small circular molecules of double-stranded DNA occurring in bacteria and yeast) and involved in their replication.
	swissmodel.expasy.org /course/text/chapter4.htm (2238 words)

	Symmetry-breaking and Molecular Evolution/1
		Primary, secondary, tertiary and global structures and conformation changes in biomolecules are the result of a fractal hierarchy of strong covalent and ionic and weaker chemical interactions - H-bonding, hydrophilic, polar and ven der Waal's interactions, arising from the unresolved non-linear nature of chemical bonding (figures from King, except (e) Watson et.
		The non-linear electromagnetic charge interactions of these asymmetric structures is responsible for both chemical bonding and the hierarchy of weak bonding interactions which result in the non-periodic secondary and tertiary structures of proteins and nucleic acids.
		These are responsible for secondary structures such as the a-helix of proteins and base-pairing and stacking of nucleic acids, and result in the tertiary effects central to enzyme action, whose energetics are determined by global interactions in complex molecules.
	www.dhushara.com /book/biocos/symevol.htm (5619 words)

	(D2OL)™ - Pathogens - Overview
		The highest level of organization in a protein is referred to as its tertiary structure and refers to the arrangement of various secondary structural elements such as alpha helices, beta pleated sheets and beta turns.
		The ribbon model of a protein shows the three dimensional arrangement secondary structural elements and is a flat ribbon like representation of the backbone of the string of amino acid residues.
		The surface of the molecule as experienced by a proto-typical solvent molecule) is useful to probe the surface of a protein for pockets and crevices as potential binding pockets.
	www.d2ol.com /pathogens.html (1137 words)

	Biopharmaceutical protein structure glossary
		The conformation into which a protein “folds.” For proteins consisting of only one polypeptide chain, it is the tertiary structure that is usually referred to by the term “the 3D structure of a protein.
		Structure determination is easiest for single- domain proteins (and these are many of the ones that have been solved).
		The organization of proteins into superfamilies based primarily on their sequences is introduced: examples are given of the methods used to cluster the related sequences and to elucidate the evolutionary history of the corresponding genes within each superfamily.
	www.genomicglossaries.com /content/protein_structure_glossary.asp (2741 words)

	76-456 Biophysical Methods -Common folding patterns of protein tertiary structure
		The protein shown is myoglobin,depicted as a ribbon tracing the path of the polypeptide chain.
		This is the structure of triose phosphate isomerase, an enzyme which has a polypeptide consisting of alternating beta strands (yellow arrow symbols and alpha helix segments (red ribbon).
		Proteins which fold into multiple domains don't necessarily repeat the same folding pattern as we have seen here for lactate dehydrogenase, but may have alpha helical bundles, and anti-parallel beta sheets and beta-alpha-beta domains all occuring in the same protein, giving the whole molecule a rather more complex appearance.
	www.chembio.uoguelph.ca /educmat/phy456/Protstr4.htm (957 words)

	Tertiary Protein - The Building Blocks For Muscle Mass (Site not responding. Last check: 2007-10-20)
		Tertiary structure describes the folding of the polypeptide chain to...
		Introduction: Denaturation of proteins involves the disruption and possible destruction of both the secondary and tertiary structures.
		Tertiary structure (from protein) The tertiary structure is the product of the interaction between the side chains (R) of the amino acids composing the protein.
	protein.muscledir.com /index.php?k=tertiary-protein (809 words)

	Protein Structure
		Proteins are linear, unbranched polymers of amino acids joined by peptide bonds formed via dehydration synthesis reactions (Figure 3.16; see also Web figure).
		Proteins can be broken down in the laboratory by acid hydrolysis to yield a mixture of amino acids.
		Proteins are, structurally speaking, the most sophisticated molecules known.
	www.people.virginia.edu /~rjh9u/IntroBio/bio201/lectures/Lecture05.html (602 words)

	Protein Tertiary Structure Prediction using KONF90, PSA/GAc, and NetSolve
		Protein is a substance directly connected to the biological phenomena and its biological functions are said to be derived from its tertiary structure.
		Thus, clarification of its tertiary structure leads to an explanation of the biological phenomena process.
		The tertiary structure of the protein is believed to correspond to the conformation with the lowest residual potential energy.
	icl.cs.utk.edu /netsolvedev/applications/gac.html (214 words)

	Tertiary protein structure - Bioinformatics Wiki
		Protein molecules are composed of linked amino acid chains that assume a three-dimensional structure which is the basis of a proteins function.
		Structural biology is the study of protein tertiary structure.
		LOOPP - Sequence to sequence, sequence to structure, and structure to structure alignment
	www.bioinformaticsinfo.com /wiki/Tertiary_protein_structure (235 words)

	Chem4Kids.com: Biochemistry: Proteins
		As proteins are being built, they begin as a straight chain of amino acids.
		The third step in the creation of a protein is the tertiary structure when the amino acid chains begin to fold even more and bond using more bridges (the disulfide bridges).
		In the quaternary structure, several amino acid chains from the tertiary structure fold together in a blob.
	www.chem4kids.com /files/bio_proteins.html (270 words)

	Protein Structure, Secondary
		Protein Loop Classification is a database containing conformational clusters and consensus sequences for protein loops that have been derived by computational analysis of their structures in a non-redundant set of 235 proteins with less than 25% sequence homology (X-ray resolution better than 2.5 A).
		A flowchart is given of a generalised approach to predicting protein structure.
		Presented in 2001, "Structural changes that accompany the self-assembly of hydrophobins" is the PhD thesis of Marcel de Vocht of the Faculty of Science at the University of Groningen.
	bioresearch.ac.uk /browse/mesh/D017433.html (2391 words)

	Gel electrophoresis, high speed gel 6 minutes
		In gel electrophoresis, a matrix consisting of either polyacrylamide (for proteins and small nucleic acids) or agarose (for larger nucleic acids) is prepared.
		SDS is used in electrophoresis to denature proteins.
		A random or irregularly bent/folded section of a polypeptide chain with a secondary structure.
	www.6mgel.com /gel_electrophoresis.htm (958 words)

	Protein Tertiary - The Building Blocks For Muscle Mass (Site not responding. Last check: 2007-10-20)
		Understand the hierarchy of protein structure: primary, secondary, tertiary, quaternary.
		segment of a polypeptide chain or of a protein is the amino-acid sequence of the polypeptide chain...
		Therefore, in this system, the protein tertiary structure is determined by minimizing...
	protein.muscledir.com /index.php?k=protein-tertiary (815 words)

	Using Computers to Study Molecular Structure (Site not responding. Last check: 2007-10-20)
		To study tertiary structure, you'll examine the enzyme lysozyme.
		These are covalent bonds that link distant parts of the protein primary structure, and are common in extracellular proteins.
		The tertiary structure of an enzyme is integral to its ability to bind with specific substrates.
	www.biology.arizona.edu /biochemistry/activities/molecular_structure/tertiary_structure.html (245 words)

	Online Analysis Tools - Protein Tertiary Structure
		With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology analysis.
		It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure.
		Since the protein is scanned in seven directions, each grid point can be defined to be part of a site up to seven times.
	molbiol-tools.ca /Protein_tertiary_structure.htm (988 words)

	Protein Structure 3: Modelling Tertiary Structure.
		It may be easier to see the likeliness and differences in the structures by viewing only the ribbons of the proteins.
		Then test the effect of moving gaps and the use of the "mean force potential", validate your alignment and request a model.
		In case a model of your protein or a close relative exists, then build your model on the structures of less related proteins and compare with the "correct" model in the end.
	virgil.ruc.dk /kurser/Sekvens/mnproteinstructure3.htm (538 words)

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