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Topic: Protein ligands

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Ligand

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	Ligand - Wikipedia, the free encyclopedia
		In biology, a ligand is an extracellular substance that binds to receptors.
		The ligand geometries are named and described as if the central atom were in the middle of a polyhedron, and the corners of that shape were the locations of the ligands.
		For example, a complex with four regularly distributed ligands would be described as tetrahedral, while one with six would be octahedral.
	en.wikipedia.org /wiki/Protein_Ligand (572 words)

	Ligand --Biotechnology Encyclopedia
		The charge on the central atom constrains the number of ligands that may be bonded, since each type of ligand donates a characteristic number of electrons and there is a requirement for overall neutrality.
		Ligands which bind to the central atom through more than one site of their own are termed polydentate; a ligand binding through two sites, for example, is bidentate.
		Complexes of polydentate ligands are called chelated complexes; they tend to be more stable than monodentate complexes as it is necessary to break all of the bonds to the central atom for the ligand to be displaced.
	www.biotech100.com /biotechnology_encyclopedia/ligand.htm (428 words)

	ipedia.com: Ligand Article (Site not responding. Last check: 2007-11-03)
		The inner-sphere ligands arrange themselves in a certain geometry, fixed for a given complex but in some cases mutable by reaction to another stable isomer.
		This is probably a carryover from the large number of binding studies on oxygen transport proteins, such as hemoglobin, where the ligand does indeed bind at a metal site, an expansion of the term to a more general case of binding.
		Protein ligands are studied in structural biology and metabolomics.
	www.ipedia.com /ligand.html (543 words)

	ligand
		In chemistry, a ligand is an atom, ion or functional group that is bonded to one or more central atoms or ions, usually metals generally through co-ordinate covalent bond.
		If the directly-bonded ligands (the "inner-sphere" ligands) do not balance the charge, this may be done by purely ionic interaction with another set of ions (the "outer-sphere" ligands).
		Radioactive ligands (radioligands) are used together with positron emission tomography to study the receptor systems of the brain.
	en.mcfly.org /ligand (476 words)

	Ligand (Site not responding. Last check: 2007-11-03)
		Some ligand molecules are able to bind to the metal ion through multiple sites, since they have free lone pairs on more than one atom; these are called ''polydentate''.
		A scorpionate ligand is an example of a tridentate ligand.Complexes of polydentate ligands are called ''chelated'' complexes; they tend to be more stable than monodentate complexes as it is necessary to break all of the bonds to the central atom for the ligand to be displaced.
		In biochemistry, '''ligand''' refers to a small molecule that binds to a larger macromolecule, whether or not the ligand actually binds at a metal site.
	q-basic.xodox.de /ligands (504 words)

	Ligand Article, Ligand Information (Site not responding. Last check: 2007-11-03)
		Ligands which bind to the central atom through morethan one site of their own are termed polydentate; a ligand binding through two sites, for example, isbidentate.
		This is probably a carryover from the large number of binding studies on oxygen transport proteins, such as hemoglobin, where the ligand does indeed bind at a metal site, an expansion ofthe term to a more general case of binding.
		Protein ligands arestudied in structural biology and metabolomics.
	www.anoca.org /ligands/atom/ligand.html (520 words)

	Ligand (Site not responding. Last check: 2007-11-03)
		Ligands which bind to the central through more than one site of their are termed polydentate ; a ligand binding through two sites example is bidentate.
		The ligand geometries are named and described if the central atom were in the of a polyhedron and the corners of that shape the locations of the ligands.
		This is probably a carryover the large number of binding studies on transport proteins such as hemoglobin where the ligand does indeed bind a metal site an expansion of the to a more general case of binding.
	www.freeglossary.com /Ligand (563 words)

	Protein ligands mediate the CRM1-dependent export of HuR in response to heat shock.
		Protein ligands mediate the CRM1-dependent export of HuR in response to heat shock.
		HuR and its ligands may be instrumental in the nuclear export of heat-shock mRNAs.
		We recently showed that HuR interacts with two protein ligands, pp32 and APRIL, which are also shuttling proteins, but rely on NES domains recognized by CRM1 for export.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/9066146.html (262 words)

	Protein ligands to HuR modulate its interaction with target mRNAs in vivo.
		Protein ligands to HuR modulate its interaction with target mRNAs in vivo.Three have been reported to be protein phosphatase 2A inhibitors.
		We show that pp32 and APRIL are nucleocytoplasmic shuttling proteins that interact with the nuclear export factor CRM1 (chromosomal region maintenance protein 1).
		Here, we identify four mammalian proteins that bind regions of HuR known to be essential for its ability to shuttle between the nucleus and the cytoplasm and to stabilize mRNA: SETalpha, SETbeta, pp32, and acidic protein rich in leucine (APRIL).
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/8628644.html (282 words)

	Profiling Charge Complementarity and Selectivity for Binding at the Protein Surface -- Sulea and Purisima 84 (5): 2883 ...
		the protein molecule is depicted schematically in Fig.
		The ligand charge is constrained within a chemically meaningful range of [-1; +1] e (unshaded) during optimization of binding affinity.
		Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.
	www.biophysj.org /cgi/content/full/84/5/2883 (7333 words)

	PSU Chemistry \| Blake R. Peterson (Site not responding. Last check: 2007-11-03)
		This research is based on our discovery that protein binding motifs linked to N-alkyl derivatives of 3beta-cholesterylamine can be directly loaded into plasma membranes of living mammalian cells to promote the endocytosis of impermeable protein ligands.
		The cellular uptake of ligands mediated by these synthetic receptors appears to mimic endocytic cellular penetration mechanisms employed by certain protein toxins and viruses.
		Our laboratory is investigating novel ligands of nuclear hormone receptors in an effort to identify compounds that block the growth of drug-resistant breast and prostate cancers.
	www.chem.psu.edu /profs/Peterson.html (842 words)

	Simulations of Cell-Surface Integrin Binding to Nanoscale-Clustered Adhesion Ligands -- Irvine et al. 82 (1): 120 -- ...
		adsorbed adhesion proteins or, as depicted in Fig.
		The interface of a cell membrane juxtaposed with a surface presenting tethered ligands is modeled as a two-dimensional square lattice.
		The spatial distribution of ligands is determined at the outset of the simulation and remains static during equilibration
	www.biophysj.org /cgi/content/full/82/1/120 (6297 words)

	G Protein-Coupled Receptor Allosterism and Complexing -- Christopoulos and Kenakin 54 (2): 323 -- Pharmacological ...
		-dependent mitogen-activated protein kinase signaling mediated by the insulin receptor tyrosine kinase, possibly by sequestering G protein in an inactive ternary complex of inverse-agonist, CB receptor, and G protein.
		In these examples, ligand affinity is either maximally diminished (A) or enhanced (B) by a factor of 10.
		Allosteric ligand-mediated receptor-G protein interactions are not restricted to the muscarinic acetylcholine receptors.
	pharmrev.aspetjournals.org /cgi/content/full/54/2/323 (8874 words)

	Protein-protein docking with multiple residue conformations and residue substitutions -- Lorber et al. 11 (6): 1393 -- ...
		Asp189 of trypsin and a bridging water molecule (2.6 Å from the docked ligand) are shown for context.
		The best-scoring CI-2 ligand (green) generated from multiconformer docking is shown with the unbound conformation of subtilisin (catalytic triad shown in cyan).
		Lee, B. and Richards, F.M. The interpretation of protein structures: Estimation of static accessibility.
	www.proteinscience.org /cgi/content/full/11/6/1393?ck=nck (7119 words)

	Annexins: From Structure to Function -- Gerke and Moss 82 (2): 331 -- Physiological Reviews
		protein ligand that is itself associated with or embedded in the
		The third annexin-S100 protein interaction described to date is that between annexin A11 and S100A6 (312).
		annexin A2 protein causing the submembraneous aggregation of annexin
	physrev.physiology.org /cgi/content/full/82/2/331 (11126 words)

	Ligand Binding to Integrins -- Plow et al. 275 (29): 21785 -- Journal of Biological Chemistry (Site not responding. Last check: 2007-11-03)
		and fibrinogen, a physiologic ligand for this integrin.
		in ligand binding to the leukocyte integrins is complicated.
		The extracellular matrix protein mindin serves as an integrin ligand and is critical for inflammatory cell recruitment
	www.jbc.org /cgi/content/full/275/29/21785 (3878 words)

	Hormonal Genomics -- Leo et al. 23 (3): 369 -- Endocrine Reviews
		(16), and of diverse ligands belonging to the cytokine (17),
		DNA sequences to gene transcript expression to protein function.
		Kudo M, Chen T, Nakabayashi K, Hsu SY, Hsueh AJ 2000 The nematode leucine-rich repeat-containing, G protein-coupled receptor (LGR) protein homologous to vertebrate gonadotropin and thyrotropin receptors is constitutively active in mammalian cells.
	edrv.endojournals.org /cgi/content/full/23/3/369 (8467 words)

	Uncovering Molecular Mechanisms Involved in Activation of G Protein-Coupled Receptors -- Gether 21 (1): 90 -- Endocrine ...
		The chemical diversity among the endogenous ligands is
		the endogenous ligands of the opioid receptors (136).
		An agonist-induced rigid-body movement of TM 6 involving a counterclockwise rotation and a movement of the cytoplasmic end of the helix away from TM 3, as indicated by the arrow, would cause Cys285-NBD to be exposed to a more polar environment in the interior of the protein.
	edrv.endojournals.org /cgi/content/full/21/1/90 (9316 words)

	Directory of open access journals
		The hydrolysis of ATP and ADP by ecto-nucleoside triphosphate diphosphohydrolase 1 (CD39) requires divalent cations, like Ca and Mg In spite of considerable work, it is not clear whether divalent cations bind to the enzyme in the absence of nucleotide or only as nucleotide-Me complex.
		When VO was used as a substitute for Ca, the ATPase activity of soluble CD39 was 25% of that with Ca as cofactor.
		Protein ligands of the VO -nucleotide complex bound to the catalytic site of soluble CD39 were characterized by electron paramagnetic resonance (EPR) spectroscopy.
	www.doaj.org /abstract?id=80498&toc=y (235 words)

	U.I.C. Biochemistry - Dr. Gettins (Site not responding. Last check: 2007-11-03)
		Serpins are large proteins (45-100kDa) that act as inhibitors, and thus regulators, of important physiological processes such as blood coagulation and fibrinolysis, and that employ a remarkable conformational change mechanism for inhibition of target proteinases.
		We are interested in determining the structural basis for the ability of LRP to bind to such a wide range of unrelated proteins.
		To address this we are detemining the structure of domains of LRP that bind ligands and of complexes of these domains, whether single or larger species, in complex with target protein ligands.
	www.uic.edu /depts/mcbtp/gettins.htm (1259 words)

	Protein-protein docking with multiple residue conformations and residue substitutions -- Lorber et al. 11 (6): 1393 -- ...
		Ritchie, D.W. and Kemp, G.J. Protein docking using spherical polar Fourier correlations.
		Shoichet, B.K. and Kuntz, I.D. Protein docking and complementarity.
		Protein Sci., May 1, 2005; 14(5): 1328 - 1339.
	www.proteinscience.org /cgi/content/full/11/6/1393 (7131 words)

	SCOL: The Structural Classification of Ligands (Site not responding. Last check: 2007-11-03)
		The objective of the SCOL project is to produce a global hierarchical clustering of all the available small molecules and protein ligands using measures of structural, chemical and biological 'similarity' between molecules.
		This classification system should prove useful for diverse studies, from the gross assessment of metabolic evolution to ligand binding studies.
		Investigate 'biological' measures of similarity derived from the evolution of ligand binding proteins, and assess the overlap with SCOL.
	www.bioinformatics.org /scol/index.html (699 words)

	Binding, internalization, and intracellular processing of protein ligands. Derivation of rate constants by computer ...
		Binding, internalization, and intracellular processing of protein ligands.
		constant for ligand- receptor complexes, and kh is the intracellular ligand
		internalized ligand of other systems taken from the literature, were in
	www.jbc.org /cgi/content/abstract/262/14/6494 (389 words)

	Profos AG
		Binding ligand from the lytic enzyme — called the 'Cellwall Binding Domain' (or CBD)
		Up to 3 types of phage ligands and a lytic enzyme per bacteria!
		Copyright: All contents, graphics, forms, programmes and the structure of profos website are subject to copyright of profos ag, unless stated otherwise.
	www.profos.de /lifecycle.php (86 words)

	biochem1_0p16abs (Site not responding. Last check: 2007-11-03)
		ligands in studies of the spatial structure of neuroreceptors are reviewed.
		Key words: neuroreceptors, photoaffinity modification, peptide and protein ligands, neurotoxins
		If you have any problems with this server, contact webmaster@maik.ru.
	maik.rssi.ru /cgi-bin/search.pl?type=abstract&name=biochem&number=1&year=0&page=16 (98 words)

	Protein ligands (Site not responding. Last check: 2007-11-03)
		You can click on this message to see their list of those items.
		Presents the use of cutting edge protein engineering technologies to create protein ligands.
		Examining the molecular surface, possible binding sites, new ligands, prediction of unknown structures and in-vivo properties, at the Insitute of Biochemistry, Charite Humboldt University, Berlin, Germany.
	www.omniknow.com /common/wiki.php?in=en&term=Protein_ligands (376 words)

	SWBIC - Compendiums & Lists of Resource Links (Site not responding. Last check: 2007-11-03)
		The large number of resource categories include academic sites, conferences, employment, genomics, proteins, grants & contracts, intellectual property, methods & protocols, software, and venture capital.
		This site contains information on their research in microbiology, natural products, cell and immune biology, molecular biotechnology, biochemical engineering, and structure research.
		Many links for ligands, protein structure, drug design, computational chemistry, bioinformatics.
	www.swbic.org /links/2.5.php (1186 words)

	The Protein Structure Database (PSdb) -- Table II (Site not responding. Last check: 2007-11-03)
		The Protein Structure Database (PSdb) -- Table II The Protein Structure Database (PSdb), Deerfield, Geigel -- Table II Table II: Contacts used in solvent accessible molecular surface area (SAMSA) computations.
		ALL Protein Contacts Plus Ligands Plus Metal Ions (including water of hydration)
		ALL Protein Contacts Plus Ligands Plus Metal Ions Plus Structural Water Molecules
	www.psc.edu /~deerfiel/PSdb/PSdbPaper/table2.html (54 words)

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