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Topic: Noncovalent

	3.5.1
		Noncovalent bonds are largely responsible for the secondary and higher order structure of macromolecules.
		However, the possibility of combining within a limited area a great number of noncovalent bonds having complementary elements allows the formation of a large specific association whose affinity may be of the same order of magnitude as a covalent bond.
		Hydrogen Bond -- A second important noncovalent interaction is the hydrogen bond, a dipole formed when a hydrogen atom covalently bonded to an electronegative atom is shared with a second electronegative atom (typically an oxygen, nitrogen or fluorine atom), such that the proton may be approached very closely by an unshared pair of electrons.
	www.nanomedicine.com /NMI/3.5.1.htm (1214 words)

	Noncovalent interactions
		Noncovalent or van der Waals interactions were first recognized by J. van der Waals in the nineteenth century [3].
		In noncovalent interactions, in turn, no overlapping is necessary because the attraction comes from the electrical properties of the building blocks.
		Noncovalent interactions comprise interactions between permanent multipoles, between a permanent multipole and an induced multipole, and between a time–variable multipole and an induced multipole.
	herkules.oulu.fi /isbn9514259971/html/x156.html (908 words)

	Noncovalent Interactions: A Challenge for Experiment and Theory
		Noncovalent interactions are known to act at distances of several angstroms or even tens of angstroms and overlap is thus unnecessary (in fact overlap between occupied orbitals leads only to repulsion).
		For noncovalent clusters, the essentially statistical quantum-chemical description at 0 K should be combined with a statistical description at nonzero temperature, because dynamical characteristics of noncovalent complexes are more pronounced than those of covalent molecules.
		Noncovalent interactions lead to the formation of noncovalently bound clusters when a compound, generally seeded in helium, neon, or argon, is expanded in a jet.
	pubs.acs.org /cgi-bin/jtextd?chreay/100/i01/html/cr9900331 (15086 words)

	Photochemistry and Photobiology: Stabilization of the optical tracer agent indocyanine green using noncovalent ... (Site not responding. Last check: 2007-10-14)
		Such noncovalent binding between dye and carrier molecules was found to preserve substantially the dye in aqueous solutions for several weeks with no apparent changes in the measured in vivo biological properties.
		The variety of colors observed in flowers and plants, for instance, is attributed to noncovalent association between the natural pigments and the carbohydrates or proteins found in plant cells (1).
		To this end, several cationic, anionic and neutral polymers were noncovalently bound to ICG and evaluated in vitro and in vivo.
	www.findarticles.com /p/articles/mi_qa3931/is_200003/ai_n8887160 (1454 words)

	BindingDB
		These noncovalent interactions can cause molecules to bind to each other in solution with binding energies that can be quite small, or as large as 100 kJ/mol.
		Specific noncovalent binding, or "molecular recognition", is fundamental to biology: examples include the recognition of substrates by enzymes, the action of biological transmitters at their receptors, the binding and inactivation of foreign proteins by antibodies, and the inhibition of enzymes by drugs.
		A database of binding measurements would facilitate the elucidation of the physical basis for noncovalent binding, and thus the development of predictive models that would be useful to industry.
	www.bindingdb.org /bind/update/workshop_rep1b.html (1152 words)

	Noncovalent Interactions (Site not responding. Last check: 2007-10-14)
		For small organic molecules it is convienent to think about covalent bonds as intramolecular (i.e as defining the structure of the molecule) and noncovalent interactions as intermolecular.
		This view is not useful for macromolecules such as proteins; in this case both covalent bonding and intramolecular noncovalent bonding are important in determining the structure of these molecules.
		Covalent and noncovalent bonds differ in their strength.
	webhost.bridgew.edu /fgorga/proteins/noncovalent.htm (176 words)

	Christa L. Colyer - Research Interests and Publications
		The determination of phycobiliproteins and investigations into the mechanism of noncovalent binding of nonfluorescent proteins with visible and near-infrared organic dyes are examples of current projects in the Colyer lab.
		By coming to understand the nature of noncovalent interactions between various dye and protein molecules, it will be possible to develop efficient, high sensitivity analytical methods with applicability to the separation and quantitation of nonfluorescent proteins in complex mixtures.
		Noncovalent labeling strategies, coupled with CE and laser-induced fluorescence (LIF), are designed to overcome the disadvantages normally associated with protein derivatization, such as increased sample preparation and handling, restrictive solution pH and temperature conditions, and decreased separation efficiency due to the formation and partial resolution of multiple, differently-labeled species.
	www.wfu.edu /academics/chemistry/faculty/ChristaColyerResearch.html (758 words)

	Reconstitution of a native-like SH2 domain from disordered peptide fragments examined by multidimensional heteronuclear ...
		N HSQC spectra for the noncovalent complex of His-tagged p85, titrated to a 1:1 complex at 100 µM (red), and native His-tagged p85 at 240 µM (fl).
		One-dimensional proton spectra at 25°, 30°, 35°, 40°, 45°, and 50°C are shown for a noncovalent complex of p85 at 100 µM peptide fragments.
		Native peaks disappear and denatured peptide peaks arise as the temperature is raised.
	www.proteinscience.org /cgi/content/full/10/11/2162 (6267 words)

	[Mechanism of aspartyl proteinase action. VII. Noncovalent complexes of HIV-1 aspartyl proteinase with substrate and ...
		A computer model of a noncovalent complex of HIV-1 aspartyl protease with substrate-like inhibitor JG-365 was a priori constructed by using the approaches of theoretical conformational analysis and molecular mechanics.
		The root mean square deviation of the calculated conformation of the inhibitor from the X-ray diffraction analysis data was 0.87 A. These results enabled the a priori calculation of the structure of noncovalent complex of HIV-1 protease with a hexapeptide fragment of its native specific substrate Ser-Gln-Asn-Tyr-Pro-Ile-Val.
		The only possible orientation of the cleavable peptide bond in this and the nucleophilic water molecule relative to the catalytically active Asp residues of the enzyme (Asp25 and Asp125) was found that provides for the chemical transformation of the substrate to a tetrahedral intermediate.
	www.aegis.com /aidsline/2000/jul/A0071284.html (440 words)

	Noncovalent Interactions in Proteins
		One of the major goals of the biochemistry curriculum is to understand the type and nature of noncovalent interactions that occur within and between biomolecules.
		The search for noncovalent interactions is possible through the use of molecular visualization software such as RasMol, RasTop and Protein Explorer.
		The search for noncovalent interactions have been undertaken by biochemistry students at all levels.
	campus.murraystate.edu /academic/faculty/ricky.cox/pi/pi_inter.htm (359 words)

	- US Patent (Site not responding. Last check: 2007-10-14)
		A process of claim 9, wherein the noncovalent linkage between the monomeric fusion proteins forming the dimeric protein is formed in vitro.
		A dimeric protein of claim 13, wherein the noncovalent interaction between the interactive peptides on each monomeric fusion protein is by intercalation.
		The term "noncovalent interaction" means every existing under normal condititions stable linkage which is not related to a covalent binding, for example linkage by Van der Waal's forces, (steric) interdigitation of amphiphilic peptides, especially peptide helices, or peptides bearing opposite charges of amino acid residues.
	www.patentstorm.us /patents/5910573.html (6424 words)

	Noncovalent complex between domain AB and domains CDEF of parvalbumin. (Site not responding. Last check: 2007-10-14)*
		Noncovalent complex between domain AB and domains CD*EF of parvalbumin.
		Noncovalent complex between domain AB and domains CDEF of parvalbumin.The interaction between domain AB and domains CDEF of pike parvalbumin III has been studied by intrinsic fluorescence spectroscopy.
		The affinity of the complex of the two fragments for calcium is 50-times higher than the affinity of the isolated fragment 38-108, but slightly lower than that of the intact protein.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/23968.html (107 words)

	A novel artificial loop scaffold for the noncovalent constraint of peptides.: Rigel Pharmaceuticals
		A method for stabilization and noncovalent constraint of relatively short peptides may allow the construction and use of intracellular peptide libraries containing protein mini-domains.
		Results: We have examined a novel method for the noncovalent constraint of peptides by attaching the peptide EFLIVKS, which forms dimers, to the N- and C-terminus of different peptide inserts.
		Use of these dimerizing peptides flanking random insert sequences may be a feasible strategy to generate heterogeneous peptide libraries with both extended and folded members.
	www.rigel.com /rigel/Rigel_Publications (352 words)

	Thermochemistry of Noncovalent Metal-Ligand Interactions in the Gas Phase
		Noncovalent interactions are attracting significant attention from the chemical and biological disciplines as a result of their scientific importance and potential technological applications.
		Technological applications that make use of noncovalent interactions are numerous and range from nanoelectronics and biochemical sensors, to a variety of pharmaceutical applications.
		Metal ion-ligand binding is one of the many types of noncovalent bonding interactions and is the focus of our work.
	scienide.uwaterloo.ca /%7Eleroy/cpseminars/0001/rodgers.htm (311 words)

	Noncovalent interactions in coal structures: effects of additives on extraction yield and solubility of extracts (Site not responding. Last check: 2007-10-14)
		Noncovalent interactions in coal structures: effects of additives on extraction yield and solubility of extracts
		All of these results suggest that the associations between coal molecules by non-covalent interactions, such as hydrogen bonds, and [pi]-[pi] interactions, influence significantly the extraction yields and the solubility of extracts; these associations are broken with additives.
		Cross-link structures of coals are discussed from the perspective of noncovalent interactions.
	www.anl.gov /PCS/bib/ref451.html (225 words)

	D0017: Crystal Structures of Human Topoisomerase I in Covalent and Noncovalent Complexes with DNA (Site not responding. Last check: 2007-10-14)
		Crystal structures of human topoisomerase I in covalent and noncovalent complexes with a 22 bp DNA duplex reveal an enzyme that wraps completely around essentially B-form DNA and makes extensive contacts with the phosphate backbone but few base specific contacts.
		Crystals structures at 2.1 and 2.5 Å resolution of reconstituted human topo I in covalent and noncovalent complexes, respectively, with DNA provide a view before and after the enzyme breaks a single strand of the DNA duplex and forms a transient phosphate-tyrosine bond with the 3' end of the broken strand.
		The 2.8 Å crystal structure of an intact 70 kDa form of topo I, including a flexible linker domain not present in the reconstituted enzyme, in noncovalent complex with DNA reveals all the structural elements necessary for a proposed mechanism for the relaxation of superhelical tension termed "controlled rotation".
	www.hwi.buffalo.edu /ACA/ACA98/abstracts/text/D0017.html (339 words)

	Discussion 1 (Site not responding. Last check: 2007-10-14)
		Purich, D. (2001) Enzyme catalysis: a new definition accounting for noncovalent substrate- and product-like states.
		The making and breaking of noncovalent bonds by energases lies at the heart of affinity-modulated binding interactions of cytoskeletal proteins.
		By building on Pauling's assertion that any long-lived, chemically distinct interaction is a chemical bond, this article redefines enzyme catalysis as the facilitated making and/or breaking of chemical bonds, not just of covalent bonds.
	www.med.ufl.edu /IDP/Core01/Outln5/S5D1.html (211 words)

	Spectroscopy: Determination of recombinant monoclonal antibodies and noncovalent antigen TNF[alpha] trimer using Q-TOF ... (Site not responding. Last check: 2007-10-14)
		Spectroscopy: Determination of recombinant monoclonal antibodies and noncovalent antigen TNF[alpha] trimer using Q-TOF mass spectrometry.
		Determination of recombinant monoclonal antibodies and noncovalent antigen TNF[alpha] trimer using Q-TOF mass spectrometry.
		In the 1980s, the molecular weight (MW) of a protein could be determined by electrophoretic, light-scattering, chromatographic, or ultracentrifugation methods; however, the MW was not very accurate.
	www.highbeam.com /library/doc0.asp?DOCID=1G1:86743445&refid=holomed_1 (187 words)

	Noncovalent Bonding
		At any given pH, proteins have charged groups that may participate in binding them to each other or to other types of molecules.
		Noncovalent interactions are individually weak but collectively strong.
		All three forms of noncovalent interactions are individually weak (on the order of 5 kcal/mole) as compared with a covalent bond (with its 90-100 kcal/mole of bond energy).
	users.rcn.com /jkimball.ma.ultranet/BiologyPages/N/Noncovalent.html (579 words)

	Sequences Within the Amino Terminus of ApoB100 Mediate Its Noncovalent Association With Apo(a) -- Gabel et al. 18 (11): ... (Site not responding. Last check: 2007-10-14)
		Western blot analysis of noncovalent binding of human apoB expressed in McA-RH7777 cells to 17K r-apo(a) affinity column.
		Positions of apoB100 and apoB48-like protein are indicated to left of the blot.
		noncovalent association of apoB and apo(a) is not affected by
	atvb.ahajournals.org /cgi/content/full/18/11/1738 (4765 words)

	Mechanism and pathway of penicillopepsin-catalyzed transpeptidation and evidence for noncovalent trapping of amino acid ... (Site not responding. Last check: 2007-10-14)
		Mechanism and pathway of penicillopepsin-catalyzed transpeptidation and evidence for noncovalent trapping of amino acid and peptide intermediates.
		Mechanism and pathway of penicillopepsin-catalyzed transpeptidation and evidence for noncovalent trapping of amino acid and peptide intermediates.Penicillopepsin acting on Nph-Ala2-amide (where Nph = p-nitrophenylalanyl) catalyzes a transpeptidation reaction which leads to the formation of Nph2-Ala2-amide, which arises from condensation of the substrate with enzyme-bound Nph, as the first product released from the enzyme.
		We propose that Nph and Nph2 as intermediates are held in the active site by hydrogen bonds and by two strong electrostatic interactions.
	www.pdg.cnb.uam.es /UniPub/iHOP/gp/7007325.html (249 words)

	JCE 2000 (77) 1424 [Nov] Teaching Noncovalent Interactions in the Biochemistry Curriculum through Molecular ...
		Inherent in this task is the introduction of the structure of the amino acids and the various types of noncovalent interactions.
		When these two topics are taught together, the students gain a better appreciation for the importance of noncovalent interactions in stabilizing the structure of proteins and protein complexes.
		To introduce these ideas, RasMol, a molecular visualization program, was used by students to search for specific examples of noncovalent interactions in a variety of protein structures.
	www.jce.divched.org /Journal/Issues/2000/Nov/abs1424.html (242 words)

	The observation of chaperone-ligand noncovalent complexes with electrospray ionization mass spectrometry (Site not responding. Last check: 2007-10-14)
		The observation of chaperone-ligand noncovalent complexes with electrospray ionization mass spectrometry.
		Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was applied for the study of noncovalent chaperone SecB-ligand complexes produced in solution and examined in the gas phase with the aid of electrospray ionization (ESI).
		A high denaturant concentration was employed to produce nonnative structures of the OppA, and microdialysis of the resulting solutions containing the chaperone-ligand complexes was carried out to rapidly remove the denaturant prior to analysis.
	www.emsl.pnl.gov /docs/msd/mass_spec/home/publications/78.html (258 words)

	Angiotensin II-Acetylcholine Noncovalent Complexes Analyzed With MALDI-Ion Mobility-TOF MS -- Woods et al. 14 (1): 1 -- ...
		Angiotensin II-Acetylcholine Noncovalent Complexes Analyzed With MALDI-Ion Mobility-TOF MS -- Woods et al.
		Noncovalent Interactions Between Acetylcholine and Phosphorylated Angiotensin II and Angiotensin II, as Measured by MALDI-IM-TOF MS
		noncovalent complexes with phosphorylated residues in a peptide.
	jbt.abrf.org /cgi/content/full/14/1/1 (2576 words)

	Monitoring ligand-mediated nuclear receptor-coregulator interactions by noncovalent mass spectrometry -- Sanglier et ... (Site not responding. Last check: 2007-10-14)
		Monitoring ligand-mediated nuclear receptor-coregulator interactions by noncovalent mass spectrometry -- Sanglier et al.
		Monitoring ligand-mediated nuclear receptor–coregulator interactions by noncovalent mass spectrometry
		Keywords: ESI-MS; noncovalent mass spectrometry; nuclear receptors; protein–protein interactions; protein–ligand interactions.
	content.febsjournal.org /cgi/content/abstract/271/23-24/4958 (280 words)

	Noncovalent Bond Finder Access (Site not responding. Last check: 2007-10-14)
		The Noncovalent Bond Finder makes it very easy to find and display the atoms closest to any ligand or group of "target atoms" you select.
		The Noncovalent Bond Finder is not yet integrated into the Protein Explorer.
		Be aware that starting the Noncovalent Bond Finder will automatically close your Protein Explorer (PE) session (due to a conflict which prevents simultaneous operation).
	www.rcsb.org /pdb/pe/explorer/finder.htm (139 words)

	Noncovalent SUMO-1 Binding Activity of Thymine DNA Glycosylase (TDG) Is Required for Its SUMO-1 Modification and ... (Site not responding. Last check: 2007-10-14)
		Noncovalent SUMO-1 Binding Activity of Thymine DNA Glycosylase (TDG) Is Required for Its SUMO-1 Modification and Colocalization with the Promyelocytic Leukemia Protein -- Takahashi et al.
		Articles by Takahashi, H. Articles by Nakayama, K. Noncovalent SUMO-1 Binding Activity of Thymine DNA Glycosylase (TDG) Is Required for Its SUMO-1 Modification and Colocalization with the Promyelocytic Leukemia Protein
		To identify molecules that bind noncovalently to SUMO-1, we
	www.jbc.org /cgi/content/abstract/280/7/5611 (392 words)

	Zenobi Web
		Our goal is the determination of the binding strength of noncovalent associates with help of electrospray (ESI) time-of-flight (TOF) mass spectrometry.
		However, the coupling of spray and TOF strategies is delicate due to the lower pressure allowed in a flight chamber.
		Electrospray ionization is a very soft ionization technique that allows large compounds such as proteins and noncovalent complexes to be ionized and transferred into the gasphase.
	www.zenobi.ethz.ch /esi.html (266 words)

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