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Topic: Tim barrel

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	TIM Barrel Analysis
		barrel (TIM barrel) is by far the most common tertiary fold observed in high resolution protein crystal structures.
		-strands of the barrel form an intrinsic network of hydrogen bonds with the neighbouring strands and are oriented in the same direction.
		As expected the residues in the barrel are shielded from solvent as evidenced from their low solvent accessibility values.
	www.mrc-lmb.cam.ac.uk /genomes/madanm/articles/timanal.htm (1388 words)

	TIM Barrel (Site not responding. Last check: 2007-10-14)
		It is argued by others that the TIM barrel, which is a very stable arrangement, has been discovered independently by nature on several occasions (convergent evolution).
		Triose Phosphate Isomerase (TIM) is a glycolytic enzyme which catalyses the rapid and reversible isomerisation of glyceraldehyde 3-phosphate (an aldose) and dihydroxyacetone phosphate (a ketose).
		TIM is a homodimer and is shown on the left with 2-phosphoglycolate - a stable transition state analogue - bound at each active site.
	www.bch.bris.ac.uk /staff/hadfield/Folding/timbarrel.htm (334 words)

	Inari Kursula. Crystallographic studies on the structure-function relationships in triosephosphate isomerase. ISBN ...
		The TIM barrel fold seems to be a good framework for many different kinds of enzymes, providing unique possibilities for both natural and human-designed evolution, as the catalytic center and the stabilizing features are separated to different ends of the barrel.
		TIM can be considered a real text-book enzyme — its catalytic properties and stucture-function relationships have been studied for decades.
		TIM is a dimeric enzyme that consists of two identical subunits of 250 residues.
	herkules.oulu.fi /isbn9514270096?tulosta=yes (430 words)

	Barrel Pump - Sustainable Technology for Watering Livestock (Site not responding. Last check: 2007-10-14)
		Equilibrium is reached when the mass of water contained in the barrel (as segments of water separated by air-spacers) is equal to the mass of water in the head (Volume is given by V = Dh * I.D. of Hose * p).
		This limit is reached when the head of water being pumped by the barrel exceeds the mass of water contained in the coils within the barrel.
		Once the barrel of the paddlewheel is immersed beyond its optimum depth, the efficiency of the paddlewheel drops dramatically.
	tim.griffins.ca /writings/old/barrel-pump.html (1163 words)

	HOME IMPROVEMENT : Metalworking : "Barreling Up" a Rifle : DIY Network
		Tim's first cut "trues up" the face of the barrel to match the refined torque surface of the receiver (figure I).
		Before removing the barrel from the lathe, Tim polishes the chamber of the barrel with 600 grit sand paper and kerosene.
		Tim inspects the spent bullet casing and determines that the lack of markings indicate that the chamber is properly polished.
	diynetworks.com /diy/tl_metalworking/article/0,2037,DIY_14390_3740198,00.html (1074 words)

	Mac1 Airgun Distributors
		Barrel is a little longer so we can have a section of full barrel dimension.
		The cost of the barrel is less when run as a bull barrel.
		We have to OD the barrel from.590 to.425" through nearly the full length when the customer opts for the extended tube arrangement.
	www.mac1airgun.com /600mac1style.html (789 words)

	[No title] (Site not responding. Last check: 2007-10-14)
		Triose phosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of glyceraldehyde-3-phosphate (GAP) to dihydroxyacetone phosphate (DHAP) via an enediol (or enediolate) intermediate (Section 14-2E).
		The enzyme is colored with the parallel beta strands of the alpha/beta barrel ("sheets") yellow, their alpha helices ("helices") orange, and the remaining parts of the protein including the loops linking successive alpha helices and beta strands of the alpha/beta barrel ("loops"), greentint.
		This beta barrel is encircled by a kind of barrel made of eight parallel alpha helices that are largely antiparallel to the beta strands.
	torre.fffcmpa.tche.br /Volumes/Bioch_Inter/Kinemage/Exercises/E12_TIM.kin (905 words)

	X-ray structure of human acid-[beta]-glucosidase, the defective enzyme in Gaucher disease
		TIM barrel, as expected for a member of the glucosidase hydrolase A clan.
		Helix 7 is at the interface between the TIM barrel and a separate immunoglobulin-like domain on which L444 is located, suggesting an important regulatory or structural role for this non-catalytic domain.
		The catalytic domain (domain III), which is a TIM barrel, is shown in blue, and the active-site residues E235 and E340 are shown as ball-and-stick models.
	www.nature.com /cgi-taf/DynaPage.taf?file=/embor/journal/v4/n7/full/embor873.html (3278 words)

	Glycolysis & Fermentation
		This inhibitor of catalysis by TIM is similar in structure to the proposed enediolate intermediate.
		TIM is considered a "perfect enzyme", because the reaction rate is limited only by the rate at which substrate collides with the enzyme.
		There is debate over whether the many different TIM barrel enzymes are evolutionarily related, since in spite of the structural similarities there is tremendous diversity in catalytic functions of these enzymes and little sequence homology.
	www.rpi.edu /dept/bcbp/molbiochem/MBWeb/mb1/part2/glycolysis.htm (1469 words)

	CiteULike: tjimenez's tim_barrel (Site not responding. Last check: 2007-10-14)
		Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways.
		One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
		Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.
	www.citeulike.org /user/tjimenez/tag/tim_barrel (97 words)

	Tim's Crappy Barrel Page
		Now note for the barrels that are listed, and there bore sizes and compare bore size to commonly used paintballs.
		Barrels will help increase some range, and shot consistancy, over many stock barrels, but for the most part, all barrels are equal, an elongated tube, with the inside made perfectly smoothed.
		Flatline- This barrel produces a back spin on the paintball allowing the ball to travel further and straighter than any other barrel can.
	www.angelfire.com /extreme2/TCPP/barrel.html (764 words)

	Partial NMR assignments and secondary structure mapping of the isolated {alpha} subunit of Escherichia coli tryptophan ...
		TIM barrel and dynamics, resulting from the absence of the ß
		Nagano, N., Orenga, C.A., and Thornton, J.M. One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
		Pujadas, G. and Palau, J. TIM barrel fold: Structural, functional and evolutionary characteristics in natural and designed molecules.
	www.proteinscience.org /cgi/content/full/12/1/185 (2354 words)

	University of Oulu \|
		Ultimately, such structural studies should allow the prediction of properties of wild type and mutated proteins and in fact one important topic of the TIM project is to engineer new substrate specificity on a monomeric variant of TIM.
		The structures of many TIMs, from many different organisms ranging from extreme thermophiles to a psychrophilic organism have been determined by this and other laboratories, allowing detailed analysis of the mechanism and also other factors such as protein stability.
		The crystal structure of this monomeric variant of TIM has been described; it does not bind the natural substrates and a search has been initiated for new substrates in which the phosphate group is replaced by a neutral group.
	www.biochem.oulu.fi /tutkimus/wierenga (914 words)

	SR127: Structure-Based Functional Annotation (Site not responding. Last check: 2007-10-14)
		SR127 is a variation of the classical TIM barrel fold.
		SR127 has an N-terminal extension (relative to the barrel) of a strand (beta-1)-loop-helix-strand (beta-2) structure, which is packed perpendicular to the axis of the barrel strands, at the location of the "missing" 8th strand.
		Structural alignments reveal that the composition of this region in SR127 is similar to that of chitinase, an O-glycosylhydrolase that hydrolyzes the glycosidic bond of chitin, a beta-1,4 N-acetylglucosamine polymer.
	trantor.bioc.columbia.edu /nesg/SR127/sr127_web.html (253 words)

	A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine ...
		The substrate fragment, desulfo-coenzyme A (dark blue), threads through the TIM barrel domain, effecting the closure of the TIM barrel to the more compact structure shown.
		The Ado moiety of AdoCbl was not observed.
		TIM barrel, is important for positioning AdoCbl outside of the
	www.pnas.org /cgi/content/full/101/45/15870 (3472 words)

	Structural ({beta}{alpha})8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase -- Casals et al. 278 (31): ...
		Structural ({beta}{alpha})8 TIM Barrel Model of 3-Hydroxy-3-methylglutaryl-Coenzyme A Lyase -- Casals et al.
		-strands of the central barrel are in orange, and the
		TIM barrels with values of number of aligned residues and percent
	www.jbc.org /cgi/content/full/278/31/29016 (4441 words)

	NCBI CDD pfam00478
		Members of this family contain a TIM barrel structure.
		In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel.
		This family is a member of the common phosphate binding site TIM barrel family.
	www.ncbi.nlm.nih.gov /Structure/cdd/cddsrv.cgi?uid=pfam00478 (47 words)

	TIM barrel glycosyl hydrolases : Pairwise sequence identity and SSAP scores
		TIM barrel glycosyl hydrolases : Pairwise sequence identity and SSAP scores
		Homologous proteins typically return a score of 80 or above, but a score as low as 65-70 for large homologous structures, primarily TIM barrels, is not uncommon.
		A list of these species representatives and their associated functions may be accessed from the main superfamily summary page.
	www.biochem.ucl.ac.uk /bsm/FAM-EC/glycosyl_hyd/ssap.html (162 words)

	TimMinear.net 4.0
		Tim, if your future work continues to be of the same quality as Wonderfalls then there's no way you can fail.
		Tim, I hope that you are able to find a place for Wonderfalls.
		Tim, you and your crew should be proud of Wonderfalls - what a great freakin' show.
	www.timminear.net /archives/press/000064.html (16387 words)

	Benchrest Central Forums - Kudos for Broughton Rifle Barrels
		If you are looking for a new barrel for this coming 1000 yd season, Tim North and Broughton Barrels is a good place to start.
		The barrel he sends you will spec out exactly as he says it will and he also gives you all the internal specs.
		I won a Broughton barrel at the IBS 1000 YD Nationals.
	www.benchrest.com /forums/showthread.php?t=8546 (287 words)

	DATE: A database of TIM barrel enzymes
		The eight-stranded a /b barrel (TIM barrel) is by far the most common tertiary fold observed in high resolution protein crystal structures.
		Click on the TIM barrel enzyme link for details about the enzyme.
		Residue preferences in different regions of the TIM barrel ezymes:
	www.mrc-lmb.cam.ac.uk /genomes/date (162 words)

	Bioline International Official Site (site up-dated regularly)
		Structurally α-amylases possess (β/α)8 or TIM barrel structures and are responsible for hydrolysis or formation of glycosidic bonds in the α-conformation.
		Hydrolysis activity where the enzymes act on the α-glycosidic bonds and hydrolyse this bond to produce α-anomeric mono-or oligosaccharides or transglycosylation activity where α-1-4 or 1-6 glycosidic linkages are formed or a combination of both activities.
		Some of these conserved amino acids form the catalytic site and some are involved in the stability of the conserved TIM barrel topology (Kuriki and Imanaka, 1999; van der Maarel et al., 2002).
	www.bioline.org.br /request?jb03116 (1637 words)

	WHY A NEW DATABASE? (Site not responding. Last check: 2007-10-14)
		TIM-DB is updated weekly (after PDB releases the new layer1 entries on Wednesday morning) and is therefore more suitable for researchers interested in TIM barrel proteins than the more general SCOP and CATH databases.
		The TIM barrel proteins are classified in TIM-DB according to their EC code.
		Historically, this is the most usual way in which TIM barrel domains have been classified (Farber, 1993; Janecek & Bateman, 1996).
	www.quimica.urv.es /~pujadas/TIM/info (169 words)

	phospholipaseC.html
		The TIM Domain is made up of X, Y, and Z regions and functions as the catalytic center of phospholipase C.
		The main components of the TIM domain are a hydrophobic ridge that promotes membrane penetration, a dished barrel containing catalytic residues, and a site for calcium binding.
		The increase in activity due to the increase in phophotadic acid is proposed to stimulate the anchoring of the enzyme to the membrane(Rebecchi, 2000).
	chat.carleton.ca /~jmcewan/phospholipaseC.html (4112 words)

	Red Bear Hunting Emporium (Site not responding. Last check: 2007-10-14)
		Modeled after the red hot short barrel, we have added a much more aggressive calling style to its design.
		This call is handsomely crafted out of our fine stock of both acrylic and wood to produce a call that will perform day in and day out under the harshest weather conditions.
		We have also laser engraved the new RNT Powers logo on the barrel, to match its outstanding performance with the high quality craftsmanship and good looks you have come to expect from RNT.
	www.redbearhunting.com /shopping.asp?CategoryID=24 (5320 words)

	Gun and Game Forums - Barrel Alternatives?
		I'm getting ready to turn down the flange on the forward end of the receiver and rebarrel it to a cartridge more suitable for a 118 lb.
		There are a few different barrels out there for a small ring,a couple in calibers for your lady.
		I don't know that the receiver date has anything to do with the barrel age.
	www.gunandgame.com /forums/showthread.php?t=1616 (498 words)

	TM0936 (Site not responding. Last check: 2007-10-14)
		PFAM classifies central three quarters of TM0936 as a chlorohydrolase from ATZ/TRZ family; the closest functionally verified homologs is N-ethylammelide chlorohydrolase with 40% sequence identity.
		Threading algorithms predicted the similarity of this domain to the TIM barrel cytosine/adenosine deaminase despite only 10-12% sequence id, as well as overall (including central, N- and C-terminal domains) similarity to urease with slightly higher sequence identity of 18%.
		Both predictions were subsequently confirmed by structure comparison; the central, catalytic domain is most similar to cytosine/adenosine deaminase structure (~2.8 angstrom rmsd over 200 residues), whereas the overall structure, including the N- and C-domains, is most similar to urease with a 3.8 angstrom rmsd over 350 residues.
	www.jcsg.org /novel_features/tm0936.html (214 words)

	ongoing · Metadata, Semantics and All That
		There is no doubt that Tim in particular would like us in the TAG to orient our work more towards the architecture of his vision of the Next Web, rather than the boring old current edition.
		I took the trouble to dive pretty deep into Prolog (something you don’t hear much about now) but at the end of the day thought it was a bunch of bullshit, and said so, and suffered some temporary career damage and subsequently some credibility enhancement.
		Having said all that, as Tim is prone to point out, lots of people also used to say (pre-Web) that Hypertext was also a grand failed experiment.
	www.tbray.org /ongoing/When/200x/2003/11/09/SemWebFirstStep (1101 words)

	Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape -- Finke and Onuchic, ...
		Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape -- Finke and Onuchic, 10.1529/biophysj.105.059147 -- Biophysical Journal
		Articles by Finke, J. Articles by Onuchic, J. Equilibrium and kinetic folding pathways of a TIM barrel with a funneled energy landscape
		The role of native contact topology in the folding of a TIM
	www.biophysj.org /cgi/content/abstract/biophysj.105.059147v1 (219 words)

	Breaking open a protein barrel -- Kallenbach 98 (6): 2958 -- Proceedings of the National Academy of Sciences
		barrel structure that is the subject of the article by Silverman
		Recognizing that burial of nonpolar side chains to form a nonpolar core structure is common to all native protein structures,
		This is a landmark study, showing that large protein structures are now amenable to rigorous testing of hypotheses about folding.
	www.pnas.org /cgi/content/full/98/6/2958 (1684 words)

	FSSA HOWTO : Software (Site not responding. Last check: 2007-10-14)
		For example, suppose you just obtained a new structure with the TIM barrel fold (SCOP fold identifier c.1), and you want to know its exact biological function.
		The problem is that this new structure has low sequence similarity (less than 30%) to any other TIM barrel proteins with known function (based on sequence and structure comparisons).
		The actual function prediction is composed of two steps: First the FSSA script calls the MAMMOTH program and generates all-against-all pairwise structure alignments for all TIM barrel proteins with known function (we use SCOP superfamily to define "same function").
	software.compbio.washington.edu /fssa/fssa-2.html (449 words)

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