Young stellar object - Revision history

77.56.53.183 at 20:09, 4 September 2014

2014-09-04T20:09:55Z

← Older revision		Revision as of 22:09, 4 September 2014
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	The '''contact order''' of a [[protein]] is a measure of the locality of the inter-[[amino acid]] contacts in the protein's [[native state]] [[tertiary structure]]. It is calculated as the average sequence distance between residues that form [[native contact]]s in the folded protein divided by the total length of the protein. Higher contact orders indicate longer [[protein folding\|folding times]],~~<ref name=plaxco>Plaxco, K~~. ~~W., Simons, K. T.,~~ and ~~Baker, D. (1998). Contact order, transition state placement, and the refolding rates of single domain proteins.~~ ''J. ~~Mol. Biol~~.'~~' 277, 985-994.</ref><ref name="Bonneau">Bonneau R, Ruczinski~~ I~~, Tsai J, Baker D. (2002). Contact order and ab initio protein structure prediction. ''Protein Sci'~~' ~~11(8):1937-44~~.<~~/ref~~> ~~and low contact order has been suggested as a predictor of potential [[downhill folding]], or protein folding that occurs without a [[Thermodynamic free energy\|free energy]] barrier.~~<~~ref name="Zuo"~~>~~Zuo G, Wang J, Wang W.~~ (~~2006). Folding with downhill behavior and low cooperativity of proteins. ''Proteins'' 63(1):165-73.</ref> This effect is thought to be due to the lower loss of~~ [~~[conformational entropy]] associated with the formation of local as opposed to nonlocal contacts.<ref name="Bonneau" />~~		Hi there, I am Andrew Berryhill. I am an invoicing officer and I'll be promoted quickly. To climb is some thing I really enjoy performing. I've usually cherished living in Kentucky but now I'm considering other choices.<br><br>Look into my webpage best psychics ([http://www.indosfriends.com/profile-253/info/ please click the following website])

	~~Contact order (CO) is formally defined as:~~
	:~~<math>CO={1 \over {L\cdot N}}\sum^{N}\Delta S_{i,j}<~~/~~math>~~
	where ''N'' is the total number of contacts, Δ''Si,j'' is the sequence separation, in residues, between contacting residues ''i'' and ''j'', and ''L'' is the total number of residues in the protein.<ref name=plaxco /> The value of contact order typically ranges from 5% to 25% for single-domain proteins, with lower contact order belonging to mainly helical proteins, and higher contact order belonging to proteins with a high beta-sheet content.

	[[Protein structure prediction]] methods are more accurate in predicting the structures of proteins with low contact orders. This may be partly because low contact order proteins tend to be small, but is likely to be explained by the smaller number of possible long-range residue-residue interactions to be considered during [[global optimization]] procedures that minimize an [[objective function\|energy function]].<ref name="Mount">Mount DM. (2004). ''Bioinformatics: Sequence and Genome Analysis'' 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.</ref> Even successful structure prediction methods such as the [[Rosetta@Home\|Rosetta]] method overproduce low-contact-order structure predictions compared to the distributions observed in experimentally determined protein structures.~~<ref name="Bonneau"~~ />

	The percentage of the natively folded contact order can also be used as a measure of the "nativeness" of folding [[transition state]]s. [[Phi value analysis]] in concert with [[molecular dynamics]] has produced transition-state models whose contact order is close to that of the folded state in proteins that are small and fast-folding.<ref name="Pandit">Pandit AD, Jha A, Freed KF, Sosnick TR. (2006). Small proteins fold through transition states with native-like topologies. ''J Mol Biol'' 361(4):755-~~70.<~~/ref> Further, contact orders in transition states as well as those in native states are highly correlated with overall folding time.<ref name="Paci">Paci E, Lindorff-Larsen K, Dobson CM, Karplus M, Vendruscolo M. (2005). Transition state contact orders correlate with protein folding rates. ''J Mol Biol'' 352(3):495-500.</~~ref>~~

	~~In addition to their role in structure prediction, contact orders can themselves be predicted based on a [[sequence alignment]], which can be useful in classifying~~ the ~~fold of a novel sequence with some degree of [[homology (biology)\|homology]~~] ~~to known sequences.<ref name="Shi">Yi Shi, Jianjun Zhou, David Arndt, David S. Wishart and Guohui Lin (2008~~)~~. Protein contact order prediction from primary sequences. ''BMC Bioinformatics.'' 9:255.</ref>~~

	~~==References==~~
	~~<references />~~

	~~[[Category:Bioinformatics]]~~
	~~[[Category:Protein structure]]~~

en>ClueBot NG: Reverting possible vandalism by 198.189.163.200 to version by Addbot. False positive? Report it. Thanks, ClueBot NG. (1578705) (Bot)

2013-04-03T21:18:43Z

Reverting possible vandalism by 198.189.163.200 to version by Addbot. False positive? Report it. Thanks, ClueBot NG. (1578705) (Bot)

← Older revision		Revision as of 23:18, 3 April 2013
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	~~Andrew Berryhill~~ is ~~what his wife loves to~~ contact ~~him~~ and ~~he completely digs that title~~. ~~My wife~~ and I ~~reside in Mississippi but now I~~'~~m considering other options~~. ~~Invoicing is my profession. Playing badminton is~~ a ~~thing~~ that he is ~~completely addicted~~ to.<br><br>~~Here~~ is ~~my weblog~~ ... ~~love psychic~~ - [~~http~~://~~www~~.~~seekavideo~~.~~com~~/~~playlist~~/~~2199~~/~~video~~/ ~~www.seekavideo.com~~],		The '''contact order''' of a [[protein]] is a measure of the locality of the inter-[[amino acid]] contacts in the protein's [[native state]] [[tertiary structure]]. It is calculated as the average sequence distance between residues that form [[native contact]]s in the folded protein divided by the total length of the protein. Higher contact orders indicate longer [[protein folding\|folding times]],<ref name=plaxco>Plaxco, K. W., Simons, K. T., and Baker, D. (1998). Contact order, transition state placement, and the refolding rates of single domain proteins. ''J. Mol. Biol.'' 277, 985-994.</ref><ref name="Bonneau">Bonneau R, Ruczinski I, Tsai J, Baker D. (2002). Contact order and ab initio protein structure prediction. ''Protein Sci'' 11(8):1937-44.</ref> and low contact order has been suggested as a predictor of potential [[downhill folding]], or protein folding that occurs without a [[Thermodynamic free energy\|free energy]] barrier.<ref name="Zuo">Zuo G, Wang J, Wang W. (2006). Folding with downhill behavior and low cooperativity of proteins. ''Proteins'' 63(1):165-73.</ref> This effect is thought to be due to the lower loss of [[conformational entropy]] associated with the formation of local as opposed to nonlocal contacts.<ref name="Bonneau" />

			Contact order (CO) is formally defined as:
			:<math>CO={1 \over {L\cdot N}}\sum^{N}\Delta S_{i,j}</math>
			where ''N'' is the total number of contacts, Δ''Si,j'' is the sequence separation, in residues, between contacting residues ''i'' and ''j'', and ''L'' is the total number of residues in the protein.<ref name=plaxco /> The value of contact order typically ranges from 5% to 25% for single-domain proteins, with lower contact order belonging to mainly helical proteins, and higher contact order belonging to proteins with a high beta-sheet content.

			[[Protein structure prediction]] methods are more accurate in predicting the structures of proteins with low contact orders. This may be partly because low contact order proteins tend to be small, but is likely to be explained by the smaller number of possible long-range residue-residue interactions to be considered during [[global optimization]] procedures that minimize an [[objective function\|energy function]].<ref name="Mount">Mount DM. (2004). ''Bioinformatics: Sequence and Genome Analysis'' 2nd ed. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.</ref> Even successful structure prediction methods such as the [[Rosetta@Home\|Rosetta]] method overproduce low-contact-order structure predictions compared to the distributions observed in experimentally determined protein structures.<ref name="Bonneau" />

			The percentage of the natively folded contact order can also be used as a measure of the "nativeness" of folding [[transition state]]s. [[Phi value analysis]] in concert with [[molecular dynamics]] has produced transition-state models whose contact order is close to that of the folded state in proteins that are small and fast-folding.<ref name="Pandit">Pandit AD, Jha A, Freed KF, Sosnick TR. (2006). Small proteins fold through transition states with native-like topologies. ''J Mol Biol'' 361(4):755-70.</ref> Further, contact orders in transition states as well as those in native states are highly correlated with overall folding time.<ref name="Paci">Paci E, Lindorff-Larsen K, Dobson CM, Karplus M, Vendruscolo M. (2005). Transition state contact orders correlate with protein folding rates. ''J Mol Biol'' 352(3):495-500.</ref>

			In addition to their role in structure prediction, contact orders can themselves be predicted based on a [[sequence alignment]], which can be useful in classifying the fold of a novel sequence with some degree of [[homology (biology)\|homology]] to known sequences.<ref name="Shi">Yi Shi, Jianjun Zhou, David Arndt, David S. Wishart and Guohui Lin (2008). Protein contact order prediction from primary sequences. ''BMC Bioinformatics.'' 9:255.</ref>

			==References==
			<references />

			[[Category:Bioinformatics]]
			[[Category:Protein structure]]

en>StringTheory11: fixed dashes using a script

2012-08-25T00:53:44Z

fixed dashes using a script

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