Magneto-optic Kerr effect - Revision history

90.218.36.242 at 17:27, 14 September 2014

2014-09-14T17:27:43Z

← Older revision		Revision as of 19:27, 14 September 2014
Line 1:		Line 1:
	[[Image:Pi helix neg55 neg70 sideview.png\|thumb\|right\|250px\|Side view of a standard π-helix of L-[[alanine]] residues in [[atom]]ic detail. Two [[hydrogen bond]]s to the same [[peptide bond\|peptide group]] are highlighted in magenta; the oxygen-hydrogen distance is 1.65 Å (165 pm). The [[protein]] chain runs upwards, ~~i.e., its N-terminus~~ is ~~at the bottom and its C-terminus at the top of the figure. Note that the sidechains point slightly ''downwards'', i.e., towards the N-terminus.]]~~		Hi there, I am Alyson Boon although it is not the title on my birth certification. My day occupation is a travel agent. Ohio is where my home is but my husband wants us to transfer. It's not a typical thing but what she likes doing is to play domino but she doesn't have the time lately.<br><br>Also visit my web-site :: [http://cartoonkorea.com/ce002/1093612 free psychic]

	A '''pi helix''' (or '''π-helix''') is a type of [[secondary structure]] found in [[protein]]s.<ref name="pmid14816373">{{cite journal \|doi=10.1073/pnas.37.4.205 \|author=Pauling L, Corey RB, Branson HR \|year=1951 \|title=The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain \|journal=Proc. Natl. Acad. Sci. U.S.A. \|volume=37 \|issue=4 \|pages=205–211 \|pmid=14816373 \|pmc=1063337}}</ref> Although thought to be rare, π-helices are actually found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an [[α-helix]].<ref name="pmid20888342">{{cite journal \|doi=10.1016/j.jmb.2010.09.034 \|author=Cooley RB, Arp DJ, Karplus PA \|year=2010 \|title=Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices enhancing protein functionality\|journal=J Mol Biol \|volume=404 \|issue=2 \|pages=232–246 \|pmid=20888342 \|pmc=2981643}}</ref> Because such insertions are highly destabilizing,<ref name="pmid8475069">{{cite journal \|author=Keefe LJ, Sondek J, Shortle D, and Lattman EE \|year=2000 \|title=The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease\|journal=Proc. Natl. Acad. Sci. U.S.A. \|volume=90 \|issue=8 \|pages=3275–3279 \|pmid=8475069 \|pmc=46282 \|doi=10.1073/pnas.90.8.3275}}</ref> the formation of π-helices would tend to be selected against unless it provided some functional advantage to the ~~protein. π-helices therefore are typically found near functional sites of proteins.<ref name="pmid20888342" /><ref name="pmid10739264">{{cite journal \|author=Weaver TM \|year=2000 \|~~title=The pi-helix translates structure into function\|journal=[[Protein Science]] \|volume=9 \|issue=1 \|pages=201–206 \|pmid=10739264 \|pmc=2144447 \|doi=10.1110/ps.9.1.201}}</ref><ref name="pmid12034854">{{cite journal \|author=Fodje MN, Al-Karadaghi S \|year=2002 \|title=Occurrence, conformational features and amino acid propensities for the pi-helix\|journal=Protein Eng \|volume=15 \|issue=5 \|pages=353–358 \|pmid=12034854 \|doi=10.1093/protein/15.5.353 }}</ref>

	~~==Standard structure==~~

	The [[amino acid]]s in a standard π-helix are arranged in a right-handed [[helix\|helical]] structure. Each amino acid corresponds to an 87° turn in the helix (i.e., the helix has 4.1 residues per turn), and a translation of 1.15 [[Ångström\|Å]] (=0.115 [[Nanometre\|nm]]) along the helical axis. Most importantly, the [[amine\|N-H]] group of an amino acid forms a [[hydrogen bond]] with the [[carbonyl\|C=O]] group of the amino acid ''five'' residues earlier; this repeated ''i''+5→''i'' hydrogen bonding '''defines''' a π-helix. Similar structures include the [[310 helix\|3<sub>10</sub> helix]] (''i''+3→''i'' hydrogen bonding) and the [[Alpha helix\|α-helix]] (''i''+4→''i'' hydrogen bonding).

	~~[[Image:Pi helix topview.png\|thumb\|left\|150px\|Top view of the same helix shown above. Four [[carbonyl]] groups are pointing upwards towards the viewer, spaced roughly 87° apart~~ on ~~the circle, corresponding to 4~~.~~1 [[amino acid\|amino-acid]] residues per turn of the helix.]]~~

	The majority of π-helices are only 7 residues in length and do not adopt regularly repeating (φ, ψ) [[dihedral angle]]s throughout the entire structure like that of α-helices or β-sheets. Because of this, textbooks that provide single dihedral values for all residues in the π-helix are misleading. Some generalizations can be made, however. When the first and last residue pairs are excluded, dihedral angles exist such that the ψ [[dihedral angle]] of one residue and the φ dihedral angle of the ''next'' residue sum to roughly -125°. The first and last residue pairs sum to -95° and -105°, respectively. For comparison, the sum of the dihedral angles for a ~~3<sub>10</sub> helix is roughly -75°, whereas that for the α-helix is roughly -105°~~. ~~Proline~~ is ~~often seen immediately following the end of π-helices. The general formula for the rotation angle Ω per residue of any polypeptide helix with ''trans'' isomers~~ is ~~given by the equation~~

	~~:<math>~~
	~~3 \cos \Omega = 1 - 4 \cos^{2} \left[ \left(\phi + \psi \right)/2 \right]~~
	~~</math>~~

	~~==Left-handed structure==~~

	~~In principle, a left-handed version of the π-helix is possible by reversing the sign of the (φ, ψ) [[dihedral angle]]s~~ to ~~(55°, 70°)~~. ~~This pseudo-"mirror-image" helix has roughly the same number of residues per turn (4.1) and helical pitch (1.5 angstroms or 150 [[picometer]]~~s~~). It is~~ not a true mirror image, because the [[amino acid\|amino-acid]] residues still have a left-handed [[chirality (chemistry)\|chirality]]. <!-- Need to make the image, and check whether hydrogen bonds are still made. --> A long left-handed π-helix is ~~unlikely~~ to ~~be observed in proteins because, among the naturally occurring amino acids, only [[glycine]] is likely to adopt positive φ dihedral angles such as 55°.~~

	~~==π-helices in nature==~~
	[[File:Pi-helix within an alpha-helix.jpg\|thumb\|left\|A short, 7 residue π-helix (orange) is embedded within a longer, α-helix (green). The "bulge" of the π-helix can be clearly seen, and was created as the result of a single amino acid that has been inserted into an α-helix. PBD code 3QHB.]]

	Commonly used automated secondary structure assignment programs, such as [[DSSP (protein)\|DSSP]], suggest <1% of proteins contain a π-helix. This mis-characterization results from the fact that naturally occurring π-helices are typically short in length (7-10 residues) and are almost always associated with (i.e. flanked by) α-helices on either end. Nearly all π-helices are therefore cryptic in that the π-helical residues are incorrectly assigned as either α-helical or as "turns". Recently developed programs have been written to properly annotate π-helices in protein structures and they have found that 1 in 6 proteins (~15%) do in fact contain at least one π-helical segment.<ref name="pmid20888342"/>

	Natural π-helices can easily be identified in a structure as a "bulge" within a longer α-helix. Such helical bulges have previously been referred to as α-aneurisms, α-bulges, π-bulges, wide-turns,looping outs and π-turns, but ~~in fact are π-helices as determined by their repeating~~ '~~'i''+5→''i'' hydrogen bonds.<ref name="pmid20888342"/> Evidence suggests that these bulges, or π-helices, are created by~~ the ~~insertion of a single additional amino acid into a pre-existing α-helix. Thus, α-helices and π-helices can be inter-converted by the insertion and deletion of a single amino acid~~.<~~ref name="pmid20888342"/~~><~~ref name="pmid8475069"/~~> ~~Given both the relatively high rate of occurrence of π~~-helices and their noted associtation with functional sites (i.e. active sites) of proteins, this ability to inter-convert between α-helices and π-helices has been an important mechanism of altering and diversifying protein functionality over the course of evolution.<ref name="pmid20888342"/>

	One of the most notable group of proteins whose functional diversification appears to have been heavily influenced by such an evolutionary mechanism is the ferritin-like superfamily, which includes [[ferritin]]s, [[bacterioferritin]]s, rubrerythrins, class I [[ribonucleotide reductase]]s and [[Methane monooxygenase#Soluble methane Monooxygenase .28MMO.29 Systems\|soluble methane monooxygenases]]. Soluble methane monooxygenase is the current record holder for the most number of π-helices in a single enzyme with 13 (PDB code 1MTY). ~~However, the bacterial homologue of a Na+~~/~~Cl− dependent neurotransmitter transporter (PDB code 2A65) holds the record for the most number of π-helices in a single peptide chain with 8.<ref name="pmid20888342"~~/>

	~~==See also==~~

	* [[alpha helix]]
	* [[3 10 helix]]
	* [[secondary structure]]

	~~== References ==~~
	~~{{reflist}}~~

	~~{{Protein secondary structure}}~~

	~~[[Category:Protein structural motifs]]~~
	~~[[Category:Helices]~~]

65.189.33.3: /* Magnetic Media */

2013-12-30T22:06:27Z

Magnetic Media

← Older revision		Revision as of 00:06, 31 December 2013
Line 1:		Line 1:
	~~They contact me Emilia~~. ~~I am~~ a ~~meter reader~~ but ~~I plan on changing~~ it. ~~South Dakota is her birth place but she needs~~ to ~~move simply because~~ of ~~her family~~. It's ~~not~~ a ~~typical factor but what she likes doing~~ is ~~base leaping~~ and ~~now she~~ is ~~trying~~ to make ~~money~~ with it.<br><br>~~My website~~ ... [~~http://www~~.~~blaze16~~.~~com~~/~~blog~~/~~257588 std testing at home~~]		[[Image:Pi helix neg55 neg70 sideview.png\|thumb\|right\|250px\|Side view of a standard π-helix of L-[[alanine]] residues in [[atom]]ic detail. Two [[hydrogen bond]]s to the same [[peptide bond\|peptide group]] are highlighted in magenta; the oxygen-hydrogen distance is 1.65 Å (165 pm). The [[protein]] chain runs upwards, i.e., its N-terminus is at the bottom and its C-terminus at the top of the figure. Note that the sidechains point slightly ''downwards'', i.e., towards the N-terminus.]]

			A '''pi helix''' (or '''π-helix''') is a type of [[secondary structure]] found in [[protein]]s.<ref name="pmid14816373">{{cite journal \|doi=10.1073/pnas.37.4.205 \|author=Pauling L, Corey RB, Branson HR \|year=1951 \|title=The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain \|journal=Proc. Natl. Acad. Sci. U.S.A. \|volume=37 \|issue=4 \|pages=205–211 \|pmid=14816373 \|pmc=1063337}}</ref> Although thought to be rare, π-helices are actually found in 15% of known protein structures and are believed to be an evolutionary adaptation derived by the insertion of a single amino acid into an [[α-helix]].<ref name="pmid20888342">{{cite journal \|doi=10.1016/j.jmb.2010.09.034 \|author=Cooley RB, Arp DJ, Karplus PA \|year=2010 \|title=Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices enhancing protein functionality\|journal=J Mol Biol \|volume=404 \|issue=2 \|pages=232–246 \|pmid=20888342 \|pmc=2981643}}</ref> Because such insertions are highly destabilizing,<ref name="pmid8475069">{{cite journal \|author=Keefe LJ, Sondek J, Shortle D, and Lattman EE \|year=2000 \|title=The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease\|journal=Proc. Natl. Acad. Sci. U.S.A. \|volume=90 \|issue=8 \|pages=3275–3279 \|pmid=8475069 \|pmc=46282 \|doi=10.1073/pnas.90.8.3275}}</ref> the formation of π-helices would tend to be selected against unless it provided some functional advantage to the protein. π-helices therefore are typically found near functional sites of proteins.<ref name="pmid20888342" /><ref name="pmid10739264">{{cite journal \|author=Weaver TM \|year=2000 \|title=The pi-helix translates structure into function\|journal=[[Protein Science]] \|volume=9 \|issue=1 \|pages=201–206 \|pmid=10739264 \|pmc=2144447 \|doi=10.1110/ps.9.1.201}}</ref><ref name="pmid12034854">{{cite journal \|author=Fodje MN, Al-Karadaghi S \|year=2002 \|title=Occurrence, conformational features and amino acid propensities for the pi-helix\|journal=Protein Eng \|volume=15 \|issue=5 \|pages=353–358 \|pmid=12034854 \|doi=10.1093/protein/15.5.353 }}</ref>

			==Standard structure==

			The [[amino acid]]s in a standard π-helix are arranged in a right-handed [[helix\|helical]] structure. Each amino acid corresponds to an 87° turn in the helix (i.e., the helix has 4.1 residues per turn), and a translation of 1.15 [[Ångström\|Å]] (=0.115 [[Nanometre\|nm]]) along the helical axis. Most importantly, the [[amine\|N-H]] group of an amino acid forms a [[hydrogen bond]] with the [[carbonyl\|C=O]] group of the amino acid ''five'' residues earlier; this repeated ''i''+5→''i'' hydrogen bonding '''defines''' a π-helix. Similar structures include the [[310 helix\|3<sub>10</sub> helix]] (''i''+3→''i'' hydrogen bonding) and the [[Alpha helix\|α-helix]] (''i''+4→''i'' hydrogen bonding).

			[[Image:Pi helix topview.png\|thumb\|left\|150px\|Top view of the same helix shown above. Four [[carbonyl]] groups are pointing upwards towards the viewer, spaced roughly 87° apart on the circle, corresponding to 4.1 [[amino acid\|amino-acid]] residues per turn of the helix.]]

			The majority of π-helices are only 7 residues in length and do not adopt regularly repeating (φ, ψ) [[dihedral angle]]s throughout the entire structure like that of α-helices or β-sheets. Because of this, textbooks that provide single dihedral values for all residues in the π-helix are misleading. Some generalizations can be made, however. When the first and last residue pairs are excluded, dihedral angles exist such that the ψ [[dihedral angle]] of one residue and the φ dihedral angle of the ''next'' residue sum to roughly -125°. The first and last residue pairs sum to -95° and -105°, respectively. For comparison, the sum of the dihedral angles for a 3<sub>10</sub> helix is roughly -75°, whereas that for the α-helix is roughly -105°. Proline is often seen immediately following the end of π-helices. The general formula for the rotation angle Ω per residue of any polypeptide helix with ''trans'' isomers is given by the equation

			:<math>
			3 \cos \Omega = 1 - 4 \cos^{2} \left[ \left(\phi + \psi \right)/2 \right]
			</math>

			==Left-handed structure==

			In principle, a left-handed version of the π-helix is possible by reversing the sign of the (φ, ψ) [[dihedral angle]]s to (55°, 70°). This pseudo-"mirror-image" helix has roughly the same number of residues per turn (4.1) and helical pitch (1.5 angstroms or 150 [[picometer]]s). It is not a true mirror image, because the [[amino acid\|amino-acid]] residues still have a left-handed [[chirality (chemistry)\|chirality]]. <!-- Need to make the image, and check whether hydrogen bonds are still made. --> A long left-handed π-helix is unlikely to be observed in proteins because, among the naturally occurring amino acids, only [[glycine]] is likely to adopt positive φ dihedral angles such as 55°.

			==π-helices in nature==
			[[File:Pi-helix within an alpha-helix.jpg\|thumb\|left\|A short, 7 residue π-helix (orange) is embedded within a longer, α-helix (green). The "bulge" of the π-helix can be clearly seen, and was created as the result of a single amino acid that has been inserted into an α-helix. PBD code 3QHB.]]

			Commonly used automated secondary structure assignment programs, such as [[DSSP (protein)\|DSSP]], suggest <1% of proteins contain a π-helix. This mis-characterization results from the fact that naturally occurring π-helices are typically short in length (7-10 residues) and are almost always associated with (i.e. flanked by) α-helices on either end. Nearly all π-helices are therefore cryptic in that the π-helical residues are incorrectly assigned as either α-helical or as "turns". Recently developed programs have been written to properly annotate π-helices in protein structures and they have found that 1 in 6 proteins (~15%) do in fact contain at least one π-helical segment.<ref name="pmid20888342"/>

			Natural π-helices can easily be identified in a structure as a "bulge" within a longer α-helix. Such helical bulges have previously been referred to as α-aneurisms, α-bulges, π-bulges, wide-turns,looping outs and π-turns, but in fact are π-helices as determined by their repeating ''i''+5→''i'' hydrogen bonds.<ref name="pmid20888342"/> Evidence suggests that these bulges, or π-helices, are created by the insertion of a single additional amino acid into a pre-existing α-helix. Thus, α-helices and π-helices can be inter-converted by the insertion and deletion of a single amino acid.<ref name="pmid20888342"/><ref name="pmid8475069"/> Given both the relatively high rate of occurrence of π-helices and their noted associtation with functional sites (i.e. active sites) of proteins, this ability to inter-convert between α-helices and π-helices has been an important mechanism of altering and diversifying protein functionality over the course of evolution.<ref name="pmid20888342"/>

			One of the most notable group of proteins whose functional diversification appears to have been heavily influenced by such an evolutionary mechanism is the ferritin-like superfamily, which includes [[ferritin]]s, [[bacterioferritin]]s, rubrerythrins, class I [[ribonucleotide reductase]]s and [[Methane monooxygenase#Soluble methane Monooxygenase .28MMO.29 Systems\|soluble methane monooxygenases]]. Soluble methane monooxygenase is the current record holder for the most number of π-helices in a single enzyme with 13 (PDB code 1MTY). However, the bacterial homologue of a Na+/Cl− dependent neurotransmitter transporter (PDB code 2A65) holds the record for the most number of π-helices in a single peptide chain with 8.<ref name="pmid20888342"/>

			==See also==

			* [[alpha helix]]
			* [[3 10 helix]]
			* [[secondary structure]]

			== References ==
			{{reflist}}

			{{Protein secondary structure}}

			[[Category:Protein structural motifs]]
			[[Category:Helices]]

80.191.138.165 at 04:55, 24 April 2012

2012-04-24T04:55:40Z

New page

They contact me Emilia. I am a meter reader but I plan on changing it. South Dakota is her birth place but she needs to move simply because of her family. It's not a typical factor but what she likes doing is base leaping and now she is trying to make money with it.<br><br>My website ... [http://www.blaze16.com/blog/257588 std testing at home]