Talk:Protein structure

message: It seems like there is way too much detailed and redundant information about amino acids in this topic.  This topic should focus on generic aspects of protein structure.  There is already ample description of amino acid chemistry in the amino acid article. Anyone else have thoughts on this? Speedyboy 21:19, 31 January 2007 (UTC)
thread_title:  Too much amino acid content? 

message: Hi, just a word about the recent edit specifying the molecular forces stabilizing different types of protein structure.  Protein 2° structure is certainly defined by its hydrogen bonds, but it might be a little misleading to say that it is stabilized by its hydrogen bonds; if that were true, then peptides taken from a protein would adopt stable 2° structure, which is extremely rare.  The reason is that water-amide hydrogen bonds are generally more favorable than amide-amide hydrogen bonds; that's why the 2° structure disintegrates when the 3° structure of a protein is unfolded by tension, pressure or cold denaturation.
Likewise, disulfide bonds are extremely rare in cytosolic proteins, since the cytosol is a reducing environment thanks to the high concentration of glutathione.  With a few exceptions in thermophiles, disulfide bonds are found only in extracellular proteins such as secreted toxins, inhibitors, digestive enzymes, etc.  So I hope you won't mind the changes I'm about to make in the edit; thanks for being understanding! :) Willow 17:35, 5 February 2007 (UTC)
replies: text: Yes, it is stabilized by hydrogen bonds (~1.5 kcal/mol per a water-inaccessible H-bond. The only stable structures adopted by peptides (unless they are cyclic) are alpha-helices or beta-hairpins - precisely for that reason. The intramolecular H-bonds in proteins are "stronger" than dynamic H-bonds with water because protein  structure represents solid state. When liquids or flexible polymers (like protein coil) are frozen, they gain enthalpy of fusion. The energy of protein H-bonds is a part of enthalpy of fusion.Biophys (talk) 01:27, 4 April 2009 (UTC)
thread_title: Dominant forces in 2° and 3° structure?

message: I'm hardly searching for an explanation for the term beta-jelly-roll motive.
Some help would be great!
Thx
Monsterous mad max 14:23, 16 August 2007 (UTC)
thread_title:  Additional structural motives 

message: Could this be replaced with this one without losing information: http://upload.wikimedia.org/wikipedia/commons/c/ce/AminoAcidball.svg
?  —Preceding unsigned comment added by 195.169.212.36 (talk) 23:42, 16 February 2009 (UTC)
thread_title:  Alpha Amino Acid picture 

message: I'm not sure how wikipedia works (usually I just leech), but "However, the current estimate for the average protein length is around 300 residues." as found in the second paragraph of the intro is citation-needed as of Mar. 24/09, and I believe that a suitable citation may be found in "Protein length in eukaryotic and prokaryotic proteomes", written by Luciano Brocchieri and Samuel Karlin in 2005 (see especially Table 2).  —Preceding unsigned comment added by 99.249.92.174 (talk) 06:08, 24 March 2009 (UTC)
replies: text: Thanks for the reference; it is a perfect one. I have added it to the article. I would like to reproduce Table 2 from this paper somewhere on Wikipedia. --Thorwald (talk) 16:24, 24 March 2009 (UTC)
thread_title:  Citation Needed for (avg)300 Residues 

message: I'm unsure, but is a beta-loop the same as beta-bend (beta-turn)? according to my prof. a beta-bend is usually found in the outskirts of a protein between two beta-sheets. My book describes beta-bends as:
*reverses the direction 
*found on the surface
*often charged residues
*connect anti-parallel b-sheets
*stabilized by hydrogen and ionic bonds
I don't think the described beta-loops are a perfect match. I they aren't b-bend should be added. If they are, the b-loop part should be edited. But as I said, I'm unsure. Help?
--Nisse1337 (talk) 11:22, 25 March 2009 (UTC)
replies: text: There is no such thing as "beta-loop". There are only beta-turns.Biophys (talk) 01:18, 4 April 2009 (UTC)
thread_title:  beta loops 

message: Did anyone notice that primary structure was described several times in this article? Same with secondary structure.Biophys (talk) 01:17, 4 April 2009 (UTC)
replies: text: .. Fix it then. Could someone who has time include a link to Conformational change and maybe improve that article too, as there should be something on this page about how phosphorylation or ligand binding can affect the protein structure and activate catalytic domains, etc. 83.146.14.63 (talk) 12:06, 9 April 2009 (UTC)
replies: text: Main problem: someone included (copy and paste) this segment of text which made this article unreadable. It also duplicates texts provided in other articles.Biophys (talk) 01:40, 15 April 2009 (UTC)
thread_title: Some problems here

message: ===Hydrogen Bonding===
Polypeptides contain numerous proton donors and acceptors both in their backbone and in the R-groups of the amino acids. The environment in which proteins are found also contains ample H-bond donors and acceptors of the water molecule. H-bonding, therefore, occurs not only within and between polypeptide chains but with the surrounding aqueous medium.
===Hydrophobic Forces===
Proteins are composed of amino acids that contain either hydrophilic or hydrophobic R-groups. It is the nature of the interaction of the different R-groups with the aqueous environment that plays the major role in shaping protein structure. The spontaneous folded state of globular proteins is a reflection of a balance between the opposing energetics of H-bonding between hydrophilic R-groups and the aqueous environment and the repulsion from the aqueous environment by the hydrophobic R-groups. The hydrophobicity of certain amino acid R-groups tends to drive them away from the exterior of proteins and into the interior. This driving force restricts the available conformations into which a protein may fold.
===Electrostatic Forces===
Electrostatic forces are mainly of three types; charge-charge, charge-dipole and dipole-dipole. Typical charge-charge interactions that favor protein folding are those between oppositely charged R-groups such as K or R and D or E. A substantial component of the energy involved in protein folding is charge-dipole interactions. This refers to the interaction of ionized R-groups of amino acids with the dipole of the water molecule. The slight dipole moment that exist in the polar R-groups of amino acid also influences their interaction with water. It is, therefore, understandable that the majority of the amino acids found on the exterior surfaces of globular proteins contain charged or polar R-groups.
===van der Waals Forces===
There are both attractive and repulsive van der Waals forces that control protein folding. Attractive van der Waals forces involve the interactions among induced dipoles that arise from fluctuations in the charge densities that occur between adjacent uncharged non-bonded atoms. Repulsive van der Waals forces involve the interactions that occur when uncharged non-bonded atoms come very close together but do not induce dipoles. The repulsion is the result of the electron-electron repulsion that occurs as two clouds of electrons begin to overlap.
Although van der Waals forces are extremely weak, relative to other forces governing conformation, it is the huge number of such interactions that occur in large protein molecules that make them significant to the folding of proteins. 
===Complex Protein Structures===
Proteins also are found to be covalently conjugated with carbohydrates. These modifications occur following the synthesis (translation) of proteins and are, therefore, termed post-translational modifications. These forms of modification impart specialized functions upon the resultant proteins. Proteins covalently associated with carbohydrates are termed glycoproteins. Glycoproteins are of two classes, N-linked and O-linked, referring to the site of covalent attachment of the sugar moieties. N-linked sugars are attached to the amide nitrogen of the R-group of asparagine; O-linked sugars are attached to the hydroxyl groups of either serine or threonine and occasionally to the hydroxyl group of the modified amino acid, hydroxylysine.
There are extremely important glycoproteins found on the surface of erythrocytes. It is the variability in the composition of the carbohydrate portions of many glycoproteins and glycolipids of erythrocytes that determines blood group specificities. There are at least 100 blood group determinants, most of which are due to carbohydrate differences. The most common blood groups, A, B, and O, are specified by the activity of specific gene products whose activities are to incorporate distinct sugar groups onto RBC membrane glycoshpingolipids as well as secreted glycoproteins. 
Structural complexes involving protein associated with lipid via noncovalent interactions are termed lipoproteins. The distinct roles of lipoproteins are described on the linked page. Their major function in the body is to aid in the storage transport of lipid and cholesterol.
===Amino-Terminal Sequence Determination===
Prior to sequencing peptides it is necessary to eliminate disulfide bonds within peptides and between peptides. Several different chemical reactions can be used in order to permit separation of peptide strands and prevent protein conformations that are dependent upon disulfide bonds. The most common treatments are to use either 2-mercaptoethanol or dithiothreitol (DTT). Both of these chemicals reduce disulfide bonds. To prevent reformation of the disulfide bonds the peptides are treated with iodoacetic acid in order to alkylate the free sulfhydryls.
There are three major chemical techniques for sequencing peptides and proteins from the N-terminus. These are the Sanger, Dansyl chloride and Edman techniques.
;Sanger's Reagent: This sequencing technique utilizes the compound, 2,4-dinitrofluorobenzene (DNF) which reacts with the N-terminal residue under alkaline conditions. The derivatized amino acid can be hydrolyzed and will be labeled with a dinitrobenzene group that imparts a yellow color to the amino acid. Separation of the modified amino acids (DNP-derivative) by electrophoresis and comparison with the migration of DNP-derivative standards allows for the identification of the N-terminal amino acid.
;Dansyl chloride: Like DNF, dansyl chloride reacts with the N-terminal residue under alkaline conditions. Analysis of the modified amino acids is carried out similarly to the Sanger method except that the dansylated amino acids are detected by fluorescence. This imparts a higher sensitivity into this technique over that of the Sanger method.
;Edman degradation: The utility of the Edman degradation technique is that it allows for additional amino acid sequence to be obtained from the N-terminus inward. Using this method it is possible to obtain the entire sequence of peptides. This method utilizes phenylisothiocyanate to react with the N-terminal residue under alkaline conditions. The resultant phenylthiocarbamyl derivatized amino acid is hydrolyzed in anhydrous acid. The hydrolysis reaction results in a rearrangement of the released N-terminal residue to a phenylthiohydantoin derivative. As in the Sanger and Dansyl chloride methods, the N-terminal residue is tagged with an identifiable marker, however, the added advantage of the Edman process is that the remainder of the peptide is intact. The entire sequence of reactions can be repeated over and over to obtain the sequences of the peptide. This process has subsequently been automated to allow rapid and efficient sequencing of even extremely small quantities of peptide.
Name  (Residue)	3-letter code	Single code	Relative abundance(%) E.C.	MW 	pK    	VdW volume (Å³)	Charged, Polar, Hydrophobic,  Neutral
Alanine             	ALA          	A          	13.0                      	71 	 	67             	H
Arginine            	ARG          	R          	5.3                       	157	12.5  	148            	C+
Asparagine          	ASN          	N          	9.9                       	114	 	96             	P
Aspartate           	ASP          	D          	9.9                       	114	3.9   	91             	C-
Cysteine            	CYS          	C          	1.8                       	103	 	86             	P
Glutamate           	GLU          	E          	10.8                      	128	4.3   	109            	C-
Glutamine           	GLN          	Q          	10.8                      	128	 	114            	P
Glycine             	GLY          	G          	7.8                       	57 	 	48             	N
Histidine           	HIS          	H          	0.7                       	137	6.0   	118            	P,C+
Isoleucine          	ILE          	I          	4.4                       	113	 	124            	H
Leucine             	LEU          	L          	7.8                       	113	 	124            	H
Lysine              	LYS          	K          	7.0                       	129	10.5  	135            	C+
Methionine          	MET          	M          	3.8                       	131	 	124            	H
Phenylalanine       	PHE          	F          	3.3                       	147	 	135            	H
Proline             	PRO          	P          	4.6                       	97 	 	90             	H
Serine              	SER          	S          	6.0                       	87 	 	73             	P
Threonine           	THR          	T          	4.6                       	101	 	93             	P
Tryptophan          	TRP          	W          	1.0                       	186	 	163            	P
Tyrosine            	TYR          	Y          	2.2                       	163	10.1  	141            	P
Valine              	VAL          	V          	6.0                       	99 	 	105            	H
This table is actually worse than a similar Table in amino acids. Please compare. This is a useless content fork.Biophys (talk) 01:44, 15 April 2009 (UTC)
thread_title: Forces Controlling Protein Structure

message: Prior to sequencing peptides it is necessary to eliminate disulfide bonds within peptides and between peptides. Several different chemical reactions can be used in order to permit separation of peptide strands and prevent protein conformations that are dependent upon disulfide bonds. The most common treatments are to use either 2-mercaptoethanol or dithiothreitol (DTT). Both of these chemicals reduce disulfide bonds. To prevent reformation of the disulfide bonds the peptides are treated with iodoacetic acid in order to alkylate the free sulfhydryls.
There are three major chemical techniques for sequencing peptides and proteins from the N-terminus. These are the Sanger, Dansyl chloride and Edman techniques.
;Sanger's Reagent: This sequencing technique utilizes the compound, 2,4-dinitrofluorobenzene (DNF) which reacts with the N-terminal residue under alkaline conditions. The derivatized amino acid can be hydrolyzed and will be labeled with a dinitrobenzene group that imparts a yellow color to the amino acid. Separation of the modified amino acids (DNP-derivative) by electrophoresis and comparison with the migration of DNP-derivative standards allows for the identification of the N-terminal amino acid.
;Dansyl chloride: Like DNF, dansyl chloride reacts with the N-terminal residue under alkaline conditions. Analysis of the modified amino acids is carried out similarly to the Sanger method except that the dansylated amino acids are detected by fluorescence. This imparts a higher sensitivity into this technique over that of the Sanger method.
;Edman degradation: The utility of the Edman degradation technique is that it allows for additional amino acid sequence to be obtained from the N-terminus inward. Using this method it is possible to obtain the entire sequence of peptides. This method utilizes phenylisothiocyanate to react with the N-terminal residue under alkaline conditions. The resultant phenylthiocarbamyl derivatized amino acid is hydrolyzed in anhydrous acid. The hydrolysis reaction results in a rearrangement of the released N-terminal residue to a phenylthiohydantoin derivative. As in the Sanger and Dansyl chloride methods, the N-terminal residue is tagged with an identifiable marker, however, the added advantage of the Edman process is that the remainder of the peptide is intact. The entire sequence of reactions can be repeated over and over to obtain the sequences of the peptide. This process has subsequently been automated to allow rapid and efficient sequencing of even extremely small quantities of peptide.
Name  (Residue)	3-letter code	Single code	Relative abundance(%) E.C.	MW 	pK    	VdW volume (Å³)	Charged, Polar, Hydrophobic,  Neutral
Alanine             	ALA          	A          	13.0                      	71 	 	67             	H
Arginine            	ARG          	R          	5.3                       	157	12.5  	148            	C+
Asparagine          	ASN          	N          	9.9                       	114	 	96             	P
Aspartate           	ASP          	D          	9.9                       	114	3.9   	91             	C-
Cysteine            	CYS          	C          	1.8                       	103	 	86             	P
Glutamate           	GLU          	E          	10.8                      	128	4.3   	109            	C-
Glutamine           	GLN          	Q          	10.8                      	128	 	114            	P
Glycine             	GLY          	G          	7.8                       	57 	 	48             	N
Histidine           	HIS          	H          	0.7                       	137	6.0   	118            	P,C+
Isoleucine          	ILE          	I          	4.4                       	113	 	124            	H
Leucine             	LEU          	L          	7.8                       	113	 	124            	H
Lysine              	LYS          	K          	7.0                       	129	10.5  	135            	C+
Methionine          	MET          	M          	3.8                       	131	 	124            	H
Phenylalanine       	PHE          	F          	3.3                       	147	 	135            	H
Proline             	PRO          	P          	4.6                       	97 	 	90             	H
Serine              	SER          	S          	6.0                       	87 	 	73             	P
Threonine           	THR          	T          	4.6                       	101	 	93             	P
Tryptophan          	TRP          	W          	1.0                       	186	 	163            	P
Tyrosine            	TYR          	Y          	2.2                       	163	10.1  	141            	P
Valine              	VAL          	V          	6.0                       	99 	 	105            	H
This table is actually worse than a similar Table in amino acids. Please compare. This is a useless content fork.Biophys (talk) 01:44, 15 April 2009 (UTC)
thread_title: Amino-Terminal Sequence Determination

message: I've removed the following section for the moment (diff). Unfortunately it is an overly-detailed bullet point summary of a relatively niche paper (only cited 7 times since 2010) so isn't really appropriate for this page. If I think of a more specialist article that could benefit from a sentence on it I'll see if I can salvage some of the info, but I suspect it's a little too obscure. T.Shafee(Evo﹠Evo)talk 11:52, 14 December 2015 (UTC)
replies: text: Sorry to revert you again, but I really think that this information would be more appropriate in the SAHG article. The information you added is too specific for this page because this page is a general description of protein structure. SAHG is only one of a great many databases of equivalent notability. T.Shafee(Evo﹠Evo)talk 00:48, 15 December 2015 (UTC)
thread_title:  Section entitled "Protein Structure Prediction Pipeline- SAHG, a comprehensive database of predicted structures of all human protein" 

message: Substituted at 03:29, 30 April 2016 (UTC)
thread_title: Assessment comment