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| - | [[Image:1eeu.jpg|left|200px]]<br /><applet load="1eeu" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1eeu, resolution 1.60Å" /> | |
| - | '''M4L/Y(27D)D/Q89D/T94H mutant of LEN'''<br /> | |
| | | | |
| - | ==Overview== | + | ==M4L/Y(27D)D/Q89D/T94H mutant of LEN== |
| - | Asp residues are significantly under represented in beta-sheet regions of, proteins, especially in the middle of beta-strands, as found by a number, of studies using statistical, modeling, or experimental methods. To, further understand the reasons for this under representation of Asp, we, prepared and analyzed mutants of a beta-domain. Two Gln residues of the, immunoglobulin light-chain variable domain (V(L)) of protein Len were, replaced with Asp, and then the effects of these changes on protein, stability and protein structure were studied. The replacement of Q38D, located at the end of a beta-strand, and that of Q89D, located in the, middle of a beta-strand, reduced the stability of the parent, immunoglobulin V(L) domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively., Because the Q89D mutant of the wild-type V(L)-Len domain was too unstable, to be expressed as a soluble protein, we prepared the Q89D mutant in a, triple mutant background, V(L)-Len M4L/Y27dD/T94H, which was 4.2 kcal/mol, more stable than the wild-type V(L)-Len domain. The structures of mutants, V(L)-Len Q38D and V(L)-Len Q89D/M4L/Y27dD/T94H were determined by X-ray, diffraction at 1.6 A resolution. We found no major perturbances in the, structures of these Q-->D mutant proteins relative to structures of the, parent proteins. The observed stability changes have to be accounted for, by cumulative effects of the following several factors: (1) by changes in, main-chain dihedral angles and in side-chain rotomers, (2) by close, contacts between some atoms, and, most significantly, (3) by the, unfavorable electrostatic interactions between the Asp side chain and the, carbonyls of the main chain. We show that the Asn side chain, which is of, similar size but neutral, is less destabilizing. The detrimental effect of, Asp within a beta-sheet of an immunoglobulin-type domain can have very, serious consequences. A somatic mutation of a beta-strand residue to Asp, could prevent the expression of the domain both in vitro and in vivo, or, it could contribute to the pathogenic potential of the protein in vivo. | + | <StructureSection load='1eeu' size='340' side='right'caption='[[1eeu]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1eeu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EEU FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1eeu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eeu OCA], [https://pdbe.org/1eeu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eeu RCSB], [https://www.ebi.ac.uk/pdbsum/1eeu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eeu ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/KV401_HUMAN KV401_HUMAN] V segment of the variable domain of immunoglobulins light chain that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref> <ref>PMID:24600447</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ee/1eeu_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1eeu ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Asp residues are significantly under represented in beta-sheet regions of proteins, especially in the middle of beta-strands, as found by a number of studies using statistical, modeling, or experimental methods. To further understand the reasons for this under representation of Asp, we prepared and analyzed mutants of a beta-domain. Two Gln residues of the immunoglobulin light-chain variable domain (V(L)) of protein Len were replaced with Asp, and then the effects of these changes on protein stability and protein structure were studied. The replacement of Q38D, located at the end of a beta-strand, and that of Q89D, located in the middle of a beta-strand, reduced the stability of the parent immunoglobulin V(L) domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively. Because the Q89D mutant of the wild-type V(L)-Len domain was too unstable to be expressed as a soluble protein, we prepared the Q89D mutant in a triple mutant background, V(L)-Len M4L/Y27dD/T94H, which was 4.2 kcal/mol more stable than the wild-type V(L)-Len domain. The structures of mutants V(L)-Len Q38D and V(L)-Len Q89D/M4L/Y27dD/T94H were determined by X-ray diffraction at 1.6 A resolution. We found no major perturbances in the structures of these Q-->D mutant proteins relative to structures of the parent proteins. The observed stability changes have to be accounted for by cumulative effects of the following several factors: (1) by changes in main-chain dihedral angles and in side-chain rotomers, (2) by close contacts between some atoms, and, most significantly, (3) by the unfavorable electrostatic interactions between the Asp side chain and the carbonyls of the main chain. We show that the Asn side chain, which is of similar size but neutral, is less destabilizing. The detrimental effect of Asp within a beta-sheet of an immunoglobulin-type domain can have very serious consequences. A somatic mutation of a beta-strand residue to Asp could prevent the expression of the domain both in vitro and in vivo, or it could contribute to the pathogenic potential of the protein in vivo. |
| | | | |
| - | ==About this Structure==
| + | Factors contributing to decreased protein stability when aspartic acid residues are in beta-sheet regions.,Pokkuluri PR, Gu M, Cai X, Raffen R, Stevens FJ, Schiffer M Protein Sci. 2002 Jul;11(7):1687-94. PMID:12070321<ref>PMID:12070321</ref> |
| - | 1EEU is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with IPA as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1EEU OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Factors contributing to decreased protein stability when aspartic acid residues are in beta-sheet regions., Pokkuluri PR, Gu M, Cai X, Raffen R, Stevens FJ, Schiffer M, Protein Sci. 2002 Jul;11(7):1687-94. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12070321 12070321]
| + | </div> |
| | + | <div class="pdbe-citations 1eeu" style="background-color:#fffaf0;"></div> |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Cai, X.]] | + | [[Category: Cai X]] |
| - | [[Category: Gu, M.]] | + | [[Category: Gu M]] |
| - | [[Category: Pokkuluri, P.R.]] | + | [[Category: Pokkuluri PR]] |
| - | [[Category: Schiffer, M.]] | + | [[Category: Schiffer M]] |
| - | [[Category: Stevens, F.J.]] | + | [[Category: Stevens FJ]] |
| - | [[Category: IPA]]
| + | |
| - | [[Category: aspartic acid in beta-sheet]]
| + | |
| - | [[Category: human kappa-4 immunoglobulin light chain]]
| + | |
| - | [[Category: mutant]]
| + | |
| - | [[Category: protein stability]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:57:01 2007''
| + | |
| Structural highlights
Function
KV401_HUMAN V segment of the variable domain of immunoglobulins light chain that participates in the antigen recognition (PubMed:24600447). Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. In the recognition phase of humoral immunity, the membrane-bound immunoglobulins serve as receptors which, upon binding of a specific antigen, trigger the clonal expansion and differentiation of B lymphocytes into immunoglobulins-secreting plasma cells. Secreted immunoglobulins mediate the effector phase of humoral immunity, which results in the elimination of bound antigens (PubMed:20176268, PubMed:22158414). The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen (PubMed:17576170, PubMed:20176268).[1] [2] [3] [4]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Asp residues are significantly under represented in beta-sheet regions of proteins, especially in the middle of beta-strands, as found by a number of studies using statistical, modeling, or experimental methods. To further understand the reasons for this under representation of Asp, we prepared and analyzed mutants of a beta-domain. Two Gln residues of the immunoglobulin light-chain variable domain (V(L)) of protein Len were replaced with Asp, and then the effects of these changes on protein stability and protein structure were studied. The replacement of Q38D, located at the end of a beta-strand, and that of Q89D, located in the middle of a beta-strand, reduced the stability of the parent immunoglobulin V(L) domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively. Because the Q89D mutant of the wild-type V(L)-Len domain was too unstable to be expressed as a soluble protein, we prepared the Q89D mutant in a triple mutant background, V(L)-Len M4L/Y27dD/T94H, which was 4.2 kcal/mol more stable than the wild-type V(L)-Len domain. The structures of mutants V(L)-Len Q38D and V(L)-Len Q89D/M4L/Y27dD/T94H were determined by X-ray diffraction at 1.6 A resolution. We found no major perturbances in the structures of these Q-->D mutant proteins relative to structures of the parent proteins. The observed stability changes have to be accounted for by cumulative effects of the following several factors: (1) by changes in main-chain dihedral angles and in side-chain rotomers, (2) by close contacts between some atoms, and, most significantly, (3) by the unfavorable electrostatic interactions between the Asp side chain and the carbonyls of the main chain. We show that the Asn side chain, which is of similar size but neutral, is less destabilizing. The detrimental effect of Asp within a beta-sheet of an immunoglobulin-type domain can have very serious consequences. A somatic mutation of a beta-strand residue to Asp could prevent the expression of the domain both in vitro and in vivo, or it could contribute to the pathogenic potential of the protein in vivo.
Factors contributing to decreased protein stability when aspartic acid residues are in beta-sheet regions.,Pokkuluri PR, Gu M, Cai X, Raffen R, Stevens FJ, Schiffer M Protein Sci. 2002 Jul;11(7):1687-94. PMID:12070321[5]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Teng G, Papavasiliou FN. Immunoglobulin somatic hypermutation. Annu Rev Genet. 2007;41:107-20. PMID:17576170 doi:http://dx.doi.org/10.1146/annurev.genet.41.110306.130340
- ↑ Schroeder HW Jr, Cavacini L. Structure and function of immunoglobulins. J Allergy Clin Immunol. 2010 Feb;125(2 Suppl 2):S41-52. doi:, 10.1016/j.jaci.2009.09.046. PMID:20176268 doi:http://dx.doi.org/10.1016/j.jaci.2009.09.046
- ↑ McHeyzer-Williams M, Okitsu S, Wang N, McHeyzer-Williams L. Molecular programming of B cell memory. Nat Rev Immunol. 2011 Dec 9;12(1):24-34. doi: 10.1038/nri3128. PMID:22158414 doi:http://dx.doi.org/10.1038/nri3128
- ↑ Lefranc MP. Immunoglobulin and T Cell Receptor Genes: IMGT((R)) and the Birth and Rise of Immunoinformatics. Front Immunol. 2014 Feb 5;5:22. doi: 10.3389/fimmu.2014.00022. eCollection 2014. PMID:24600447 doi:http://dx.doi.org/10.3389/fimmu.2014.00022
- ↑ Pokkuluri PR, Gu M, Cai X, Raffen R, Stevens FJ, Schiffer M. Factors contributing to decreased protein stability when aspartic acid residues are in beta-sheet regions. Protein Sci. 2002 Jul;11(7):1687-94. PMID:12070321
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