1mcd

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[[Image:1mcd.jpg|left|200px]]<br /><applet load="1mcd" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1mcd, resolution 2.7&Aring;" />
 
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'''PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS'''<br />
 
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==Overview==
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==PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS==
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An immunoglobulin light chain dimer with a large generic binding cavity was used as a host molecule for designing a series of peptide guest ligands. In a screening procedure peptides coupled to solid supports were systematically tested for binding activity by enzyme linked immunosorbent assays (ELISA). Key members of the binding series were synthesized in milligram quantities and diffused into crystals of the host molecule for X-ray analyses. These peptides were incrementally increased in size and affinity until they nearly filled the cavity. Progressive changes in binding patterns were mapped by comparisons of crystallographically refined structures of 14 peptide-protein complexes at 2.7 A resolution. These comparisons led to guidelines for ligand design and also suggested ways to modify previously established binding patterns. By manipulating equilibria involving histidine, for example, it was possible to abolish one important intramolecular interaction of the bound ligand and substitute another. These events triggered a change in conformation of the ligand from a compact to an extended form and a comprehensive change in the mode of binding to the protein. In dipeptides of histidine and proline, protonation of both imidazolium nitrogen atoms was used to program an end-to-end reversal of the direction in which the ligand was inserted into the binding cavity. Peptides cocrystallized with proteins produced complexes somewhat different in structure from those in which ligands were diffused into preexisting crystals. In such a large and malleable cavity, space utilization was thus different when a ligand was introduced before the imposition of crystal packing restraints.
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<StructureSection load='1mcd' size='340' side='right'caption='[[1mcd]]' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1mcd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MCD FirstGlance]. <br>
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1MCD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=ACE:'>ACE</scene> and <scene name='pdbligand=NH2:'>NH2</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MCD OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=BAL:BETA-ALANINE'>BAL</scene>, <scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene>, <scene name='pdbligand=DPR:D-PROLINE'>DPR</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1mcd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mcd OCA], [https://pdbe.org/1mcd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mcd RCSB], [https://www.ebi.ac.uk/pdbsum/1mcd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mcd ProSAT]</span></td></tr>
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Principles and pitfalls in designing site-directed peptide ligands., Edmundson AB, Harris DL, Fan ZC, Guddat LW, Schley BT, Hanson BL, Tribbick G, Geysen HM, Proteins. 1993 Jul;16(3):246-67. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8346191 8346191]
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</table>
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[[Category: Single protein]]
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== Function ==
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[[Category: Edmundson, A B.]]
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[https://www.uniprot.org/uniprot/IGL1_HUMAN IGL1_HUMAN] 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:22158414, PubMed:20176268). 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:20176268, PubMed:17576170).<ref>PMID:17576170</ref> <ref>PMID:20176268</ref> <ref>PMID:22158414</ref>
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[[Category: Fan, Z C.]]
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== Evolutionary Conservation ==
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[[Category: Guddat, L W.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Harris, D L.]]
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Check<jmol>
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[[Category: ACE]]
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<jmolCheckbox>
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[[Category: NH2]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mc/1mcd_consurf.spt"</scriptWhenChecked>
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[[Category: immunoglobulin]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:53:49 2008''
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</jmolCheckbox>
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</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=1mcd ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Synthetic construct]]
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[[Category: Edmundson AB]]
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[[Category: Fan Z-C]]
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[[Category: Guddat LW]]
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[[Category: Harris DL]]

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PRINCIPLES AND PITFALLS IN DESIGNING SITE DIRECTED PEPTIDE LIGANDS

PDB ID 1mcd

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