McGill NMR Lab

Posted on August 5, 2011 by Admin

Our interests are centered on the application of Nuclear Magnetic Resonance (NMR) spectroscopy to the study of protein and nucleic acid structures. Previous structures included a peptide binding domain (PDZ domain) involved in signal transduction and a protein homeodomain (PBX) ternary complex with DNA and a small peptide. Our principal studies are on the structure and function of the C-terminal PABC domain of poly(A) binding proteins and apoptotic proteins of the Bcl-2 family. We also study the solution structure of nucleic acid hairpins, calnexin, CNP, aIF2-beta, YbcJ, alpha- & gamma-adaptins and other proteins. We work as well on developing new methodology for measuring residual dipolar couplings using polymer stabilized liquid crystalline media with a website agency. Our laboratory combines techniques from chemistry, molecular biology and bioinformatics in the quest for a deeper understanding of molecular recognition in biological systems.

Present equipment includes seven UNIX-SGI stations, an isothermal titration calorimeter and a new Bruker DRX 600 MHz NMR spectrometer with cryoprobe. Two Varian Unity Inova spectrometers at 800 MHz and 500 MHz with cryoprobes are installed in 2004 as part of the Quebec/Eastern Canada NMR Centre.

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ProtSkin

Posted on August 5, 2011 by Admin

Protein sequence conservation can be a valuable tool to assess functional regions of a protein.
But sequence information can be complemented by the tridimensional structure of the protein of interest to give new insights on the structure-function relationship.

Protein sequence conservation can be obtained from alignement engines such as BLAST, CLUSTAL W or GCG…
Numerous molecular modelisation programs exist to assist vizualising a 3D protein structure.

ProtSkin converts a protein sequence alignment in BLAST, CLUSTAL or MSF format to a property file used to map the sequence conservation onto the structure of a protein using the GRASP program or the MOLMOL program or the PyMOL program. A pseudo-PDB file with the sequence conservation score in place of the temperature factor is also provided, to use with programs such as InsightII (accelrys).

You will be guided through the three following steps :

Determine a sequence alignment for your protein,
Convert this alignement,
Use the generated file to visualize sequence conservation onto the 3D structure of your protein of interest using GRASP or MOLMOL or PyMOL.

You can also use ProtSkin to map any scalar data, such as heteronuclear NOE or chemical shift differences onto your protein structure. Prepare a plain text file (first column : residue numbers, second column : values to map) and go directly to step 2 to generate a GRASP property file, a MOLMOL macro or a PyMOL macro.

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Poly-A Binding Proteins – Ctermini alignements

Posted on August 5, 2011 by Admin

Organism Length Sequence Accession # Blast
Anemia Phyllitidis 638

MPALASALAS ASPEEQRVML GEQLYPLVDR LEH–DHAGK VTGMLLEMDQ PEVLHLIDLL RQLKAKVAEA MDVL

CAA81127
A.Thaliana 668

ISKLASDLAL ASPDKHPRML GDHLYPLVEQ QEP–ANAAK VTGMLLEMDQ AEILHLLESP EALKAKVSEA LDVL

AAF43230
Bos Taurus 636

EPLTASMLAS APPQEQKQML GERLFPLIQA MHP–TLAGK ITGMLLEIDN SELLHMLESP ESLRSKVDEA VAVL

CAA62006
C. Elegans 646

EPLTSAMLAA AAPQEQKQLL GERIYALIEK LYPGHKDAGK ITGMMLEIDN SELIMMLQDS ELFRSKVDEA ASVL

CAA21572
C. Reinhardtii 623

QPLTASALAA AAPEQQKMMI GERLYPQVAE LQP–DLAGK ITGMLLEMDN AELLMLLESH EALVSKVDEA IAVL

AAC39368
Cucumis sativus 649

VGALASALAN ATPDQQRTML GENLYPLVEQ LEP–DNAAK VTGMLLEMDQ TEVLHLLESP EALKAKVAEA MEVL

AAF53202
Daucus Carota 658

ITALASALAN APADQQRTML GENLYPLVDQ LEH–DHAAK VTGMLLEMDQ TEVLHLLESP DALKAKVAEA MDVL

AF349964
D.Melanogaster 632

EKLIASLLAN AKPQEQKQIL GERLYPMIEH MHA–NLAGK ITGMLLEIEN SELLHMIEDQ EALKAKVEEA VAVL

P21187
E. Nidulans 705

VGVLTAQALS AAPPQQQKQM LGEALYPKIQ ATQ–PELAG KITGMLLEMD NTELLGLLRM TRLCAPRSTK PLAF

AAB16848
Homo Sapiens 636

EPLTASMLAS APPQEQKQML GERLFPLIQA MHP–TLAGK ITGMLLEIDN SELLHMLESP ESLRSKVDEA VAVL

P11940 structure
Leishmania Major 603

PPITPQELES MSPQEQRAAL GDRLFLKVYE IPP–DVAPK ITGMFLEMKP KEAYELLNDQ KRLEERVTEA LCVL

AAC64372
M. Crystallinum 176

VGTLATLLAN ATPEQQRLLL GENLYPLVEQ LEP–EMAAK VTGMLLEMDQ TEVLHLLESP EALKSKVAEA MEVL

AAB61594
Mus Musculus 636

EPLTASMLAS APPQEQKQML GERLFPLIQA MHP–SLAGKIT GMLLEIDN SELLHMLESP ESLRSKVDEA VAVL

CAA46522
Nicotiana Tabacum 649

VGALATALAN SSPTEQRTML GENLYPLVEQ LEP–ETAAK VTGMLLEMDQ TEVLHLLESP EALKAKVAEA MEVL

AAF66823
P. Marinus 630

EPLTASMLAA APPHEQKQML GERLFPLIHG MYP–TLAGK ITGMLLEIDN SELLHMLESP ESLRAKVEEA VAVL

AAB8849
Rattus Norvegicus 636

EPLTASMLAS APPQEQKQML GERLFPLIQA MHP–SLAGK ITGMLLEIDN SELLHMLESP ESLRSKVDEA VAVL

CAC21554
S.Cerevisiae 478

FPRNANDNNQ FYQQKQRQAL GEQLYKKVSA KTSNEEAAGK ITGMILDLPP QEVFPLLESD ELFEQHYKEA SAAY

P04147
S.Pombe 653

ERFTAADLAA VPEESRKQVL GELLYPKVFV REE–KLSGK ITGMLLEMPN SELLELLEDD SALNERVNEA IGVL

T38950
Triticum Aestivum 651

IGALASALAN SPPETQRMML GENLYPLVDQ LEH–DQAAK VTGMLLEMDQ TEVLHLLESP DALKAKVAEA MEVL

AAB38974
Trypanosoma Brucei 555

GQNLSTVLAS MTPDQQKNVL GERLYNYIVR NNP–SFAAK VTGMLLEMDN SEILNLLDNH SLLDTKVQEA LDVL

AAD13337
Trypanozoma Cruzi 550

GQNLSTVLAN LTPEQQKNVL GERLYNHIVA INP–AAAAK VTGMLLEMDN GEILNLLDTP GLLDAKVQEA LEVL

AAC46487
Xenopus Laevis 633

EPLTASMLAA APPQEQKQML GERLFPLIQA MHP–TLAGK ITGMLLEIDN SELLHMLESP ESLRSKVDEA VAVL

CAA40721
Related proteins
Drosophila HYD 496

TDNATPESLN DHLSVHLQQI GERLYPKIHS INQ–THAPK ITGMLLEIPT PQLLSVISSD ETLRQKVNEA IEII

AF252698
Human HYD 2798

ASEGNPSDDP EPLPAHRQAL GERLYPRVQA MQP–AFASK ITGMLLELSP AQLLLLLASE DSLRARVDEA MELI

AAF88143 structure
Rat 100 kDa 889

ASEGNPSDDP DPLPAHRQAL GERLYPRVQA MQP–AFASK ITGMLLELSP AQLLLLLASE DSLRARVEEA MELI

Q62671

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