itrans database sorting structural motifs in cellular transporters afonso m.s. duarte biological...
TRANSCRIPT
![Page 1: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/1.jpg)
ITRANS database Sorting structural motifs in cellular transporters
Afonso M.S. DuarteBiological Energy Transduction Lab
ITQB-UNL, Portugal
![Page 2: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/2.jpg)
Cellular membrane transporters
Takamori et al, Cell. 2006 Nov 17;127(4):831-46
• Nutrients uptake
• “Waste disposal”
• Signal transduction
• Energy production
• Drug targets
![Page 3: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/3.jpg)
Ion transporters
Activity
Regulation
Molecular mechanism
Protein structure at different levels
Atomic resolution
Structural motifs
Repeats
![Page 4: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/4.jpg)
What are the basic features of repeats ?
Can repeats be systematized and characterized at sequence and
structural level?
? ? ? ? ? ?
Structural motifs and repeats
![Page 5: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/5.jpg)
Structural motifs
Repeats
transport mechanism
inhibition
activation
Post-translational modifications
# TMs# # β
# kinks
ions
repeat orientation
Ion transporters
Charges
hydrophobicity
Itrans DB
![Page 6: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/6.jpg)
Itrans – Data sources
Itrans DB
literature
DB of ion and small molecules transporters
with known 3D structure
![Page 7: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/7.jpg)
Itrans – Structure
![Page 8: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/8.jpg)
Itrans – Structure
![Page 9: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/9.jpg)
Itrans – input
![Page 10: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/10.jpg)
Itrans – full table
≠ query –> custom-made tables
![Page 11: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/11.jpg)
Itrans – repeats table
![Page 12: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/12.jpg)
Itrans – transporter entry
![Page 13: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/13.jpg)
Itrans - Statistics
![Page 14: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/14.jpg)
Acknowledgments ITQB-UNL
Manuela Pereira
Guilherme BeneditoJosé SilvaDalila FernandesJoana SimõesCátia CostaAna Batista Bruno Marreiros
Filipa CalistoFilipa Sena Patrícia RefojoPaulo CastroAndreia Silva
![Page 15: ITRANS database Sorting structural motifs in cellular transporters Afonso M.S. Duarte Biological Energy Transduction Lab ITQB-UNL, Portugal](https://reader035.vdocuments.us/reader035/viewer/2022062502/570638711a28abb823907918/html5/thumbnails/15.jpg)