ITRANS database Sorting structural motifs in cellular transporters

Afonso M.S. DuarteBiological Energy Transduction Lab

ITQB-UNL, Portugal

Cellular membrane transporters

Takamori et al, Cell. 2006 Nov 17;127(4):831-46

• Nutrients uptake

• “Waste disposal”

• Signal transduction

• Energy production

• Drug targets

Ion transporters

Activity

Regulation

Molecular mechanism

Protein structure at different levels

Atomic resolution

Structural motifs

Repeats

What are the basic features of repeats ?

Can repeats be systematized and characterized at sequence and

structural level?

? ? ? ? ? ?

Structural motifs and repeats

Structural motifs

Repeats

transport mechanism

inhibition

activation

Post-translational modifications

# TMs# # β

# kinks

ions

repeat orientation

Ion transporters

Charges

hydrophobicity

Itrans DB

Itrans – Data sources

Itrans DB

literature

DB of ion and small molecules transporters

with known 3D structure

Itrans – Structure

Itrans – Structure

Itrans – input

Itrans – full table

≠ query –> custom-made tables

Itrans – repeats table

Itrans – transporter entry

Itrans - Statistics

Acknowledgments ITQB-UNL

Manuela Pereira

Guilherme BeneditoJosé SilvaDalila FernandesJoana SimõesCátia CostaAna Batista Bruno Marreiros

Filipa CalistoFilipa Sena Patrícia RefojoPaulo CastroAndreia Silva