Algorithmic and Artificial Intelligence Methods for Protein Bioinformatics

Chapter 25

MeTaDoR: Online Resource and Prediction Server for Membrane Targeting Peripheral Proteins

NITIN BHARDWAJ, MORTEN KäLLBERG, WONHWA CHO, and HUI LU

25.1 Introduction

Cell signaling is a complex system of communication that governs basic cellular activities and coordinates cell actions. The process involves complex arrays of inter-molecular interactions, including protein–protein, protein–lipid, protein–carbohydrate, protein–nucleic acid, and protein–small molecule interactions [1]. As a part of this highly organized process, many proteins are redistributed within the cell to various cellular compartments [2]. A large majority of these dynamic proteins target various cellular membranes by recognizing specific lipids and/or proteins. These proteins, collectively known as peripheral proteins [3], are different from integral membrane proteins in that they interact with membranes mostly reversibly in response to specific signals. Peripheral proteins also play crucial roles in other cellular processes, including membrane trafficking, cell motility, apoptosis, viral infection, and cell metabolism. Many of these peripheral proteins have been implicated in major human diseases, such as cancer [4] and AIDS [5].

Most peripheral proteins interact with cell membranes via one or more modular domains, known either as membrane targeting domains (MTDs) or as lipid binding domains (LBDs), which are specialized in lipid binding [6, 7]. The MTDs and LBDs are referred to the same class of ...