Classi cation of Membrane Proteins by Types ofTransmembrane Helices Using SOSUI System
Shigeki Mitaku 1

mitaku@cc.tuat.ac.jp
12

Takatsugu Hirokawa 12
hirokawa@cc.tuat.ac.jp

Mitsuo Ono 1

mitsuo@cc.tuat.ac.jp

Tokyo University of Agriculture and Technology, Department of Biotechnology, Tokyo
184-5855, Japan
Present address: Ryoka System Inc., Computational Science and Technology Division

1 Introduction
There are many amino acid sequences in proteomes which are not homologous to any other sequences.
Therefore, methods to classify proteins independent of the sequence homology are strongly requiredfor computational analysis of proteomes. Proteins may be divided into two categories: soluble andmembrane proteins. Since membrane proteins are characterized by the existence of long hydrophobictransmembrane helices, the classi cation of amino acid sequences into two types of proteins, soluble
and membrane proteins, is possible with considerably high accuracy. The classi cation of all aminoacid sequences in several proteomes was reported recently, leading to the conclusion that the fractionof membrane proteins is about 30% [1]. However, those methods provided only the information about
the number of transmembrane helices. We have previously proposed a new method (SOSUI) to classify
amino acid sequences by two types of transmembrane helices, primary and secondary transmembranesegments. In this work, we have analyzed four kinds of dataset including two set of all amino acidsequences from proteomes, using the SOSUI system [2] which not only predicts transmembrane helix
regions but also classi es them by the strength of interaction with lipid membranes.

2 Methods
We have prepared four kinds of dataset of amino acid sequences: (1) ORFs of Mycoplasma genitalium,(2) ORFs of Methanococcus jannaschii, (3) membrane proteins of known topology, and (4) membraneproteins whose 3D-structure is known. The number of membrane proteins were 105, 359, 80 and 17,
respectively.
All amino acid sequences were analyzed by a SOSUI system by which the number of transmembrane
helices and the fraction of primary and secondary transmembrane segments were obtained. The
performance of the SOSUI system was reported in ref. [2]. The SOSUI system is available at URL:
http://www.tuat.ac.jp/~mitaku/.

3 Results and Discussion
The distribution of the number of transmembrane helices showed two peaks. The largest peak wasfound at the single spanning membrane proteins and a broad peak was observed at the helix number ofsix or seven. This characteristics of the number distribution was common to three dataset except formembrane proteins with known 3D-structure. Because histograms of the number of transmembrane
helices for two biological species is similar to that for the dataset from membrane proteins of known
topology, it is expected that membrane proteins with seven transmembrane helices, many of which
are receptor proteins are abundant in biological systems.
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Statistical analysis showed that two thirds of transmembrane segments were primary transmembrane helices, which will be able to penetrate into membrane by themselves, while the remaining
transmembrane helices were secondary ones, which are considered to be stabilized by the interaction
with other transmembrane segments. However, fty percent of transmembrane helices were secondary
ones in the dataset of known 3D-structures. Although the statistical signi cance of the increased
fraction of secondary transmembrane helices is not clear yet because of the paucity of data, this typeof transmembrane helices may stabilize the tertiary structure of membrane proteins.
Functionally important residues usually have polar groups. Therefore, functionally important
helices should have polar residues, which are the characteristics of secondary transmembrane helices.
The number of secondary transmembrane helices in most membrane proteins was less than three. Theclassi cation of membrane proteins by the fraction of secondary transmembrane helices may provide
information about the functional features of the proteins.

Acknowledgements
This work was supported in part by a Grant-in-Aid for Scienti c Research on Priority Areas, \GenomeScience", from the Ministry of Education, Science, Sports and Culture of Japan.

References[1] Frishman, D. and Mewes, H.W., Protein structural classes in ve complete genomes, Naturestructural biology, 4:626{628, 1997.
[2] Hirokawa, T., Seah, B.-C., and Mitaku, S., SOSUI: classi cation and secondary structure prediction system for membrane proteins, Bioinformatics Application Note, 14, 1988.

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