+ Site Statistics
+ Search Articles
+ PDF Full Text Service
How our service works
Request PDF Full Text
+ Follow Us
Follow on Facebook
Follow on Twitter
Follow on LinkedIn
+ Subscribe to Site Feeds
Most Shared
PDF Full Text
+ Translate
+ Recently Requested

Prediction of rotational orientation of transmembrane helical segments of integral membrane proteins using new environment-based propensities for amino acids derived from structural analyses



Prediction of rotational orientation of transmembrane helical segments of integral membrane proteins using new environment-based propensities for amino acids derived from structural analyses



Febs Journal 274(10): 2653-2660



Alpha-helical integral-membrane proteins (IMPs) play a key role in many biological processes, such as signal transduction, and are targets for >50% of current therapeutic drugs. In contrast to their significant abundance and biological importance, they comprise <1% of structurally solved proteins. In the absence of experimental evidence, molecular modeling of IMP structures is an alternative for providing structural information and aiding further experimental design. In the current work, we propose two new amino acid lipid-facing propensity scales derived from the structural analysis of a nonredundant set of water-soluble proteins. The new scales, pi and delta, perform as well or better than published scales (Carugo's hydrophobicity and kPROT scales) in predicting the lipid-facing side of helical segments of a set of structurally solved IMPs, thus indicating (a) that the folding properties of water-soluble proteins and IMPs are similar, and (b) that the new scales will prove useful in modeling the transmembrane segments of IMPs.

Please choose payment method:






(PDF emailed within 0-6 h: $19.90)

Accession: 013796156

Download citation: RISBibTeXText

PMID: 17451441

DOI: 10.1111/j.1742-4658.2007.05800.x


Related references

Uncoupling hydrophobicity and helicity in transmembrane segments. a-helical propensities of the amino acids in non-polar environments. The Journal of Biological Chemistry 273(37): 645-8, 1998

Uncoupling hydrophobicity and helicity in transmembrane segments. Alpha-helical propensities of the amino acids in non-polar environments. Journal of Biological Chemistry 273(37): 23645-8, 1998

A simple flexible program for the computational analysis of amino acyl residue distribution in proteins: application to the distribution of aromatic versus aliphatic hydrophobic amino acids in transmembrane alpha-helical spanners of integral membrane transport proteins. Journal of Computational Biology 3(1): 185-190, 1996

Modeling of the structural features of integral-membrane proteins reverse-environment prediction of integral membrane protein structure (REPIMPS). Protein Science 10(8): 1529-1538, 2001

Using biophysical and biochemical experimental information to generate 3-D structural models of transmembrane domains of helical, integral membrane proteins. Biophysical Journal 74(2 Part 2): A249, 1998

Discrimination of Golgi type II membrane proteins based on their hydropathy profiles and the amino acid propensities of their transmembrane regions. Bioscience Biotechnology and Biochemistry 75(1): 82-88, 2011

K-2 -12K-2-amide A new peptide model of helical hydrophobic transmeMbrane segments of membrane segments of membrane proteins. Biophysical Journal 66(2 Part 2): A57, 1994

Prediction of membrane proteins based on classification of transmembrane segments. Protein Engineering 11(11): 961-970, 1998

Peptide models of helical hydrophobic transmembrane segments of membrane proteins. 1. Studies of the conformation, intrabilayer orientation, and amide hydrogen exchangeability of Ac-K2-(LA)12-K2-amide. Biochemistry 34(7): 2348-2361, 1995

kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction. Journal of Molecular Biology 294(4): 921-935, 1999

Non-random distribution of amino acids in the transmembrane segments of human type I single span membrane proteins. Journal of Molecular Biology 229(3): 602-608, 1993

Neural network-based prediction of transmembrane beta-strand segments in outer membrane proteins. Journal of Computational Chemistry 25(5): 762-767, 2004

The composition of transmembrane segments of human type I integral membrane proteins that span the membrane once. Biophysical Journal 70(2 Part 2): A181, 1996

Empirical lipid propensities of amino acid residues in multispan alpha helical membrane proteins. Proteins 59(3): 496-509, 2005

Determining the orientation of uniaxially rotating membrane proteins using unoriented samples: a 2H, 13C, AND 15N solid-state NMR investigation of the dynamics and orientation of a transmembrane helical bundle. Journal of the American Chemical Society 129(17): 5719-5729, 2007