PNAS | July 22, 2003 | vol. 100 | no. 15 | 8670-8675


Determining the basis of channel-tetramerization specificity by x-ray crystallography 
and a sequence-comparison algorithm: Family values (FamVal) 

Max H. Nanao *a , Wei Zhou *, Paul J. Pfaffinger **, and Senyon Choe *b  

*Structural Biology Laboratory, The Salk Institute, La Jolla, CA 92037; and 
**Division of Neuroscience, Baylor College of Medicine, Houston, TX 77030 

Communicated by Stephen F. Heinemann, The Salk Institute for Biological Studies, 
La Jolla, CA, May 12, 2003 (received for review September 20, 2002)


We have developed a semiempirical algorithm called Family Values (FamVal), which 
identifies residues that encode functional specificity in a protein sequence. Given 
a multiple sequence alignment (MSA) grouped into functionally distinct subfamilies, 
FamVal calculates a specificity score for each subfamily at every amino acid position 
of an MSA. This algorithm was used to predict specificity-encoding positions within 
the tetramerization assembly (T1) domain of voltage-gated potassium (Kv) channel 
subfamilies Kv3 and Kv4. The importance of one such position (Arg to Ala at MSA 
position 93) was confirmed by in vitro pull-down assays. The structural basis of 
this assembly discrimination was elucidated by determining the crystal structure of 
the Kv4 T1 domain and comparing it to the Kv3 T1 domain. 



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Abbreviations: FamVal, Family Values; Kv, voltage-gated potassium; MSA, multiple 
sequence alignment; NTA, nitrilotriacetic acid; PDGF, platelet-derived growth factor; 
T1, tetramerization assembly. 

Data deposition: The atomic coordinates for the T1 domain of rat voltage-gated K 
channel 4.2 (rKv4.2T1) have been deposited in the Protein Data Bank, www.rcsb.org 
(PDB ID code 1NN7). 

a-Present address: Institut de Biologie Structurale, 41 Avenue Jules Horowitz, 
38027 Grenoble Cedex 1, France. 

b-To whom correspondence should be addressed. E-mail: choe@salk.edu. 



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Copyright © 2003 by the National Academy of Sciences