Erich Bornberg-Bauer, Eric Rivals, Martin Vingron
Nucleic Acids Res., 26(11):2740-2746;(1998)

Abstract:
The leucine zipper is a dimerisation domain occurring mostly in regulatory and thus in many oncogenic proteins. The leucine repeat in the sequence has been traditionally used for identification, however with poor reliability. The coiled-coil structure of a leucine zipper is required for dimerisation and can be predicted with reasonable accuracy by existing algorithms. We exploit this fact for identification of leucine zippers from sequence alone. We present a program, 2ZIP, which combines a standard coiled coil prediction algorithm with an approximate search for the characteristic leucine repeat. No further information from homologues is required for prediction. This approach improves significantly over existing methods, especially in that the coiled coil prediction turns out to be highly informative and avoids large numbers of false positives. Many problems in predicting zippers or assessing prediction results stem from wrong sequence annotations in the database.

pdf-file of publication in NAR

• You may download the perl script for Leucine Zipper prediction: LZpred.pl
• LZpred.pl has to be accompanied by ncoils-binary version 2.2 : ncoils 2.2 at EBI ftp server
• here is the old program: LZprediction-1.0.tar.gz

Copy a sample sequence

>CNN_DROME
MDQSKQVLRDYCGDGNGTCASSLKEITLIETVTSFLEENGAAEIDRRVLR
KLAEALSKSIDDTSPGALQDVTMENSYASFDVPRPPGGGNSPLPSQGRSV
RELEEQMSALRKENFNLKLRIYFLEEGQPGARADSSTESLSKQLIDAKIE
IATLRKTVDVKMELLKDAARAISHHEELQRKADIDSQAIIDELQEQIHAY
MAESGGQPVENIAKTRKMLRLESEVQRLEEELVNIEARNVAARNELEFM
LAERLESLTACEGKIQELAIKNSELVERLEKETASAESSNANRDLGAQLA
DKICELQEAQEKLKERERIHEQACRTIQKLMQKLSSQEKEIKKLNQENEQ
SANKENDCAKTVISPSSSGRSMSDNEASSQEMSTNLRVRYELKINEQEEK
IKQLQTEVKKKTANLQNLVNKELWEKNREVERLTKLLANQQKTLPQISEE
SAGEADLQQSFTEAEYMRALERNKLLQRKVDVLFQRLADDQQNSAVIGQL
RLELQQARTEVETADKWRLECVDVCSVLTNRLEELAGFLNSLLKHKDVLG
VLAADRRNAMRKAVDRSLDLSKSLNMTLNITATSLADQSLAQLCNLSEIL
YTEGDASHKTFNSHEELHAATSMAPTVENLKAENKALKKELEKRRSSEGQ
RKERRSLPLPSQQFDNQSESEAWSEPDRKVSLARIGLDETSNSLAAPEQA
ISESESEGRTCATRQDRNRNSERIAQLEEQIAQKDERMLNVQCQMVELDN
RYKQEQLRCLDITQQLEQLRAINEALTADLQAIGSHEEERMVELQRQLEL
KNQQIDQLKLAHSTLTADSQITEMELQALQQQMQEIEQQHADSVETLQSQ
LQKLKLDAVQQLEEHERLHREALERDWVALTTYQEQAQQLLELQRSLDYH
QENEKELKQTLVENELATRALKKQLDESTLQASKAVMERTKAYNDKLQLE
KRSEELRLQLEALKEEHQKLLQKRSNSSDVSQSGYTSEEVAVPWGHLRVR
LQRANRLLPQFWARGEHIISDLGHEAMPAGYLA

>MYC1_CYPCA
MPVSASLAYKNYDYDYDSIQPYFYFDNDDEDFYHHQQGQTQPPAPSEDIW
KKFELLPTPPLSPSRRQSLSTAEQLEMVSEFLGDDVVNQSFICDADYSQS
FIKSIIIQDCMWSGFSAAAKLEKVVSERLASLHAARKELMSDSSSNRLNA
SYLQDVSTSASECIDPSVVFPYPLPESGKSSKVAPSEPMPVLDTPPNSSS
SSGSDSEEEEEEEEEEEEEEEEEEIDVVTVEKRQKKNETAVSDSRYPSPL
VLKRCHVSTHQHNYAAHPSTRHDQPAVKRLRLEASSNSNSRHVKQRKCTS
PRTSDSEDNDKRRTHNVLERQRRNELKLSFFALRDEIPDVANNEKAAKVV
ILKKATECIHSMQLDEQRLLSIKEQLRRKSEQLKHRLQLLRSSH

>VCG3_NPVAC
MEFVKLQCNICFSVAEIKNYFLQPIDRLTIIPVLELDTCKHQLCSMCIRK
IRKRKKVPCPLCRVESLHFNVYSVNRNVVDVIKCSASSVAQWNKINANFD
AASLASVLFEKSLLDDAEDNNANADDTMLSEAQAILKKLQVDIAEQTQLN
IKQQLDLDKLQQTSVSMQEKLDKIKSDYNNMHKSFKELQLKRITTEKALK
SLNDDYAKLASKNAKLSSENKVLSNKNIELIKHKNLLQNEYTTLQSYKCI
TNATITTNVTINVD

>XBP1_HUMAN
MVVVAAAPNPADGTPKVLLLSGQPASAAGAPAARLPLMVPAQRGASPEAA
SGGLPQARKRQRLTHLSPEEKALRRKLKNRVAAQTARDRKKARMSELEQQ
VVDLEEENQKLLLENQLLREKTHGLVVENQELRQRLGMDALVAEEEAEAK
GNEVRPVAGSAESAALRLRAPLQQVQAQLSPLQNISPWILAVLTLQIQSL
ISCWAFWTTWTQSCSSNALPQSLPAWRSSQRSTQKDPVPYQPPFLCQWGR
HQPSWKPLMN
                    

The following lines give an example for an annotation:


1) number of potential LEUCINE ZIPPERS: 1     Annotations:
     |
1---------11--------21--------31--------41--------51--------     |
MVVVAAAPNPADGTPKVLLLSGQPASAAGAPAARLPLMVPAQRGASPEAASGGLPQARKR     |
     |
     |
     |
     |
61--------71--------81--------91--------101-------111-------     |position 
QRLTHLSPEEKALRRKLKNRVAAQTARDRKKARMSELEQQVVDLEEENQKLLLENQLLRE     |sequence
                CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC     |coiled coil 
                L------L------L------L--     |L-Repeats
                LZLZLZLZLZLZLZLZLZLZLZLZ     |LeucineZipper
     |
121-------131-------141-------151-------161-------171-------     |
KTHGLVVENQELRQRLGMDALVAEEEAEAKGNEVRPVAGSAESAALRLRAPLQQVQAQLS     |
CCCCCCCCCCCC             |
----L------L             |
LZLZLZLZLZLZ             |
     |
181-------191-------201-------211-------221-------231-------     |
PLQNISPWILAVLTLQIQSLISCWAFWTTWTQSCSSNALPQSLPAWRSSQRSTQKDPVPY     |
     |
     |
     |
     |
241-------251-------     |
QPPFLCQWGRHQPSWKPLMN     |