

PFRMAT ABF1
TARGET T0011
AUTHOR 9293-6602-8904   J. Fernando Bazan, DNAX, bazan@dnax.org
REMARK
REMARK =============================================================
REMARK Completed Thursday to Friday, August 29-30, 1996
REMARK
REMARK This file contains an 'ab initio' prediction for target T0011, 
REMARK the N-terminal domain of Yeast Hsp90 (aa 1-220, swissprot file
REMARK hs82_yeast), due August 30, 1996.  The registered predictor is 
REMARK J. Fernando Bazan from DNAX Research Institute in Palo Alto, 
REMARK CA (email bazan@dnax.org).  Below is attached a 1.1 (secondary
REMARK structure string) and 2.1 (segment pairing and contact) 
REMARK prediction in (hopefully) the right format. The following
REMARK concerns the methods used to arrive at these predictions.
REMARK I first conducted an exhaustive survey of Hsp90 homologs from
REMARK the nonredundant NCBI databases using the BLAST server with
REMARK Gonnet, Blosum45 and 30 comparison matrices.  These sequences
REMARK were collected and aligned with ClustalW to make Gribskov-type
REMARK profiles, used to screen again for more distant relatives. 
REMARK From both the BLAST and profile searches, the human TRAP1 and
REMARK a C. elegans ORF sequences (Genbank Acc. #'s U12595 and U00036
REMARK were incorporated to the profile.  Next, in the same fashion, a 
REMARK hypothetical prokaryotic protein (swissprot yd3m_herau) was  
REMARK found. The augmented profiles, and the MPSRCH server (DISC in 
REMARK Japan) located a significant, albeit faint, similarity to 
REMARK bacterial MutL proteins (involved in DNA mismatch repair 
REMARK complexes) centering around an Hsp90 conserved motif of DxGxG 
REMARK (aa 79-83 in target). All MutL-like sequences were separately
REMARK harvested and aligned (including MLH1 and PMS1-like proteins 
REMARK in eukaryotes, with some quite distant homologs found as ORFs
REMARK in the yeast genome) with ClustalW, and BLAST/profile searches
REMARK next revealed two interesting matches (that had appeared as
REMARK bottom-type hits with the Hsp90 profile) with a number of
REMARK bacterial sensor proteins from two-component signaling pathways
REMARK - to central regions that correspond to identified Histidine 
REMARK Kinase domains - and to the N-terminal segments of bacterial
REMARK gyrase subunit-B sequences - also ATPase domains.   Both
REMARK of these divergent families also preserve DxGxG motifs
REMARK at approximately the same spot as Hsp90s/MutLs, about 1/3
REMARK of the way into the chain; another centrally located
REMARK Gly-rich motif also cemented the relationship. 
REMARK
REMARK    Throughout the exercise, the growing multiple alignments 
REMARK were submitted to the PHD neural network prediction server at 
REMARK the EMBL, and to the PSSP server at Baylor, with Solovyev's 
REMARK SSP and NNSSP programs that are also quite good prognosticators.
REMARK The Hsp90 and MutL predictions were quite similar, with an
REMARK alpha+beta pattern of a-a-b-b-a-a-b-b-b-b-a-b-b. The His
REMARK kinase domains, smaller in size (CheA aa 370-514 works as
REMARK a kinase) feature a pattern of a-a-b-b-a-b-b-a-b-b (less
REMARK two strands), while the gyraseB-like sequences (clustering
REMARK in prokaryotic and eukaryotic families) are Hsp90/MutL-like
REMARK in length, and give similar alpha+beta patterns.  Routine
REMARK checks were run of representative members of the Hsp90, MutL,
REMARK HisKin and GyrB families with the threading programs 123D 
REMARK (Alexandrov, NCI), topits (Rost, EMBL), Pscan (Eloffson, 
REMARK Stockholm) and ProFIT on my SGI and nothing appeared
REMARK significantly in common, although most of the top hits 
REMARK were with alpha+beta, or alpha/beta folds.  
REMARK
REMARK     It has not escaped attention that the York group has
REMARK earlier solved the X-ray structure of E. coli gyraseB 
REMARK (Wigley et al., Nature 351, 624, 1991) but no coordinates 
REMARK have been deposited in the PDB. The gyrase B fold is composed
REMARK of two distinct domains: an N-terminal, 220 aa novel ATPase
REMARK structure (with AMPNP bound as a non-hydrolyzable analog) formed
REMARK by a mixed beta-sheet with helices packed on one side, and
REMARK a C-terminal a/b fold related to domains in ribosomal proteins
REMARK and EF-G (Murzin, 1995 letter in Nat. Struc. Biol.). The
REMARK location of the GyrB ATPase secondary structural elements
REMARK correspond quite well with the PHD/PSSP-derived helices and
REMARK strands. From this template fold, the likely topology of the
REMARK predicted Hsp90 secondary structure can be deduced, as well 
REMARK as the strand pairing/contacts.  Viewing the sheet from above
REMARK (looking down at the helices lying on top of the sheet), the 
REMARK eight strands are in order 5-4-3-6-2-1-7-8, all antiparallel 
REMARK save for the 1-7 pair, which are parallel to each other. Two
REMARK helices precede the first b-strand, and then also form links
REMARK between strands 1-2, and 6-7. The more economical His Kinase
REMARK sequences may lack the edge 5-4 hairpin - this looks to be
REMARK allowed by the fold. The ATP-binding site, as mapped by the
REMARK presence of the ADPNP, is on top of the sheet, protected by
REMARK various loops and helices.  The noted DxGxG motif lies in 
REMARK a loop just after strand 2; in the GyrB-ADPNP complex, the
REMARK Asp73 side chain interacts with the amino side group of the
REMARK adenine ring.  Tyr109 H-bonds to the N3 atom of the adenine
REMARK ring; while the Hsp90s have no equivalent Tyr at that position,
REMARK there is a totally conserved Lys98 residue that could play a
REMARK similar role.  The phosphates in ADPNP rest against a Gly motif
REMARK in GyrB (Glys 114, 117 and 119); in Hsp90, the equivalent Gly
REMARK residues are at positions 118, 121 and 123.   More recently
REMARK Wigley (now at Oxford) has solved the GyrB str bound to 
REMARK the antibiotic novobiocin, and seen that this molecule overlaps
REMARK the ADPNP only in the adenine ring site (described in an
REMARK Ann. Rev. Biophys. Biomol. Str. 1995 article on topoisomerase
REMARK structures by Wigley).  
REMARK
REMARK     On the 1.1 and 2.1 predictions below, the former lists
REMARK the 3-state prediction as well as the accessibility forecast.
REMARK Both are derived from the column format PHD output from the 
REMARK alignment of only the Hsp90 immediate homologs (including
REMARK Trap1, the C.elegans ORF and sequence yd3m_herau), with some
REMARK hand tuning to reflect the PSSP input, and the alignments 
REMARK of the Hsp90s to GyrBs via MutL sequences.  I have gotten
REMARK ahold of the Lesk J. Molec. Graphics article and am attempting
REMARK to decipher the format (just what are 'elevenses'?) to describe 
REMARK the predicted pairing of strands (mostly) and the mode of
REMARK helix packings on the sheet (less importantly).
REMARK 
REMARK      The biological implications of this predicted fold?
REMARK Well, first of all, the Hsp90 N-terminal domain appears to
REMARK contain all the residues that mark it as an active ATPase
REMARK using the GyrB protein scaffold.  This is somewhat 
REMARK controversial, as a recent paper concludes after a broad
REMARK experimental review that "highly purified Hsp90 does not
REMARK bind ATP" (Jakob et al., J. Biol. Chem. 271, 10035, 1996).
REMARK Secondly, this ATPase is coupled to the activity of the
REMARK C-terminal domain of Hsp90, like the GyrB is tied to other
REMARK domains, or MutLs and His Kinases interact with yet other
REMARK protein modules.  This has precedents in the heat shock
REMARK field, as both Hsp60 and Hsp70-class proteins have distinct
REMARK ATPase catalytic domains, accessorized to other protein
REMARK interaction domains. 
REMARK
REMARK       The 'style' of this prediction is more closely akin to 
REMARK the Pearl and Taylor modeling of the retroviral Asp protease 
REMARK structure after aligning faint motifs and secondary 
REMARK structure patterns in the aggregate sequences of
REMARK divergent families of proteins.  Here, the relationship of
REMARK Hsp90 domains to MutLs and His Kinases and ultimately GyrB
REMARK ATPase domains led directly to a template for the fold; 
REMARK without this fortuitous guide, the prediction would have 
REMARK just as accurate at the secondary structure level, but
REMARK likely would not have reached the present topology as most
REMARK prediction methods -threading, Barton's mapping, etc. - rely
REMARK one way or another on the desired fold residing, well digested
REMARK and understood, in the PDB or SCOP or FSSP.  This isn't the 
REMARK case with the well protected GyrB fold (ever curious, I inquired
REMARK by email with Wigley as to the availability of the coordinates,
REMARK and rather shockingly, he emailed back that he was only selling
REMARK the structure, cold cash or credit card!, given that funds in the
REMARK lab go to supplies or trips, I had to graciously decline his
REMARK offer, although I almost asked what it was going for, in a 
REMARK nice way). Given time (and not at last minute as this is
REMARK progressing), the chosen strands could be assembled into a 
REMARK sheet (perhaps taking other a/b proteins as skeletal guides) 
REMARK and the helices combinatorically packed on top.  
REMARK 
REMARK     Specifics on the prediction:
REMARK   
REMARK     This is a crude topology cartoon with labeled elements:
REMARK
REMARK                     1                 
REMARK                    a1 
REMARK               nh2-hhhh--\
REMARK                    _____|____                h=helices
REMARK     ___           /    _h_   |  ____
REMARK    |   ^    |\   ^    | h ^  h ^    |  up/down arrows=b-strands
REMARK    |   |    | h  |    | h |  h |    | 
REMARK    |   |    | h  |    | h |  h |    |
REMARK    v   |    v h  |    v h |  h |    v
REMARK    |   \____/ |  |   *  \/   |_/    \cooh   *=DxGxG motif
REMARK    \__________h__/  /
REMARK               h____/
REMARK
REMARK    b5  b4  b3 a4 b6  b2 a2b1 a5 b7  b8 <--b-strands,a-helices     
REMARK               a3                                     
REMARK
REMARK    9   8   7  5-6 10  4 2 3  11 12  13  <-2o str # for 2.1
REMARK                                
REMARK
REMARK   (helix a3-a4 loop between strands b2 and b3 is not depicted
REMARK    well in this rough figure - just to see connectivity & 
REMARK    topology)
REMARK
REMARK The amino acid limits of the predicted 2o str for 1.1:
REMARK a1 or 1 (aa 8-16), a2 or 2 (26-44), b1 or 3 (62-68),
REMARK b2 or 4 (73-79), a3 or 5 (101-110), a4 or 6 (122-130),
REMARK b3 or 7 (133-139), b4 or 8 (144-150), b5 or 9 (155-160), 
REMARK b6 or 10 (171-177), a5 or 11 (183-198), b7 or 12 (204-209),
REMARK b8 or 13 (212-217).
REMARK 
REMARK The predicted pairings of strands (see cartoon) for 2.1:
REMARK b1-b2 or 3-4 (HH), b2-b6 or 4-10 (HH), b3-b6 or 7-10 (HH),
REMARK b3-b4 or 7-8 (HH), b4-b5 or 8-9 (HH), b1-b7 or 3-12 (KK),
REMARK b7-b8 or 12-13 (HH).
REMARK
REMARK The helix-helix pairings:
REMARK a1-a4 or 1-6 (RD), a2-a5 or 2-11 (PD), a2-a4 or 2-6 (OT),
REMARK a3-a4 or 5-6 (RD).
REMARK
REMARK Strand-helix pairings, bit tougher to gauge:
REMARK a2-b1 or 2-3 (OT), a2-b2 or 2-4 (PD), a3-b3 or 5-7 (OT),
REMARK a3-b4 or 5-8 (PE), a4-b3 or 6-7 (OT), a4-b6 or 6-8 (PD),
REMARK a5-b7 or 11-12 (OT), a5-b8 or 11-13 (PD).
REMARK
REMARK Specific residue contacts to deduce register of pairings:
REMARK b1-b2 or 3-4 w/ aa L62-D79, b6-a4 or 10-6 w/ aa L175-F124,
REMARK b3-b4 or 7-8 w/ aa K139-E144, b6-b3 or 10-7 w/ aa T171-S138,
REMARK b5-b4 or 9-8 w/ aa T159-Q145, b6-b2 or 10-4 w/ aa I172-R78,
REMARK a4-a1 or 6-1 w/ aa V130-I12, a2-a5 or 2-11 w/ aa I29-E186,
REMARK b7-b8 or 12-13 w/ aa I205-K215, b7-b1 or 12-3 w/ aa I205-L62.
REMARK
REMARK This is the extent of the work - Cheers, Fernando.
REMARK Emailed in to LLNL on Friday, August 30, ~4:45 pm PST.
REMARK
REMARK =============================================================
BEGDAT 1.1 1 1.00
SS 220 1
M    C    1.0    
A    C    1.0    
S    C    1.0    
E    C    1.0    
T    C    1.0    
F    C    1.0    
E    C    1.0    
F    H    1.0    
Q    H    1.0   
A    H    1.0    
E    H    1.0    
I    H    1.0    
T    H    1.0    
Q    H    1.0    
L    H    1.0    
M    H    1.0    
S    C    1.0     
L    C    1.0    
I    C    1.0   
I    C    1.0    
N    C    1.0    
T    C    1.0   
V    C    1.0     
Y    C    1.0    
S    C    1.0       
N    H    1.0        
K    H    1.0       
E    H    1.0       
I    H    1.0         
F    H    1.0        
L    H    1.0        
R    H    1.0        
E    H    1.0       
L    H    1.0        
I    H    1.0         
S    H    1.0        
N    H    1.0    
A    H    1.0        
S    H    1.0         
D    H    1.0        
A    H    1.0        
L    H    1.0         
D    H    1.0        
K    H    1.0       
I    C    1.0         
R    C    1.0       
Y    C    1.0         
K    C    1.0        
S    C    1.0        
L    C    1.0         
S    C    1.0       
D    C    1.0       
P    C    1.0       
K    C    1.0       
Q    C    1.0        
L    C    1.0         
E    C    1.0        
T    C    1.0       
E    C    1.0        
P    C    1.0       
D    C    1.0        
L    E    1.0       
F    E    1.0        
I    E    1.0        
R    E    1.0      
I    E    1.0       
T    E    1.0       
P    E    1.0      
K    C    1.0        
P    C    1.0       
E    C    1.0        
Q    C    1.0        
K    E    1.0        
V    E    1.0        
L    E    1.0         
E    E    1.0         
I    E    1.0         
R    E    1.0        
D    E    1.0        
S    C    1.0       
G    C    1.0         
I    C    1.0         
G    C    1.0       
M    C    1.0         
T    C    1.0        
K    C    1.0       
A    C    1.0        
E    C    1.0       
L    C    1.0         
I    C    1.0        
N    C    1.0        
N    C    1.0        
L    C    1.0         
G    C    1.0        
T    C    1.0        
I    C    1.0         
A    C    1.0        
K    C    1.0       
S    C    1.0       
G    C    1.0         
T    H    1.0        
K    H    1.0      
A    H    1.0         
F    H    1.0         
M    H    1.0         
E    H    1.0        
A    H    1.0         
L    H    1.0         
S    H    1.0        
A    H    1.0        
G    C    1.0         
A    C    1.0         
D    C    1.0        
V    C    1.0        
S    C    1.0         
M    C    1.0        
I    C    1.0         
G    C    1.0         
Q    C    1.0       
F    C    1.0         
G    C    1.0         
V    H    1.0         
G    H    1.0         
F    H    1.0        
Y    H    1.0        
S    H    1.0        
L    H    1.0         
F    H    1.0         
L    H    1.0         
V    H    1.0         
A    C    1.0        
D    C    1.0        
R    E    1.0        
V    E    1.0         
Q    E    1.0         
V    E    1.0        
I    E    1.0         
S    E    1.0        
K    E    1.0        
S    C    1.0        
N    C    1.0        
D    C    1.0      
D    C    1.0        
E    E    1.0        
Q    E    1.0        
Y    E    1.0         
I    E    1.0         
W    E    1.0         
E    E    1.0       
S    E    1.0         
N    C    1.0        
A    C    1.0        
G    C    1.0        
G    C    1.0       
S    E    1.0        
F    E    1.0         
T    E    1.0        
V    E    1.0         
T    E    1.0        
L    E    1.0        
D    C    1.0        
E    C    1.0       
V    C    1.0        
N    C    1.0        
E    C    1.0        
R    C    1.0        
I    C    1.0        
G    C    1.0        
R    C    1.0        
G    C    1.0        
T    E    1.0         
I    E    1.0        
L    E    1.0        
R    E    1.0        
L    E    1.0         
F    E    1.0        
L    E    1.0        
K    C    1.0       
D    C    1.0       
D    C    1.0     
Q    C    1.0        
L    C    1.0         
E    H    1.0        
Y    H    1.0         
L    H    1.0        
E    H    1.0        
E    H    1.0       
K    H    1.0       
R    H    1.0     
I    H    1.0        
K    H    1.0       
E    H    1.0        
V    H    1.0        
I    H    1.0       
K    H    1.0      
R    H    1.0       
H    H    1.0       
S    H    1.0      
E    C    1.0     
F    C    1.0      
V    C    1.0      
A    C    1.0     
Y    C    1.0    
P    E    1.0      
I    E    1.0     
Q    E    1.0      
L    E    1.0    
V    E    1.0    
V    E    1.0     
T    C    1.0    
K    C    1.0     
E    E    1.0      
V    E    1.0      
E    E    1.0      
K    E    1.0     
E    E    1.0     
V    E    1.0       
P    C    1.0     
I    C    1.0       
P    C    1.0    
ACC 220 1
M    49    0.40    
A    36    0.10    
S     0    0.10    
E    49    0.40    
T    36    0.20    
F     0    0.20    
E     0    0.00    
F     0    0.20    
Q    36    0.20    
A     0    0.40    
E    49    0.30    
I     0    0.60    
T     0    0.10    
Q    36    0.20    
L     0    0.50    
M     0    0.70    
S     0    0.10    
L     0    0.50    
I     0    0.70    
I     0    0.70    
N     0    0.20    
T     0    0.20    
V     0    0.20    
Y    16    0.20    
S    36    0.10    
N     0    0.00    
K    49    0.50    
E    36    0.10    
I     0    0.30    
F     0    0.50    
L     0    0.70    
R    36    0.20    
E    36    0.10    
L     0    0.50    
I     0    0.50    
S    49    0.40    
N    49    0.50    
A     0    0.40    
S     0    0.00    
D    49    0.60    
A     0    0.30    
L     0    0.30    
D    49    0.40    
K    49    0.60    
I     0    0.40    
R    25    0.20    
Y     0    0.30    
K    36    0.20    
S     0    0.20    
L     0    0.10    
S    49    0.40    
D    49    0.40    
P    49    0.40    
K    49    0.30    
Q    36    0.10    
L     0    0.00    
E    49    0.40    
T    81    0.50    
E    49    0.50    
P    49    0.40    
D    49    0.50    
L     0    0.40    
F     0    0.20    
I     0    0.80    
R    36    0.20    
I     0    0.50    
T     0    0.10    
P    36    0.10   
K    49    0.50    
P    49    0.50    
E    49    0.40    
Q    49    0.40    
K    49    0.40    
V     0    0.00    
L     0    0.30    
E     0    0.00    
I     0    0.60    
R     0    0.00    
D    49    0.20    
S     0    0.00    
G     0    0.20    
I     0    0.00    
G    49    0.40    
M     0    0.20    
T     0    0.00    
K    36    0.10    
A    36    0.00    
E    36    0.10    
L     0    0.50    
I     0    0.40   
N    49    0.40    
N    36    0.10    
L     0    0.40    
G     0    0.10    
T    36    0.20    
I     0    0.50    
A     0    0.50    
K    49    0.50    
S    49    0.50   
G     0    0.00    
T     0    0.00    
K    49    0.50    
A     0    0.10    
F     0    0.40    
M     0    0.50    
E    49    0.50    
A     0    0.20    
L     0    0.40    
S    49    0.40    
A    49    0.30    
G     0    1.00    
A     0    0.10    
D    49    0.30    
V     0    0.50    
S     0    0.10    
M     0    0.60    
I     0    0.60    
G     0    0.30    
Q    36    0.10    
F     0    0.40    
G     0    0.30    
V     0    0.30    
G     0    0.20    
F     0    0.50    
Y     0    0.20    
S     0    0.60    
L     0    0.80    
F     0    0.30    
L     0    0.30    
V     0    0.50    
A     0    0.50    
D    49    0.30    
R    36    0.10    
V     0    0.70    
Q     0    0.00    
V     0    0.60   
I     0    0.50    
S     0    0.40   
K    49    0.50    
S    36    0.10    
N    49    0.40    
D    49    0.30    
D    49    0.40    
E    49    0.50    
Q    49    0.30    
Y     0    0.00    
I     0    0.30    
W     0    0.10    
E    49    0.30    
S     0    0.10    
N    36    0.10    
A    81    0.30    
G    49    0.50    
G    49    0.30    
S    36    0.10    
F     0    0.20    
T     0    0.00    
V     0    0.50    
T     0    0.20    
L    25    0.00    
D    49    0.30    
E    36    0.00    
V    49    0.30    
N    49    0.30    
E    49    0.40    
R    49    0.30    
I     0    0.00    
G    49    0.40    
R    49    0.50    
G     0    0.00    
T     0    0.10    
I    36    0.20    
L     0    0.60    
R     0    0.30    
L     0    0.50    
F     0    0.20    
L     0    0.50    
K    49    0.60    
D    49    0.50   
D    49    0.50    
Q    49    0.40    
L     0    0.00    
E    36    0.20    
Y     0    0.10    
L     0    0.40    
E    49    0.50    
E    49    0.50    
K    36    0.10    
R    36    0.20    
I     0    0.30    
K    49    0.60    
E    49    0.60    
V     0    0.30    
I     0    0.60    
K    49    0.60    
R    49    0.70    
H     0    0.00    
S     0    0.30    
E    49    0.40    
F     0    0.40    
V     0    0.40    
A     0    0.20    
Y     0    0.00    
P     0    0.20    
I     0    0.60    
Q     0    0.00    
L     0    0.30    
V     0    0.10    
V     0    0.40    
T    36    0.10    
K    49    0.60    
E    49    0.40    
V    36    0.10    
E    49    0.50    
K    49    0.50    
E    49    0.60    
V     0    0.00    
P    49    0.30    
I    81    0.50    
P    81    0.90    
ENDDAT 1.1
BEGDAT 2.1 1 1.00 1 
19 
 3   4   HH   1.00    62   79  1.00
 4  10   HH   1.00    78  172  1.00
 7   8   HH   1.00   139  144  1.00
 7  10   HH   1.00   138  171  1.00
 8   9   HH   1.00   145  159  1.00
 3  12   KK   1.00    62  205  1.00
12  13   HH   1.00   205  215  1.00
 1   6   RD   1.00    12  130  1.00
 2   3   OT   1.00     0    0  0.00
 2   4   PD   1.00     0    0  0.00
 2   6   OT   1.00     0    0  0.00
 2  11   PD   1.00    29  186  1.00
 5   6   RD   1.00     0    0  0.00
 5   7   OT   1.00     0    0  0.00
 5   8   PE   1.00     0    0  0.00
 6   7   OT   1.00     0    0  0.00
 6  10   PD   1.00   124  175  1.00
11  12   OT   1.00     0    0  0.00
11  13   PD   1.00     0    0  0.00
ENDDAT 2.1
END

