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Predicting the flavodoxin secondary and
tertairy structure
Flavodoxins are electron-transfer proteins involved in a variety
of photosynthetic and non-photosynthetic reactions
The redox activity of flavodoxin derives from its bound flavin
mononucleotide cofactor (FMN), whose intrinsic properties are
profoundly modified by the host protein.
In the last decade of flavodoxin research, the following has
been revealed:
o the folding pathway
o the structure and stability of the apoprotein,
o the mechanism of FMN recognition,
o the interactions that stabilize the functional complex and
tailor the redox potentials
o many details of the binding and electron transfer to partner
proteins
Predicting the flavodoxin secondary and
tertairy structure
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The next decade should witness an even deeper understanding
of the flavodoxin molecule and a greater comprehension of its
many physiological roles.
The fact that flavodoxin is essential for the survival of some
human pathogens could make it a drug target on its own.
Predicting the flavodoxin secondary and
tertairy structure
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Predict using a multiple alignment of 13 flavodoxin
sequences
• Redox protein
• Involved in photosynthesis and other crucial processes
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The 14th sequence on the bottom of the alignment is a
VERY distantly related protein cheY
• Chemotaxis protein
• For example, it interacts with proteins at the base of the
flagellar apparatus of E. coli and promotes clockwise
flagellar rotation
Flavodoxin-cheY multiple sequence alignment:
1fx1
FLAV_DESDE
FLAV_DESVH
FLAV_DESSA
FLAV_DESGI
2fcr
FLAV_AZOVI
FLAV_ENTAG
FLAV_ANASP
FLAV_ECOLI
4fxn
FLAV_MEGEL
FLAV_CLOAB
3chy
-PKALIVYGSTTGNT-EYTAETIARQLANAG-YEVDSRDAASVEAGGLFEGFDLVLLGCSTWGDDSI------ELQDDFIPLF-DSLEETGAQGRKVACF
MSKVLIVFGSSTGNT-ESIaQKLEELIAAGG-HEVTLLNAADASAENLADGYDAVLFgCSAWGMEDL------EMQDDFLSLF-EEFNRFGLAGRKVAAf
MPKALIVYGSTTGNT-EYTaETIARELADAG-YEVDSRDAASVEAGGLFEGFDLVLLgCSTWGDDSI------ELQDDFIPLF-DSLEETGAQGRKVACf
MSKSLIVYGSTTGNT-ETAaEYVAEAFENKE-IDVELKNVTDVSVADLGNGYDIVLFgCSTWGEEEI------ELQDDFIPLY-DSLENADLKGKKVSVf
MPKALIVYGSTTGNT-EGVaEAIAKTLNSEG-METTVVNVADVTAPGLAEGYDVVLLgCSTWGDDEI------ELQEDFVPLY-EDLDRAGLKDKKVGVf
--KIGIFFSTSTGNT-TEVADFIGKTLGA---KADAPIDVDDVTDPQALKDYDLLFLGAPTWNTG----ADTERSGTSWDEFLYDKLPEVDMKDLPVAIF
-AKIGLFFGSNTGKT-RKVaKSIKKRFDDET-MSDA-LNVNRVS-AEDFAQYQFLILgTPTLGEGELPGLSSDCENESWEEFL-PKIEGLDFSGKTVALf
MATIGIFFGSDTGQT-RKVaKLIHQKLDG---IADAPLDVRRAT-REQFLSYPVLLLgTPTLGDGELPGVEAGSQYDSWQEFT-NTLSEADLTGKTVALf
SKKIGLFYGTQTGKT-ESVaEIIRDEFGN---DVVTLHDVSQAE-VTDLNDYQYLIIgCPTWNIGEL--------QSDWEGLY-SELDDVDFNGKLVAYf
-AITGIFFGSDTGNT-ENIaKMIQKQLGK---DVADVHDIAKSS-KEDLEAYDILLLgIPTWYYGE--------AQCDWDDFF-PTLEEIDFNGKLVALf
-MK--IVYWSGTGNT-EKMAELIAKGIIESG-KDVNTINVSDVNIDELL-NEDILILGCSAMGDEVL-------EESEFEPFI-EEIS-TKISGKKVALF
MVE--IVYWSGTGNT-EAMaNEIEAAVKAAG-ADVESVRFEDTNVDDVA-SKDVILLgCPAMGSEEL-------EDSVVEPFF-TDLA-PKLKGKKVGLf
-MKISILYSSKTGKT-ERVaKLIEEGVKRSGNIEVKTMNLDAVD-KKFLQESEGIIFgTPTYYAN---------ISWEMKKWI-DESSEFNLEGKLGAAf
ADKELKFLVVDDFSTMRRIVRNLLKELGFN--NVEEAEDGVDALNKLQAGGYGFVI---SDWNMPNM----------DGLELL-KTIRADGAMSALPVLM
1fx1
FLAV_DESDE
FLAV_DESVH
FLAV_DESSA
FLAV_DESGI
2fcr
FLAV_AZOVI
FLAV_ENTAG
FLAV_ANASP
FLAV_ECOLI
4fxn
FLAV_MEGEL
FLAV_CLOAB
3chy
GCGDS-SY-EYFCGA-VDAIEEKLKNLGAEIVQD---------------------GLRIDGD--PRAARDDIVGWAHDVRGAI-------ASGDQ-EY-EHFCGA-VPAIEERAKELgATIIAE---------------------GLKMEGD--ASNDPEAVASfAEDVLKQL-------GCGDS-SY-EYFCGA-VDAIEEKLKNLgAEIVQD---------------------GLRIDGD--PRAARDDIVGwAHDVRGAI-------GCGDS-DY-TYFCGA-VDAIEEKLEKMgAVVIGD---------------------SLKIDGD--PE--RDEIVSwGSGIADKI-------GCGDS-SY-TYFCGA-VDVIEKKAEELgATLVAS---------------------SLKIDGE--PD--SAEVLDwAREVLARV-------GLGDAEGYPDNFCDA-IEEIHDCFAKQGAKPVGFSNPDDYDYEESKS-VRDGKFLGLPLDMVNDQIPMEKRVAGWVEAVVSETGV-----GLGDQVGYPENYLDA-LGELYSFFKDRgAKIVGSWSTDGYEFESSEA-VVDGKFVGLALDLDNQSGKTDERVAAwLAQIAPEFGLS--L-GLGDQLNYSKNFVSA-MRILYDLVIARgACVVGNWPREGYKFSFSAALLENNEFVGLPLDQENQYDLTEERIDSwLEKLKPAV-L-----GTGDQIGYADNFQDA-IGILEEKISQRgGKTVGYWSTDGYDFNDSKA-LRNGKFVGLALDEDNQSDLTDDRIKSwVAQLKSEFGL-----GCGDQEDYAEYFCDA-LGTIRDIIEPRgATIVGHWPTAGYHFEASKGLADDDHFVGLAIDEDRQPELTAERVEKwVKQISEELHLDEILNA
G-----SY-GWGDGKWMRDFEERMNGYGCVVVET---------------------PLIVQNE--PDEAEQDCIEFGKKIANI--------G-----SY-GWGSGEWMDAWKQRTEDTgATVIGT----------------------AIVNEM--PDNA-PECKElGEAAAKA--------STANSIAGGSDIA---LLTILNHLMVKgMLVYSG----GVAFGKPKTHLGYVHINEIQENEDENARIfGERiANkVKQIF----------VTAEAKK--ENIIAA---------AQAGAS-------------------------GYVV-----KPFTAATLEEKLNKIFEKLGM------
Iteration 0
T
G
SP= 136944.00
AvSP= 10.675
SId= 4009
AvSId= 0.313
Rules of thumb when looking at a
multiple alignment (MA)
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Hydrophobic residues are internal
Gly (Thr, Ser) in loops
MA: hydrophobic block -> internal -strand
MA: alternating (1-1) hydrophobic/hydrophilic =>
edge -strand
• MA: alternating 2-2 (or 3-1) periodicity => -helix
• MA: gaps in loops
• MA: Conserved column => functional? => active
site
Rules of thumb when looking at a
multiple alignment (MA) … cont.
• Active site residues are together in 3D structure
• Helices often cover up core of strands
• Helices less extended than strands => more
residues to cross protein
• -- motif is right-handed in >95% of cases
(with parallel strands)
• MA: ‘inconsistent’ alignment columns and
match errors!
• Secondary structures have local anomalies, e.g.
-bulges
Amino acid
properties
Amino acid hydrophobicity scale
hydrophobic
hydrophilic
Burried and Edge strands
Parallel -sheet
Anti-parallel -sheet
Periodicity patterns within
secondary structures
Burried -strand
Edge -strand
-helix
= hydrophilic
= hydrophobic
TOPS diagrams
Circle = helix
Triangle = strand
-- motif is right-handed in
>95% of cases
RH
LH
Building flavodoxin
RH