The overlap feature of hemoglobin

Hemoglobin was used in 1962 by Zuckerkandl and Pauling to derive data that led to the molecular clock idea.  Here I examined the overlap feature using human Hemoglobin alpha 1 (AAK61216, hba1) to compare with horse and chicken, in a way similar to what Zuckerkandl and Pauling had done.

Hs, Human [Homo sapiens]

Ec, Horse [Equus caballus]

Gg, Chicken [Gallus gallus]

Hs     1    MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG  60

Hs=Ec       MVLS ADKTNVKAAW KVG HAGEYGAEALERMFL FPTTKTYFPHFDLSHGSAQVK HG

Ec     1    MVLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHG  60

Hs=Gg       MVLS ADK NVK  + K+  HA EYGAE LERMF ++P TKTYFPHFDLSHGSAQ+KGHG

Gg     1    MVLSAADKNNVKGIFTKIAGHAEEYGAETLERMFTTYPPTKTYFPHFDLSHGSAQIKGHG  60

Overlap         x          x   x               x 

Non-overlap                                                          *           

Hs     61   KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP  120

Hs=Ec       KKV DALT AV H+DD+P ALS LSDLHAHKLRVDPVNFKLLSHCLL TLA HLP +FTP

Ec     61   KKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTP  120

Hs=Gg       KKV  AL  A  H+DD+   LS LSDLHAHKLRVDPVNFKLL  C LV +A H PA  TP

Gg     61   KKVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPAALTP  120

Overlap        x    x  x x  x x   x                            x    x

Non-overlap                                                *       *           

 

Hs     121  AVHASLDKFLASVSTVLTSKYR  142

Hs=Ec       AVHASLDKFL+SVSTVLTSKYR

Ec     121  AVHASLDKFLSSVSTVLTSKYR  142

Hs=Gg        VHASLDKFL +V TVLT+KYR

Gg     121  EVHASLDKFLCAVGTVLTAKYR  142

Overlap               x

 

Results:

Of 17 variants between human and horse, 14 are also variants between human and chicken.  So there are 14 overlaps and 3 non-overlaps. 

Molecular clock prediction:  17/142 x 42/142 x 142 = 5 overlap residues, accounting for 36% of total overlap.  If we generously grant 50% positions as absolutely non-variable, we have 17/71 x 42/71 x 71 = 10 overlap residues, accounting for only 71% of total overlap.  To account for 14 overlaps, we need 91 absolutely non-variable residues or require that there are only 51 residues that can vary.  But we know that there are at least 71 variable positions between human and fish.  So, molecular clock simply cannot account for the 14 overlaps.  But the existence of significant overlap is a prime prediction of the MGD hypothesis.

In fact, there are only 21 residues that are absolutely conserved among human, bony fish, lungfish, coelacanths, and sharks.  So, a most realistic calculation of overlap should be 17/121x42/121x122=5.9 residues, far short of 14. 

BTW, chicken is equidistant (70% identity) to human and horse as shown below.  Of 17 variants between human and horse, 14 are also variant between horse and chicken, a significant overlap.

Human-Horse [Equus caballus]:

Identities = 125/142 (88%)

Hs     1    MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG  60

            MVLS ADKTNVKAAW KVG HAGEYGAEALERMFL FPTTKTYFPHFDLSHGSAQVK HG

Ec     1    MVLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHG  60

 

Hs     61   KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP  120

            KKV DALT AV H+DD+P ALS LSDLHAHKLRVDPVNFKLLSHCLL TLA HLP +FTP

Ec     61   KKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTP  120

 

Hs     121  AVHASLDKFLASVSTVLTSKYR  142

            AVHASLDKFL+SVSTVLTSKYR

Ec     121  AVHASLDKFLSSVSTVLTSKYR  142

 

Human-Chicken [Gallus gallus]

Identities = 100/142 (70%)

Hs     1    MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG  60

            MVLS ADK NVK  + K+  HA EYGAE LERMF ++P TKTYFPHFDLSHGSAQ+KGHG

Gg     1    MVLSAADKNNVKGIFTKIAGHAEEYGAETLERMFTTYPPTKTYFPHFDLSHGSAQIKGHG  60

 

Hs     61   KKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTP  120

            KKV  AL  A  H+DD+   LS LSDLHAHKLRVDPVNFKLL  C LV +A H PA  TP

Gg     61   KKVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPAALTP  120

 

Hs     121  AVHASLDKFLASVSTVLTSKYR  142

             VHASLDKFL +V TVLT+KYR

Gg     121  EVHASLDKFLCAVGTVLTAKYR  142

 

Horse-Chicken [Gallus gallus]

Identities = 100/142 (70%),

Ec     1    MVLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHG  60

            MVLSAADK NVK  ++K+ GHA EYGAE LERMF  +P TKTYFPHFDLSHGSAQ+K HG

Gg     1    MVLSAADKNNVKGIFTKIAGHAEEYGAETLERMFTTYPPTKTYFPHFDLSHGSAQIKGHG  60

 

Ec     61   KKVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTP  120

            KKV  AL  A  H+DD+ G LS LSDLHAHKLRVDPVNFKLL  C L  +A+H P   TP

Gg     61   KKVVAALIEAANHIDDIAGTLSKLSDLHAHKLRVDPVNFKLLGQCFLVVVAIHHPAALTP  120

 

Ec     121  AVHASLDKFLSSVSTVLTSKYR  142

             VHASLDKFL +V TVLT+KYR

Gg     121  EVHASLDKFLCAVGTVLTAKYR  142