Domain-specific analysis of collagen code Mammalian collagen 1α1

1. Domain-specific analysis of collagen code
Mammalian collagen 1α1
Anne Kleinnijenhuis
anne.kleinnijenhuis@triskelion.nl
May 2017

2. Introduction
Collagen is the most abundant protein in mammals and an important
structural protein.
The amino acid sequence contains large stretches of repetitive Gxy triplets
(Gxy region) involved in the helical structure, where G represents glycine and
x and y represent another amino acid (often proline).
In Triskelion study 20959 a comprehensive investigation of collagen DNA and
protein code was performed. In the current presentation some of the findings
during the analysis of mammalian collagen 1α1 are highlighted.
The results are presented using a novel nomenclature for nucleotide changes
and a novel codon table.

3. Nomenclature: novel codon table
Percodonavaluehasbeenprovided,whichindicatesthe
robustnessofthecode.Inprinciplethereare9possiblechanges
toacodon,excludingchangeswhichresultinaframeshift.
Thevaluebehindthecodonindicatesthenumberofpossible
changesinthatparticularcodonwhichdonotresultinachange
intheeventuallytranslatedaminoacid.

4. Nomenclature: nucleotide changes
Inprinciplethereareintotal20possible(combinationsof)
nucleotidechangeswhichwouldnotleadtoadifferentamino
acidaftertranslation(synonymouschanges),seetable.
Theappliednomenclatureforcodongroupandaminoacid
changesisstraightforward,e.g.AS2meansthatthecodongroup
changesfromAtoS2andtheaminoacidfromAtoS.

5. Nomenclature: change order

6. Comparison to Homo sapiens collagen 1α1
The collagen 1α1 Gxy regions of
the following species were
compared to Homo sapiens:
(source: www.ebi.ac.uk/ena)
Pan troglodytes
Chimpanzee
Macaca mulatta
Rhesus monkey
Mus musculus
House mouse

7. Nucleotide changes (Pan troglodytes)
NucleotidedifferencesbetweenthePantroglodytesandHomo
sapienscollagen1α1Gxyregion.SharedchangeswithMacaca
mulattaonlyarehighlightedinyellow,withMusmusculusonlyin
redandwithMacacamulattaANDMusmusculusinorange.
Therearenoaminoaciddifferences.

8. Pan troglodytes
Nucleotide changes projected
on chimpanzee coding DNA

9. Nucleotide changes (Macaca mulatta)
NucleotidedifferencesbetweentheMacacamulattaandHomo
sapienscollagen1α1Gxyregion.SharedchangeswithMus
musculusarehighlightedinyellow.Orangehighlightmeansthat
Musmusculushasadifferentchangeinthesamenucleotide,
comparedtoMacacamulatta.

10. Macaca mulatta
Nucleotide changes projected
on rhesus monkey coding
DNA

11. Nucleotide changes (Mus musculus) 1
NucleotidedifferencesbetweentheMusmusculusandHomo
sapienscollagen1α1Gxyregion.Multiplechangeswithin1codon
arehighlightedinyellow.

12. Nucleotide changes (Mus musculus) 2

13. Nucleotide changes (Mus musculus) 3

14. Nucleotide changes (Mus musculus) 4

15. Mus musculus
Nucleotide changes projected
on murine coding DNA

16. Summary table
Summary of the changes between
human and chimpanzee / rhesus
monkey / murine collagen 1α1

17. Codon group involvement
Codon table with color ranges indicating, from white to red, the increasing
involvement of codon groups in amino acid changes in the Gxy region between
chimpanzee and murine collagen 1α1 and, from white to blue, the codon usage
in chimpanzee collagen 1α1. Especially the S2N change route is notable.

18. Codon usage 1
Arginine
Histidine
Lysine
Positivelychargedaminoacids.

19. Codon usage 2
Aspartic acid
Glutamic acid
Negativelychargedaminoacids.

20. Codon usage 3
Serine
Threonine
Asparagine
Glutamine
Aminoacidswithpolarsidechains.

21. Codon usage 4
Alanine
Isoleucine
Leucine
Methionine
Valine
Aminoacidswithhydrophobicsidechains.

22. Codon usage 5
Phenylalanine
Tryptophan
Tyrosine
Aminoacidswithhydrophobicsidechains
andaconjugatedsystem.

23. Codon usage 6
Cysteine
Glycine
Proline
Aminoacidswith–H,-SHandpyrrolidine
sidechains(other).
Proline codon
usage in the 2nd &
3rd Gxy position

24. Amino acid usage per position
AminoacidusageperpositionintheGxy
tripletsofhumancollagen1α1.

25. Alanine codon usage in human collagen 1α1
Alanine codon usage in the
2nd & 3rd Gxy position

26. Trypsin cleavage sites
Homosapienscollagen1α1proteinsequenceshowingthetrypsin
cleavagesitesKinlightblueandRinlightgreenwhichoccurat
regularintervals.
Amongstothers,KandRarehighlyconservedaminoacidsin
collagenGxyregionswhichofferstheopportunityfortheanalysis
ofanalogoustrypticpeptidesusingbottomupLC-MS

27. Analogous targets
WhenchangesinKorRdooccur,mostlybetweenlessrelated
collagens,theyareusuallyswitchesbetweenthesepositively
chargedaminoacids(seeorangeboxes).
Apartofthealignedsequencesofseveralcollagentypesfrom
severalspeciesisshowntoillustratethepresenceofanalogous
tryptictargetpeptides

28. Conclusions
In the present study collagen sequences from the Gxy region were analyzed
on the nucleotide, codon group, amino acid and target peptide level.
To describe the changes between collagens a novel nomenclature and codon
table were proposed.
Several biases were observed in codon usage, codon usage related to Gxy
position and amino acid usage related to Gxy position.
The conserved position of positively charged amino acids K and R offers the
opportunity for selection of analogous tryptic target peptides.

29. SlideShare series Anne Kleinnijenhuis
Domain-specific analysis of collagen code (May 2017)
Exploring LC-MS peptide dynamic range (December 2016)
Strategies for bioanalysis of proteins using LC-MS (May 2016)
Proposal for the absolute quantification of modular molecules
(October 2015)