Computational Problems in Molecular Biology Dong Xu Computer Science Department 109 Engineering Building West

Lecture Outline l From DNA to gene l Protein sequence and structure l Gene expression l Protein interaction and pathway l Provide a roadmap for the entire course l Biology from system level (computational perspective)

About Life l Life is wonderful: amazing mechanisms l Life is not perfect: errors and diseases l Life is a result of evolution

Cells l Basic unit of life l Prokaryotes/eukaryotes l Different types of cell: å Skin, brain, red/white blood å Different biological function l Cells produced by cells å Cell division (mitosis) å 2 daughter cells

DNA l Double Helix (Watson & Crick) l Nitrogenous Base Pairs å Adenine  Thymine [A,T] å Cytosine  Guanine [C,G] å Weak bonds (can be broken) å Form long chains

Genome l Each cell contains a full genome (DNA) l The size varies: å Small for viruses and prokaryotes (10 kbp-20Mbp) å Medium for lower eukaryotes X Yeast, unicellular eukaryote 13 Mbp X Worm (Caenorhabditis elegans) 100 Mbp X Fly, invertebrate (Drosophila melanogaster) 170 Mbp å Larger for higher eukaryotes X Mouse and man 3000 Mbp å Very variable for plants (many are polyploid) X Mouse ear cress (Arabidopsis thaliana) 120 Mbp X Lilies 60,000 Mbp

Differences in DNA ~2%~4% ~0.2%

Genes l Chunks of DNA sequence that can translate into functional biomolecules (protein, RNA) l 2% human DNA sequence for coding genes l 32,000 human genes, 100,000 genes in tulips

Gene Structure l General structure of an eukaryotic gene l Unlike eukaryotic genes, a prokaryotic gene typically consists of only one contiguous coding region

Informational Classes in Genomic DNA l Transcribed sequences (exons and introns) l Messenger sequences (mRNA, exons only) l Coding sequences (CDS, part of the exons only) l Heads and tails: untranslated parts (UTR) l Regulatory sequences l... and all the rest  Identify them: gene-finding

Genetic Code A=Ala=Alanine C=Cys=Cysteine D=Asp=Aspartic acid E=Glu=Glutamic acid F=Phe=Phenylalanine G=Gly=Glycine H=His=Histidine I=Ile=Isoleucine K=Lys=Lysine L=Leu=Leucine M=Met=Methionine N=Asn=Asparagine P=Pro=Proline Q=Gln=Glutamine R=Arg=Arginine S=Ser=Serine T=Thr=Threonine V=Val=Valine W=Trp=Tryptophan Y=Tyr=Tyrosine

Protein Synthesis AGCCACTTAGACAAACTA (DNA) å Transcribed to: AGCCACUUAGACAAACUA (mRNA) å Translated to: SHLDKL (Protein)

About Protein 10s – 1000s amino acids (average 300) Lysozyme sequence (129 amino acids): KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDITA SVNCAKKIVS DGNGMNAWVA WRNRCKGTDV QAWIRGCRL Protein backbones: Side chain

Evolution of Genes: Mutation l Genes alter (slightly) during reproduction å Caused by errors, from radiation, from toxicity å 3 possibilities: deletion, insertion, alteration l Deletion: ACGTTGACTC  ACGTGACTC l Insertion: ACGTTGACTC  AGCGTTGACTC l Substitution: ACGTTGACTC  ACGATGACTC l Mutations are mostly deleterious

Ancestor Gene duplication X Y Recombination 75%X 25%Y Paralogs (related functions) Mixed Homology Orthologs (similar function) Evolution and Homology Twilight zone: undetectable homology (<20% sequence identity)

Sequence Comparison o Pairwise sequence comparison o multiple alignment SAANLEYLKNVLLQFIFLKPG--SERERLLPVINTMLQLSPEEKGKLAAV O15045 NEKNMEYLKNVFVQFLKPESVP-AERDQLVIVLQRVLHLSPKEVEILKAA P34562 KNEKIAYIKNVLLGFLEHKE----QRNQLLPVISMLLQLDSTDEKRLVMS Q06704 REINFEYLKHVVLKFMSCRES---EAFHLIKAVSVLLNFSQEEENMLKET Q92805 MLIDKEYTRNILFQFLEQRD----RRPEIVNLLSILLDLSEEQKQKLLSV O42657 EPTEFEYLRKVMFEYMMGR-----ETKTMAKVITTVLKFPDDQAQKILER O70365 DPAEAEYLRNVLYRYMTNRESLGKESVTLARVIGTVARFDESQMKNVISS Q21071 STSEIDYLRNIFTQFLHSMGSPNAASKAILKAMGSVLKVPMAEMKIIDKK Q18013

Phylogenetic Trees Understand evolution

Protein Structure Lysozyme structure: ball & stick strand surface

Structure Features of Folded Proteins l Compact l Secondary structures: loop  -helix  -sheet Protein cores mostly consist of  -helices and  -sheets

Protein Structure Comparison Structure is better conserved than sequence Structure can adopt a wide range of mutations. Physical forces favor certain structures. Number of fold is limited. Currently ~700 Total: 1,000 ~10,000 TIM barrel

Protein Folding Problem A protein folds into a unique 3D structure under the physiological condition Lysozyme sequence: KVFGRCELAA AMKRHGLDNY RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC SALLSSDITA SVNCAKKIVS DGNGMNAWVA WRNRCKGTDV QAWIRGCRL

Structure-Function Relationship Certain level of function can be found without structure. But a structure is a key to understand the detailed mechanism. A predicted structure is a powerful tool for function inference. Trp repressor as a function switch

Structure-Based Drug Design HIV protease inhibitor Structure-based rational drug design is still a major method for drug discovery.

Gene Expression Same DNA in all cells, but only a few percent common genes expressed (house-keeping genes). A few examples: (1) Specialized cell: over-represented hemoglobin in blood cells. (2) Different stages of life cycle: hemoglobins before and after birth, caterpillar and butterfly. (3) Different environments: microbial in nutrient poor or rich environment. (4) Special treatment: response to wound.

Eucaryote Gene Expression Control DNA Primary RNA transcript mRNA nucleuscytosol RNA transport control inactive mRNA degradation control translation control nucleus membrane transcriptional control protein inactive protein activity control RNA processing control Methods: Mass-spec Microarray

Gene Regulation DNA sequence Start of transcription promoter operator

Microarray Experiments Microarray data  Regulation/function/pathway/cellular state/phenotype  Disease: diagnosis/gene identification/sub-typing Microarray chip

Genetic vs. Physical Interaction Regulatory network Genetic interaction Complex system Physical interaction Gene/protein interaction Expressed gene Transcription factor

Biological Pathway

Studying Pathways through Systems Biology Approach RGYSLGNWVC AAKFESNFNT QATNRNTDGS TDYGILQINS RWWCNDGRTP GSRNLCNIPC sequence structure functionprotein interaction gene regulation pathway (cross-talk)

Discussion l Possible impacts of biotechnology to our life

Assignments l Required reading: * Chapter 13 in “Pavel Pevzner: Computational Molecular Biology - An Algorithmic Approach. MIT Press, 2000.” * Larry Hunter: molecular biology for computer scientists l Optional reading: