Simplify the display

Show only alpha carbons

Turn off show backbone oxygen

Colour secondary structure

Turn 3 D display on

1HEW

Backbone as alpha carbons

Sidechains only Tyr62

Substrate with VDW surface and CPK colors

1bmf

1bmf

Colored by chain

(discuss similarity to helicase and T3SS)

1bmf

Open pdb – check chain idSelect Chain E (by clicking in

column designation in Control Panel)

Safe selected residues in current layer as betaTP

Repeat for betaDP, betaE, alpha TP, alphaDP, and alpha E.

The save menu

1bmf

Open the three beta SU

<SHIFT> Color inin secondary structure (shift makes it act on the 3 layers simultaneously)

1bmf 3 beta subunits Use Magic fit and interative magic fit to align the three subunits

(use betDB as reference layer) <ctrl>tab allows you to move through the three layers

For an animated GIF see http://web2.uconn.edu/gogarten/F1ATPasecatcycle.htm

Layer Info Window

Checkmarks in the vis and mov columns provide a fast way to change settings for the different layers

betaTB and betaE with RMS coloring compared to betaDP

Magic fit -> fit molecules -> RMS coloring

RED: Long wavelength =long distance between structures

BLUE: Short wavelength =short distance between structures

If you need to switch the reference layer, you can do so in the SwissModel menu

The 3 point alignment tool If you want to compare the structure of very

dissimilar proteins that use a similar substrate, sometimes it helps to align the substrates.

This can be done through the 3 point alignment tool.

Homing

Homing cycle of a parasitic genetic element (modified from [3, 13]). Recent findings suggest that due to complex population structure the cycle might not operate in synchrony in different subpopulations. The red arrows indicate the trajectory of the functioning HE and the black arrows the fate of the host gene. The precise loss can occur through recombination with an intein or intron free allele, or, in case of introns, through recombination with a reverse transcript of the spliced mRNA [39, 40].

XXAlleles with empty

Target Site

ZZAlleles invaded by a functional Homing

Endonuclease

YYAlleles harboring a

dysfunctional Homing

Endonuclease

(I) X-alleles are converted to Z-

alleles through the function of

the homing endonuclease,

leading to super Mendelian

inheritance of Z

X < Z

Y > Z(II) Carriers of the Y-allele are more fit than carriers of the Z

allele. The presence of a dysfunctional homing endonuclease provides

immunity to invasion by Z

(III)

Carri

ers o

f the

Y-all

ele ar

e

less fi

t tha

n ca

rrier

s of t

he X

allele

. Y <

X

"Nothing in biology makes sense except in the light of evolution"

Theodosius Dobzhansky

Homology

bird wing bat wing

human arm

by B

ob F

riedm

an

homology vs analogy

  Homology (shared ancestry) versus  Analogy (convergent evolution)

A priori sequences could be similar due to convergent evolution

bird wing butterfly wing

bat wing fly wing

What does Bioinformatics have to do with Molecular Evolution? Problem: Application of first principles does not (yet) work:

Most scientists believe in the principle of reductionism (plus new laws and relations emerging on each level), e.g.:

DNA sequence ->transcription ->translation ->protein folding ->protein function (catalytic and other properties) ->properties of the organism(s) ->ecology

At several steps along the way from DNA to function our understanding of the chemical and physical processes involved is incomplete and computational simulations are so time consuming that prediction of protein function based on only a single DNA sequence is at present impossible (at least for a protein of reasonable size).

Related Proteins

Present day proteins evolved through substitution and selection from ancestral proteins. Related proteins have similar sequence AND similar structure AND similar function.

In the above mantra "similar function" can refer to:

•identical function,

•similar function, e.g.:•identical reactions catalyzed in different organisms; or •same catalytic mechanism but different substrate (malic and lactic acid dehydrogenases); •similar subunits and domains that are brought together through a (hypothetical) process called domain shuffling, e.g. nucleotide binding domains in hexokinse, myosin, HSP70, and ATPsynthases.

homologyTwo sequences are homologous, if there existed an ancestral molecule in the past that is ancestral to both of the sequences

Homology is a "yes" or "no" character (don't know is also possible). Either sequences (or characters share ancestry or they don't (like pregnancy). Molecular biologist often use homology as synonymous with similarity of percent identity. One often reads: sequence A and B are 70% homologous. To an evolutionary biologist this sounds as wrong as 70% pregnant.

Sequence Similarity vs Homology

The following is based on observation and not on an a priori truth:

If two (complex) sequences show significant similarity in their primary sequence, they have shared ancestry, and probably similar function.(although some proteins acquired radically new functional assignments, lysozyme -> lactalbumin).

The Size of Protein Sequence Space (back of the envelope calculation)

For comparison the universe contains only about 1089 protons and has an age of about 5*1017 seconds or 5*1029 picoseconds.

If every proton in the universe were a super computer that explored one possible protein sequence per picosecond, we only would have explored 5*10118 sequences, i.e. a negligible fraction of the possible sequences with length 600 (one in about 10662).

Consider a protein of 600 amino acids. Assume that for every position there could be any of the twenty possible amino acid. Then the total number of possibilities is 20 choices for the first position times 20 for the second position times 20 to the third .... = 20 to the 600 = 4*10780 different proteins possible with lengths of 600 amino acids.

no similarity vs no homology If two (complex) sequences show significant similarity in their primary sequence, they have shared ancestry, and probably similar function.

THE REVERSE IS NOT TRUE:

PROTEINS WITH THE SAME OR SIMILAR FUNCTION DO NOT ALWAYS SHOW SIGNIFICANT SEQUENCE SIMILARITYfor one of two reasons:

a)  they evolved independently (e.g. different types of nucleotide binding sites); or b)   they underwent so many substitution events that there is no readily detectable similarity remaining.

Corollary: PROTEINS WITH SHARED ANCESTRY DO NOT ALWAYS SHOW SIGNIFICANT SIMILARITY.