Lecture 9:Protein A

rchitecture V:Evolution, Function &

Classification

Margaret A

. Daugherty

Fall 2003

BIOC 205

Definitions

Biochemical evolution: study of how proteins (and other

molecules) and biochem

ical pathways have changedthrough tim

e.

Hom

ologous proteins: those derived from a com

mon

ancestor; share a significant degree of sequencesim

ilarityi). paralogs - hom

ologs present within a species;

ii). orthologs: -homologs that are present in

different species

Divergent evolution: Proteins derived from

comm

onancestors

Orthologs vs. Paralogs

35% sequence identity

Sequence alignments: statistical survey of sequences

In this example

we are lookingat identicalm

atches;

Slide onesequence alongother and countup m

atches

Insertion of gaps helps alignments

36 matches

Conservative substitutions Replacing one am

ino acid by another similar in size & charge

e.g., asp -> glu can you name other conservative changes?

Rule of thumb: (assum

ing a 100 residue protein)>25%

identity : homologous sequence

<15% identity: probably not hom

ologous

Paralogs: the oxygen binding heme proteinsBIO

C 205

Tertiary structure is more conserved than prim

ary structure

PHYLO

GENETIC TREE FO

R THE GLO

BINSBIO

C 205

* gene duplication events play a major role here!

*

*

**

CONSERVA

TION

IN TH

E GLO

BIN FO

LD

BIOC 205

Sequence Alignm

ent: Identification of homologous proteins

cytochrome c: a favorite exam

ple

Yellow - invariant; blue - conservative; unshaded; non-conserved

BIOC 205

Comparison of sequence differences

# of differences is proportional to the phylogenetic differenceBIO

C 205

Phylogenetic trees: evolutionary relatedness

BIOC 205

# of changes is

proportional toevolutionary tim

esince the com

mon

ancestor

How hum

an cyt c compares with its ancestral progenitor

BIOC 205

A). Tuna (5cyt)

B). TunaC). Rice (1cc4)D

). Yeast(1ycc)E). Bacterial (1hro)

Conservation in structure

BIOC 205

Convergent evolution: different evolutionary paths lead tothe sam

e solutionThe serine proteases: cleave peptide bonds by hydrolysis

Active sites

Protein structure

Genetic VariabilityGene m

utations (base substitutions) can lead to alteredam

ino acid substitutions; can be neutral, aberrant or non-functional

BIOC 205

Hb S: Sickle cell H

b

Hb S:

A case study

BIOC 205

High incidence of sickle cell allele

generally coincides with highincidence of m

alaria;H

eterozygotes have a higherresistance to m

alaria;The fragility of the RBCs tendsto interrupt the m

alarialparasites life cycle;Therefore, heterozygotes have ahigher survival rate & are m

orelikely to pass on their genes!

•Sickle hem

oglobin(H

bS);

•M

utation β6 E -> V;•

Most com

mon in people

of African and

Caribbean descent–

1 in 10-40 carry thetrait

–1 in 60-200 have thedisease

β6 glutamic acid --> valine m

utationStructural consequence of the m

utationBIOC 205

β6 glutamic acid --> valine m

utationStructural consequence of the m

utation

Clinical Manifestations

•D

ue to their shape, sickled RBCscan't squeeze through sm

allblood vessels as easily as thealm

ost donut-shaped normal

cells;

•This can lead to these sm

allblood vessels getting blocked,which stops the oxygen fromgetting through to where it isneeded;

•This in turn can lead to severepain and dam

age to organs.

BIOC 205

Classification: we’ve seen this

Enzymes - catalyze chem

ical reactionsRegulatory proteins - control physiological functionTransport proteins - m

ove substances around/between cellsStorage proteins - provide a reservoir for a substanceM

otor proteins - endow cells with capability of movem

entStructural proteins - create and m

aintain biological structureProtective proteins -active role in cell defense or protectionExotic proteins - have specialized adaptive functions

The simplification: A

nd all this with just 20 amino acids

and some post-translational m

odifications!

The reality: many proteins contain other chem

ical groups BIOC 205

Conjugated ProteinsN

omenclature: the word "conjugated" is from

the Latin,con = withjugum

= yoke

Thus, the protein and non-protein moieties are yoked

with one another (like oxen) to work together.

Apoprotein = the protein without its non-protein

component;

Prosthetic group = the non-protein portion alone;what wecall the non-am

ino acid component if it is crucial to

function or influences the conformation of the protein.

Conjugated or holo- protein = the apoprotein + prostheticgroup.

BIOC 205

Classification ofconjugated proteins

GlycoproteinsLipoproteinsN

ucleoproteinsPhosphoproteinsM

etalloproteinsH

emoproteins

Flavoproteins

BIOC 205

Examples of Prosthetic Groups

Hem

e

Phosphate

Carbohydrate Lipid

Stephen Everse © 2001

BIOC 205

Metalloproteins

Metals found as prosthetic groups of proteins include:

Mg, Ca, V, Cr, M

n, Fe, Co, Cu, Zn and Mo.

These metals can form

coordination complexes. They accept

electron pairs from atom

s with unshared electron pairs. The electron

pairs fill vacant orbitals of the metal ion, such as sp

3d2 orbitals. Som

eof these m

etals can easily undergo oxidation-reduction,e.g.

Fe(II) = Fe(III) + e-

All are relatively sm

all; note, no heavy metals (e.g., Pb, H

g) areincluded!

Stephen Everse © 2001

BIOC 205

Roles for Bound Metals

• The m

etal acts as a polydentate ligand, thereby stabilizing the three-dim

ensional structure of the protein.

Example: The gam

ma dom

ain of fibrinogen looses its structure if

Ca2+ is rem

oved & can no longer clot.

• M

etals frequently participate in oxidation-reduction. Sometim

es boundm

etals participate directly in biological oxidation-reduction reactions byaccepting or donating an electron (changing oxidation state).

Example: Cytochrom

es

• H

olding the protein and some other m

olecule together (e.g., an enzyme

and its substrate are ligands of the metal ion sim

ultaneously).

Example: D

NA

polymerases with M

g ++ ligated by 2-3 conserved

acidic AA

s and the triphosphate tail of the dNTP

BIOC 205

Mg, Ca, V, Cr, M

n, Fe, Co, Cu, Zn and Mo.

GlycoproteinsProteins with carbohydrate prosthetic groups

Functions:•

First, recognition. Carbohydrate prosthetic groups serve asantigenic sites (e.g., blood group antigens are carbohydrateprosthetic groups), intracellular sorting signals (m

annose 6-phosphate bound to a newly synthesized protein sends it tothe lysosom

es), proteins which have lost their terminal sialic

acid(s) are cleared by the liver, etc.

•Second, structural. Structural com

ponents of the organism:

e.g., the proteoglycans of cartilage.

Stephen Everse © 2001

BIOC 205

GlycosylationTypical structure -- one or m

ore chains of monosaccharide units, 1 to

30 units long. It may be straight or branched, and it is usually

covalently linked to the apo-protein in one of two major ways.

BIOC 205

ABO

Blood Group Antigens

•Type A

cells–

A antigen on cells

–anti-B antibodies

•Type B cells–

B antigen on cells–

anti-A antibodies

•Type A

B cells–

A & B antigens on cells

–no antibodies

•Type O

cells–

H antigen on cells

–both anti-A

& -B antibodies

BIOC 205

When does glycosylation occur?

•Can start asthe protein isbeingsynthesizedon the ER;

•U

suallycom

pleted inthe golgi.

BIOC 205

Computer Sim

ulation ofGlycoslyated proteins

•Superim

posed“snapshots” over tim

e;•

Oligosaccharides are

conformationally

mobile;

•M

ay shield proteinsurface, thusprotecting it fromproteolysis.

Stephen Everse © 2001

BIOC 205

REVIEW

BIOC 205

1). Sequence similarities between proteins im

ply evolutionary relatedness.

2). Hom

ologous proteins are those that perform the sam

e function indifferent organism

s.

3). Related proteins are that have related functions.

4). Invariant amino acids are crucial to either structure or function.

5). The number of sequence changes in hom

ologous proteins isproportional to the phylogenetic difference betw

een the organisms.

6). Length of branches in phylogenetic trees are proportional to time.

7). Conservation of sequence is followed by conservation of structure.

8). Genetic variability exist in large populations.

9). Proteins can be classified according to function or chemistry.

10). Familiarize yourself with the classifications!