Lecture 5' - Introduction to Protein Struct II Spr08

8/14/2019 Lecture 5' - Introduction to Protein Struct II Spr08

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Lecture 5 Protein Structure II

Protein Structure (cont.)

Super-secondary structure

Turns

Motifs

Tertiary Structure

Protein Domains

3o Structure Representation Methods:

visual methods non-visual methods of representation:

contact plots

Quaternary structure


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The Structure of GlobularProteins

Fibrous structural proteins are long helices. e.g., collagen (C), -, -keratin.

Water-soluble and membrane proteins more globular. therefore, adopt more complex folds

that vary greatly from protein to protein.

the 3o

structure describes the global conformation.

However, different proteins often locally similar: will generally have regions of similar 2

ostructure.

may also contain similar groups of helices:

super-secondary structure. there are numerous common groups, called motifs.

3o

structure can also often be segregated into domains: independently folding units, with discrete function. thus, we first discuss these 2 intermediate levels of

structure.


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Type I and Type II -turns

There are 2 typical -turnsobserved in proteins: distinguished by the orientation of the

peptide bond connecting residues 2 and

3. Type I keto-O of res. 2 pointed away

from R2, R3 (shown in peptide

bond 3). no steric problems. the turn in our previous slide was type I.

Type II keto-O of residue 2 pointed

towards R2, R3.

steric problems b/w the keto-O and the C

of R3.

thus, a Glycine often observed at R3

(no

C).


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The Motif

A 2-stranded parallel -sheet: must incorporate a longer turn.

at least the length of 1 -strand.

often adopts an -helix. to accommodate H-bond donors

and acceptors in the stretch. eliminates interaction with H20.

the motif. The 2 -strands are H-bonded

in spite of the intervening helix.


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Motifs Involving only -helices

Finally, there are motifs involving only -helices: e.g.: The unit, or -helix hairpin.


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The Domainal Picture ofProtein Structure

Many globular proteins containindependentlyfolding elements: each of which is independently stable, with specific

function.

longer than super-2o structures (30-300 residues).

such elements called Domains. Many proteins have separate domains:

for binding of substrates;

for binding of effectors; for enzymatic activity.

most proteins contain overlapping regions.

Mosaic proteins: consist exclusively of a chain of non-overlapping

domains.


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Example: Calmodulin

Calmodulin is anintercellular protein: regulates the behavior of many other proteins.

is a transducer: Ca+

sensor.

Ca+

binding converts it to an active form.

has a clear, domainal structure:

Calmodulin composed of 2

Ca+- binding domains.

2 separate binding domains. each domain = a pair of EF-hands.

domains connected by a long -helix.

helix shortens on Ca+

binding

allowing folding into active form.


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Protein Tertiary Structure

Tertiary Structure (3o):

the overall 3-D conformation of the polypeptidechain.

may be determined, for instance, by X-ray

crystallography.

How do we represent this overall structure? many methods, with different degrees of detail

atomic coordinate models.

various visual inspection models: Stick model.

van der Waals surface (CPK) model.

Ribbon model.

Solvent accessible surface (SAS) area model.

Simple caricature (exaggerated cartoon).


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Representation 1 - AtomicCoordinates

The most detailed representation is a list: atomic coordinates for each atom in the polypeptide.

each list element specifies:

atom name;

type, number of the residue;

spatial coordinates, (x,y,z).

conceptually simple, but focus is not conformation.

not very intuitive (not a picture): does not indicate helices, or

super-2o

structures...

Visual models focus on conformation. easily produced (by computer) from atomic

coordinates.


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Visual Model 1 Stick Model

Each bond represented as a stick in 3-D. i.e., a line connecting each bonded pair of atoms in

3-space.

correctly represents atomic positions, relative bond

lengths. gives a notion of overall shape.

clearly shows residue adjacencies.

Atomic sizes not included.

no indication of steric interactions.

Helical structure not indicated. helical structure not shown.

does not show super-2o

structure.

does not indicate domains.


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Visual Model 2van der Waals Surface Model

Developed by Corey, Pauling, and Kultun: also called CPK models. includes the size of each atom:

represents each atom as a vdW sphere.

radius = van der Waals radius. atom types distinguished by color.

Various Disadvantages: protein interior obscured.

primarily a surface plot. backbone not distinguished from

side-chains.

no indication of helical structure.

Vi l M d l 3 Ribb


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Visual Model 3 RibbonModel

The Ribbon Model: removes the vdW spheres to reveal interior atoms.

backbone traced by a ribbon. aids in visualization of helices.

still may be too much information. 2

ostructure obscured.

often, only critical residues retained. such as those at an active site.

much more informative.Numerous variations on the

ribbon model. residues may be completely omitted.

choice depends on purpose.


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Solvent Accessible SurfaceModel

In a Solvent-Accessible Surface (SAS) model: new focus: interaction of the macromolecule with

H20.

backbone may still be represented by a ribbon:

to indicate the helical structure.

Residues are not explicitly modeled. instead, modeled implicitly.

residues exclude solvent differently,

based on hydrophobicity: Limits the solvents accessibility.

Resulting water boundary depictedas a transparent surface

the solvent accessible surface (SAS).


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Visual Model 5 Caricature

Finally, we may represent the protein using acaricature (cartoon) model: here, our focus is again on conformation. atoms in the backbone replaced by simple symbols.

side-chains may be retained in stick form.Each symbol represents a 2

ostructure.

each helix represented by a cylinder. each -strand represented by an arrow.

points N to C.

greatly simplifies inspection: location of 2

ostructures.

types of super-2o

structures. domains clearly shown.

The best model depends on focus.


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Non-visual Methods

Conformation may also be represented non-visually. alternative: define helical structures analytically in terms of the mean values of (,) required:

for a given residue to adopt each type of helix structure.Simple method for a protein of interest: calculate the (,) value for each residue in the chain.

from the list of atomic coordinates. assign a structure to each residue.

i.e.,-helix (H), -sheet (E), or random coil (c). Example: N-ccHHHHcccEEEEEcc-C

Problem: mapping not unique actual distributions of each type of structure overlap. H-bonding patterns may also be considered

Kabsch and Sanders (1983).o


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Contact Plots

Alternative method of representing proteinstructure:

is by a plot of residue adjacency called a contact, or diagonal plot.

Method: Calculate the distance (dij) b/w each pair of residues

(i,j).

distance b/w C carbons.

Construct a sequence vs. sequence grid: assign residue contacts at each grid point, (i,j) based on

dij:

dij = 0 nm (white)

dij = 0.4-0.5 nm (gray)

dij = 0.5-0.6 nm (black).


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Definition of Close Contact

Definition of close contact: dij = 0.4-0.6 nm. excludes successive residues (i,i+1)

In particular: -helix helical rise, h = 0.15 nm;

-strand helical rise, h = 0.34 nm; Trans-conformation helical rise = 0.36 nm (max helical

rise).

includes residues that bond to form helices andsheets.

Residue self-contact, so that dii = 0 nm produces a set of white points along the main

diagonal, i = j. Note that contacts will be mirror symmetric about

i=j.


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Contact Signature of anAntiparallel -sheet

An anti-parallel -sheet: has a local hairpin structure. places residues i and j in close

contact,

for i,j symmetric about the centralresidue of the hairpin.

An anti-parallel -sheet willtherefore generate: 2 linear sets of points;

perpendicular to the main diagonal; centered about the residue which

makes the hairpin turn.

Shown at right, for a 12 residuesheet:

centered at residue i=7, the centralresidue of the hairpin.


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Contact Signature of aParallel -sheet

Consider a parallel -sheet: of length L residue pairs, with

a spacing chain of length N, for convenience, let K = L+N;

total chain length = K + L =2L+N

residues i will be in closecontact with residue j =(L+N)+ i = K+ i.

A parallel -sheet willtherefore generate: 2 linear sets of points

each parallel to the main

diagonal; And offset K residues to either


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Contact Plots: Example

Example: Protein with a pair ofadjacent -helices, each helix produces a

characteristic signature.

details of 2o structure. helix-to-helix contact also

indicated: by points at the corners of the

box formed by the 2 helices.

thus, reveals details of 3ostructure.

Particularly useful when: applied to data from of a

technique that measuresdistance, directly:


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Protein Quaternary Structure

Protein Quaternary Structure (4o) describes:

formation of a multimeric complex from 2 or morepolypeptides (= units);

by non-covalent association.

4o

structure defined by thetype and numberof each unit. For instance, there are 2 broad types of dimers:

homodimer - complex formed by 2 identical units.

heterodimer - complex formed by 2 different units.

3o

and 4o

structures generally play differentroles: 3

ostructure provides basic functionality;

4o structure provides organized contact;

The Significance of 4


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The Significance of 4Structure

Example: Myoglobin (Mb) vs. Hemoglobin (Hb). Very similar:

each binds Oxygen

1o, 2

o, and 3

ostructures nearly identical.

However, each has a different, specific function: Mb: O2 storage in muscle cells.

Hb: transports O2 from the lungs.

Difference: 4o

structure. Mb is a monomer; Hb is a tetramer:

2 units; 2 units. Hb does not function as 4 Mb units:

each unit has lower O2 affinity.

O2 binding of units cooperative.

Cooperativity arises from the contact; contact allows communication.


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Symmetry in Hb 4o

Structure

Complexes of identical subunits typicallysymmetric. description of 4

ostructure includes subunit symmetry.

Symmetry of Hb: 1 true C2 symmetry axis

(perpendicular to plane of slide).

2 pseudo-C2 axes (x and y)

relate , dimers, by 180o

rotation.

O2

binding breaks the symmetry: Fe pulled out of the porphyrin plane.

tugging on the distal histidine. Large conformational change in Mb. In Hb, this change resisted by the

other subunits. Hbs tendency to maintain symmetry:

Hi h S i i P i


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Higher Symmetries in Protein

4o

Structure

Higher symmetries in 4o structure alsopossible when proteins exist in large clusters. there are many examples:

Hemocyanin: D5.

Virus Coat Proteins: Icosahedral.

Example: Aspartate Transcarbomylase(ATCase) Catalyzes 1st step in pyrimidine synthesis;

structure (X-ray crystallography) symmetric arrangement (12 subunits):

6 C subunits (catalytic). 6 R subunits (regulatory).

D3 symmetry:

One C3 axis (perp. to the plane). also 3 C axes in the lane .


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Why Symmetric Clusters?

Reasonable Question: why do proteins tend to aggregate in symmetric

clusters?

Thermodynamic reason: aggregation is entropically unfavorable (So < 0).

Thus, a very negative interaction Enthalpy, Ho

required. symmetric aggregation maximizes the interaction

number:

thereby maximizing -H

o

.Example: Homodimer Association each monomer: up to 2 interactions. Symmetric conformation:

2 subunit-subunit interactions.

Nonsymmetric conformation:


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Conclusion

In this Lecture, we have discussed: The intermediate level structure of Proteins:

Super-2o

and Domainal structure of Proteins.

Methods of Visualization of the overall 3-D structures

of Proteins. Protein 3

ostructure:

contact plots.

Protein 4o

structure.

In Lecture 5, we will turn to polynucleotidestructure.

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Lecture 5' - Introduction to Protein Struct II Spr08