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Lecture #9

• Prediction of protein structure

• Chou-Fasman rules

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Prediction of protein structure

Why predict?

• 1. Spectroscopic methods estimate

% 2o structure in proteins, but cannot

locate precisely the helical, sheet,

turn, and random regions (unless X-

ray or NMR structure determinationis performed).

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Prediction of protein structure

2. Renaturation experiments have

shown that information for folding

into 2o and 3o structure is coded

in the amino acid sequence.

• Combined knowledge of

sequence/structure can provideinsight into how proteins function.

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How to predict

• Minimum energy calculations can

locate low energy regions for protein

backbone and side chain rotationalangles.

• These calculations predict

the

existence of favoured secondarystructures.

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How to predict

• The a-helix and b-sheet therefore involvelocal regions in which each residue

repeats stereochemically-desirableangles.

• These procedures have led to theRamachandran plots (f, y maps).

• But these calculations give informationonly about

“

short-range interactions”

.

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Ramachandran Plot

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How to predict

• Thus, protein tertiary structure

(overall folding) cannot be predicted

on this basis alone.

• At least two other factors must be

considered:

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How to predict

• Environment (e.g ., water ormembrane) must be taken into

account; most calculations are donein a vacuum: small energyincrements gained or lost at

hundreds of sites contribute tofolding.

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How to predict

• 2. Long-range protein/proteininteractions must be considered toobtain the overall protein structure.

• Especially pertinent to formation ofinter-molecularly H-bonded structuressuch as b-sheets (from sequentiallydistant segments of a protein).

• This is very complex: challenges themost sophisticated computers.

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Develop empirical rules

• Analyze known protein structures.

• Find patterns.

• Assume these patterns are typical of

universal protein features.

• Formulate rules from an existing

database.

• Apply the rules to future cases.

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Develop empirical rules

• Analyze known protein structures.

• Find patterns.

• Hypothesize that these patterns are

typical of universal protein features.

• Operationalize patterns into rules.

• Test the rules against future cases.

• Modify rules as needed.

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Chou-Fasman rules

• 30 protein structures solved by X-ray

crystallography were considered.

• Each residue in each protein wasassigned as occurring in an a-helix,

b-sheet, b-turn, or random

(unstructured) region of the protein.

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Chou-Fasman rules

• Conformation of a given residue wasdetermined by its f, y) angles.

• Consecutive sequences of 4 or more

helical residues are helix .• Consecutive sequences of 3 or more b-

sheet residues are“

beta-sheet”

.

• Residues not in either region are assigned

“

random”

independent of f, y) angles.

Residues in b-turns were assigned upon

inspection of protein structure.

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Parameter designations

• Pa, Pb, and Pt refer to values forindividual amino acids.

• (Pa), (Pb) and (Pt) refer to AVERAGEvalues over the length of a givensegment.

•

To obtain average values, add upindividual values and divide bynumber of residues.

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Chou-Fasman results

• In C.-F.

s sample:

• Average freq. (f a

) = 0.38 (ahelix)

(f b

) = 0.20 (b-sheet)

(f t) = 0.32 (b-turns)

•

Random regions = 0.10

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Chou-Fasman results

• Conformational parameters (P-values)were obtained from % occurrences ofeach residue in each structural form,

compared to the overall occurrence ofthat form.

• Thus, if all Ala residues in the 30proteins are considered, and 45% of

them are in helical regions, then:

Ala Pa

= 0.45/0.38 = 1.18

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Chou-Fasman results

•

P-values were developed similarly for thethree types of secondary structure:

• Pa

= propensity of a given residue to

be helical.

• Pb

= propensity of a given residue to

be b -sheet.

• Pt = propensity of a given residue to

be in a b-turn.

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Amino acid preferences for

a-helix, b -sheet, and b-turn

Pa

Pb

P

Chou & Fasman, 1978

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Chou-Fasman outcomes

• Top helix-forming residues:

Glu, Met, Ala, Leu, Lys

• Best helix-breaking residues:

Gly, Pro, Asn, Tyr, Cys

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• Top b-sheet-forming residues:

Val, Ile, Tyr, Phe, Trp

• Bestb

-sheet-breaking residues:

Glu, Asp, Pro, Gly, Lys

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• Top b-turn-occurring residues:

Asn, Gly, Pro, Asp, Ser, Cys, Tyr

• Leastb

-turn-occurring residues:

Ile, Val, Leu, Phe, Met

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b-turns:

Pro most common at i+1

Gly most common at i+2

Best b-turn:

-Asn-Pro-Gly-Gly-

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• Top helix-forming residues:

Glu, Met, Ala, Leu, Lys

• Top b-sheet-forming residues:

Val, Ile, Tyr, Phe, Trp

• Top b-turn-occurring residues:

Asn, Gly, Pro, Asp, Ser

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Chou-Fasman results

• Rules were formulated based on P-values

• Computer algorithms were applied to

assign each residue, and eachprotein segment

• Results: 81% of helices, 85% of b-

sheets, 78% of b-turns were localizedcorrectly

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Summary

• Analysis of protein structures has revealed

that certain amino acids tend to be found in

certain secondary structural elements• Chou-Fasman rules can be used to predict

secondary structure in a protein sequence

• We can not yet predict the final tertiary protein structure for its sequence

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Secondary Structure

Prediction

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