Protein Structure (Pauling)

8/14/2019 Protein Structure (Pauling)

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Protein Structure(in a nutshell)

Guy Ziv

December 26th, 2006

Myoglobin (1958)


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Proteins

From the Greek proteios meaningof first importance

The basic building blocks of almost all life Constitutes the majority of the cell, and perform nearly all

enzymatic activities

Composed of 20 naturally occurring amino-acids

varying moiety

called side chain


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Protein Synthesis In-vivo

1. Transcription:

DNA messenger RNA (mRNA)

2. Translation:

mRNA Linear chain of a.a.(Ribosome)

3. Folding:Linear chain Structure

Peptide bond

Protein chains have direction N-terminal C-terminal


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X-Rays crystallography

the tool of structural biology

Why X-ray?

Wavelength of visible light: ~500 nmBond lengths in proteins: ~0.15 nmTypical X-ray wavelength: ~0.15 nm

X-ray are (weakly) scattered by electrons

Diffraction from a single molecule is weakso use a crystal: Multiple copies of the molecule increases diffraction Crystalline structure imposes constraints on diffraction

pattern


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Diffraction occurs at particular angles

Diffraction spotsare the result ofconstructiveinterferencefrom multiplescatterers

satisfyingBraggs Law: = 2 d sin


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Bragg planes intersect the unit cell in

particular indices

0,0

h=1, k=1

h

k

h=4, k=-2


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Each Spot Represents a Unique Set of

Bragg Planes

h=2, k=1, l=3

h=10, k=3, l=8

1 2 3

detector

= 2 d sin

Points in k-space(Fourier Space)


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Modern X-Ray Crystallography

Need good crystals for better resolution,which is difficult in proteins (need right conditions)and sometimes nearly impossible

(e.g. membranal proteins)

High resolution details are faint requiresgood experimental apparatus

Recorded intensity give only the magnitudebut not the phase of the complex form factor

Error in density map lead to un-realisticatom assignment, requiring iterative refinementprocess

Early 1950s
http://en.wikipedia.org/wiki/Image:X_ray_diffraction.pnghttp://en.wikipedia.org/wiki/Image:X_ray_diffraction.png


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Historical perspective to

Pauling and Corey paper series

X-ray crystallography, invented in the beginning

of the 20th century, has been used to solvestructures of some amino-acids, syntheticpolymers (poly-glu) and small organic molecules

Some fibrous materials such as wool and

-keratin are sufficiently crystalline to givediffraction patterns

Evidence suggested that these proteinsstructure involve mainly translation and rotation


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Pauling and Corey

Robert Corey (1897-1971)

Linus Pauling (1901-1994)


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Pauling and Corey papers series

PNAS April 1951

1. Pauling, L., Corey, R.B. and Branson H. R. The Structure of Proteins:Two Hydrogen-Bonded Helical Configurations of the PolypeptideChain. PNAS, 37, 205-211, (1951).

2. Pauling, L. & Corey, R. B. Atomic Coordinates and Structure Factors forTwo Helical Configurations of Polypeptide Chains. PNAS, 37, 235-240,(1951).

3. Pauling, L. & Corey, R. B. The Structure of Synthetic Polypeptides.PNAS, 37, 241-250, (1951).

4. Pauling, L. & Corey, R. B. The Pleated Sheet, A New LayerConfiguration of Polypeptide Chains. PNAS, 37, 251-256, (1951).

5. Pauling, L. & Corey, R. B. The Structure of Feather Rachis Keratin.PNAS, 37, 256-261, (1951).6. Pauling, L. & Corey, R. B. The Structure of Hair, Muscle, and Related

Proteins. PNAS, 37, 261-271, (1951).7. Pauling, L. & Corey, R. B. The Structure of Fibrous Proteins of the

Collagen-Gelatin Group. PNAS, 37, 272-281, (1951).8. Pauling, L. & Corey, R. B. The Polypeptide-Chain Configuration in

Hemoglobin and Other Globular Proteins. PNAS, 37, 282-285, (1951).


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Pauling and Corey papers series

PNAS April 1951

1. Pauling, L., Corey, R.B. and Branson H. R. The Structure of Proteins:Two Hydrogen-Bonded Helical Configurations of the PolypeptideChain. PNAS, 37, 205-211, (1951).

2. Pauling, L. & Corey, R. B. Atomic Coordinates and Structure Factors forTwo Helical Configurations of Polypeptide Chains. PNAS, 37, 235-240,(1951).

3. Pauling, L. & Corey, R. B. The Structure of Synthetic Polypeptides.PNAS, 37, 241-250, (1951).

4. Pauling, L. & Corey, R. B. The Pleated Sheet, A New LayerConfiguration of Polypeptide Chains. PNAS, 37, 251-256, (1951).

5. Pauling, L. & Corey, R. B. The Structure of Feather Rachis Keratin.PNAS, 37, 256-261, (1951).6. Pauling, L. & Corey, R. B. The Structure of Hair, Muscle, and Related

Proteins. PNAS, 37, 261-271, (1951).7. Pauling, L. & Corey, R. B. The Structure of Fibrous Proteins of the

Collagen-Gelatin Group. PNAS, 37, 272-281, (1951).8. Pauling, L. & Corey, R. B. The Polypeptide-Chain Configuration in

Hemoglobin and Other Globular Proteins. PNAS, 37, 282-285, (1951).


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Linus Carl Pauling

The Nobel Prize in Chemistry 1954

"for his research into the natureof the chemical bond and itsapplication to the elucidation

of the structure of complexsubstances"


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Determinants of helical structure

Distances and anglesBetween atoms

Resonant partial double bond character ofpeptide bond induces planar arrangement of

atoms

All hydrogen bonds should be satisfied,i.e. distance N-O of about 2.7 and anglebetween C = O and H N less then ~30

superposition


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Building a model

similar to building with LEGO blocks

Start assembling monomers(amino-acids) with fixedtranslation and rotation

Look for configurations whichhave no steric hindrance (i.e.

clashes) Calculate N-HO=C distances

andangles (3-d trigonometry..)


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2 models satisfies all constraints


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The -helix one of the two common

structural elements in proteins

Completes one turn every 3.7residues

Rises ~5.4 with each turn Has hydrogen bonds between

the C=O of residue i and the

N-H of residue i+4 Is right-handed

i

i+4

C

N

O


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Alpha-helices appear a lot in trans-

membranal proteins

E.g. Lactose permease (LacY)

1pv6.pdbmembrane


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Why did Pauling and Corey succeed

where others failed?

Understanding the importance of hydrogenbonds

Taking into account the planar peptide bond Better knowledge of covalent bond lengths

and angles

MOST IMPORTANTLY they were NOTcrystallographers, and did not consider onlymodels with integer number of residues perturn!


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Proof came 7 years later

Kendrew, J. C., Bodo, G., Dintzis, H. M. Parrish, R. G., Wyckoff, H.,

and Phillips, D. C. A Three-Dimensional Model of the Myoglobin Molecule

Obtained by X-ray Analysis. Nature, 181, 662 (1958).

John Cowdery KendrewThe Nobel Prize in Chemistry 1962


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Hierarchy of Protein Structure

Linear chain made of 20 possibleamino acids Alpha-helices, beta-sheets, turns

Motifs, domains

Oligomers, complexes


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The Protein Data Bank (www.pdb.org)


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The PDB contains over 40,000

structures (as of December 2006)

NMR - Nuclear magnetic resonanceAllows structure determination based ondistance and angular constraints in solution


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Proteins Structure is Dynamic

Fluctuations exists in all proteins

Conformational changes FunctionAdenylate kinaseAn enzyme that catalyzesthe production of ATP from ADP
http://en.wikipedia.org/wiki/Enzymehttp://en.wikipedia.org/wiki/Enzyme


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Protein Folding still an open

question

1954 Christian B. Anfinsen proved that theprotein structure is determined by its

sequenceProtein Denatured (unfolded) Protein

1969 Levinthal paradox For a 100 a.a.sequence there are 9100 possibleconfigurations. If sampled randomly everynanosecond, it will take longer then the ageof the universe to fold a single protein

+ Urea DilutionRNaseenzyme


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Protein folding research continues

Late 1980s - Wolynes et al. present the

Energy Landscape or Folding Funnel modelfor protein folding

2006 There is still no precise understandinghow proteins fold fast (up to sec!), reliably and

accurately to their native structure

Energy

Entropy

Native(folded) state
http://www.dillgroup.ucsf.edu/energy.htmhttp://www.dillgroup.ucsf.edu/energy.htmhttp://www.dillgroup.ucsf.edu/energy.htm

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Protein Structure (Pauling)