Protein structure and folding Some facts and fundamental conepts Cherri Hsu 02-2789-8658 Institute of Chemistry B307 [email protected].

Protein structure and folding

Some facts and fundamental conepts

Cherri Hsu

02-2789-8658

Institute of Chemistry B307

[email protected]

Goals and plans Understand basic facts of protein structures. Understand general concepts that determines

structure and dynamics. Physics Evolution

Go through Chapters 8 and 9 of V&V book. A few more stories I’ve learned. My own review in protein folding prediction and

simulation.

Structural basis:

Hierarchy of protein structures Primary: sequence Secondary: local structures Tertiary: 3-dimension structure of a peptide chain. Quaternary: assembly of protein subunits (multiple

chains) Local structural characteristics:

- angles; Ramachandran plots. -Helixes -Sheets Loops

Methods for determing protein structures

X-ray diffraction

NMR

Determining molecular structures

Method Uses Limits

Infrared Absorption

Assigning local bonding types and structures

Small organic molecules.

NMRAssigning local bonding types and structures; Measuring distances

Small molecules

Small proteins (< 40 kDa?)

X-ray diffraction

Atomic resolution of molecular structures

Virtually no limit over the sizes of the molecules. Single crystals needed.

Electron microscopy & 2-D diffraction

Good for large proteins. No crystals needed.

Large, low resolution structures.

IR (Absorption) Spectra

3000 2000 1000Wavenumber (cm-1)

0.0

0.5

1.0

Transmittance

1030.49

1385.89

1412.02

1449.48

2831.01

2944.26

3327.53

3646.35

3000 2000 1000Wavenumber (cm-1)

0.0

0.5

1.0

Transmittance

428.61

804.7

879.57

1044.11

1085.9

1320.08

1381.02

1448.06

1924.26

2883.64

2974.18

3310.22

3315.44

3342.43

3356.36

3634.95

3000 2000 1000Wavenumber (cm-1)

0.0

0.5

1.0

Transmittance

937.8 1

103.03

1116.14

1166.85

1177.34

1191.33

1453.6

1462.34

2047.21

2118.9

2818.3

2831.41

2887.36

2922.33

2980.03

2995.77

Methanol: CH3OH

Ethanol:C2H5OHC2H6O

Methyl ether:CH3OCH3

C2H6O

Nuclear Magnetic Resonance

NMR is an important tool in chemistry

QuickTime™ and aTIFF (LZW) decompressor

are needed to see this picture.

2D NMR?

A table that lists different 2D NMR techniques.

Can be used to determine distance between atoms.

Will be further introduced in next semester.

X-ray diffraction

X-ray diffraction:Physics2000: wave Physics2000: two slits

http://www.ysbl.york.ac.uk/~cowtan/fourier/fourier.html

Basic building blocks of protein structures

Are proteins sticky tapes?

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Figure 8-1 The trans-peptide group.

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Figure 8-2 The cis-peptide group.

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“trans” is more stable “cis” conformation is

rarely seen. For the peptide

bonds follow proline residue, ~10% are “cis”.

Fibrous proteins

Keratin

A mechanically durable, chemically unreactive protein.

-keratin occur in mammals (hair) -keratin occur in birds (feather) and

reptiles.

-Keratin From x-ray, structure expected: -helix But, the pitch is 5.1Å, rather than normal 5.4 Å. Coiled coil is expected. Rich in Cys residues, form disulfide bonds and cross-

link adjacent peptide chains. “hard” or “soft” : high or low in sulfur content. Hard: hair, horn, nail Soft: skin

When disulfide bonds cleaved, an -keratin can be streched to become a -pleated sheet.

-Keratin From x-ray, structure expected: -helix But, pitch is 5.1Å, rather than normal 5.4 Å. Coiled coil is expected. Rich in Cys residues, form disulfide bonds and

cross-link adjacent peptide chains. “hard” or “soft” : high or low in sulfur content. Hard: hair, horn, nail Soft: skin

When disulfide bonds cleaved, an -keratin can be streched to become a -pleated sheet.

Collagen

Occurs virtually in every tissue. Connective tissues. Mammals have at least 33 genetically

distinct polypeptide chains. 20 distinct collagen types in different tissues.

Hyp: A special residue found in collagens

Collagen Nearly 1/3 of its residues are Gly. 15-30% are Hyp residues. Hyp are converted to Hyp after collagen

polypeptides are synthesized. The conversion is through prolyl hudroxylase,

and it requires Ascorbic acid (vit. C). Hyp offers extra H-bondings. (possibly to

peptides and to water)

Globular proteins

Enzymes

Transport and receptor proteins

Soluable proteins

Membrane proteins

Physical forces determining protein structures

H-bonding

Electro-static interactions

Hydrophobic forces

H-bonds

D-H … A Assignment: if D…A < 3.7 Å in crystal

structure. (normally 2.7-3.1 Å). Energy of stablization: -12~-40 kJ/mol) Tends to be linear. Only weakly stabilize proteins. (!?)

A survey over H-bonds in globular proteins (J. Mol. Biol. (1992) 226, 1143)

Most H-bonds are local.

Most H-bonds are between beckbone atoms.