Protein structure and folding Some facts and fundamental conepts Cherri Hsu Institute of Chemistry B307

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 MethodUsesLimits Infrared Absorption Assigning local bonding types and structures Small organic molecules. NMR Assigning 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 Methanol: CH 3 OH Ethanol: C 2 H 5 OH C 2 H 6 O Methyl ether: CH 3 OCH 3 C 2 H 6 O

Nuclear Magnetic Resonance

NMR is an important tool in chemistry

2D NMR? A table that lists different 2D NMR techniques. 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: wavePhysics2000: wave Physics2000: two slitsPhysics2000: two slits

Basic building blocks of protein structures

Are proteins sticky tapes?

Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 8-1The trans-peptide group. Page 220

Voet Biochemistry 3e © 2004 John Wiley & Sons, Inc. Figure 8-2The cis-peptide group. Page 220

“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 % 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 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.