Physical interactions that determine the properties of...
Transcript of Physical interactions that determine the properties of...
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Physical interactions that determine the properties
of proteins
Petsko-Ringe 1.0 to 1-9Proteins. Creighton 4
The biological activities of proteins
Unique environments and orientations of the functional groups
Interactions with the environment:
WaterSaltsMembranesOther proteinsNucleic Acids
Noncovalent interactions
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Noncovalent interactions
• Short range• Ionic • Hydrogen bonds• van der Waals
Short range repulsions
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Electrostatic forces
• strength depends on the distance of the charges and what occupies the space between the charges
+ - + -non-polarsubstanceor vacuum
polar, e.g.water
strong attraction weak attraction
Dielectric Constants and Permanent Molecular Dipole Moments
of Some Common Solvents
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Voet
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chem
istry
3e©
2004
Joh
n W
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& So
ns, I
nc.
Figure 8-57 Dipole-dipole interactions.
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Hydrogen bonding
• requires one donor and one acceptor• bonds are directional (distance and angle
between donor and acceptor are important)
\C=O/
Preferred area for accepting H-bondsD-H |A
donor acceptor
Donor, hydrogen and acceptor atomare arranged along a straight line
Hydrogen atom is located near thelone pair electrons of the acceptor
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Hydrogen bonds (~1.9-2 Ǻ)• N-H O=• O-H -O-• S-H -N=• C-H -S-
• -S-• π electrons
Solubilities:
Relative hydrophilicities
of amino acids side chains
Biochemistry 198120, 849-55
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Interactions between molecules in water
• A + B ↔ AB Kassoc=[AB]/([A].[B])
• Interactions between individual molecules in solution are very weak
Kassoc~0.02 M-1
Debye-Hückel screening
• Deff = Dwater . exp(+κd)
• Dwater decrease at higher temperatures
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Voet
Bio
chem
istry
3e©
2004
Joh
n W
iley
& So
ns, I
nc.
Figure 8-58 The orientational preference of water molecules next to a nonpolar solute.
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•H2O forms an ordered clathrate cage around non-polar substances.
•This is energetically unfavorable because of the high negative ΔS.
Interaction of water with non-polar substances
The hydrophobic effect
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© 2004 New Science Press Ltd new-science-press.com
What drives protein folding?
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© 2004 New Science Press Ltd new-science-press.com
© 2004 New Science Press Ltd new-science-press.com
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© 2004 New Science Press Ltd new-science-press.com
pKa values of the ionizable groupsof proteins (Prot. Sci. 2006 15,1-5)
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© 2004 New Science Press Ltd new-science-press.com
© 2004 New Science Press Ltd new-science-press.com
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NSP In association withBioMed Central
Proteins: Inside and outside
Slice through a globular protein
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23 1: Hydrophobic core
2: Protein surface3: Water (solvent)