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Crowded Channels and Active Sites. Active Sites of Proteins are Very Charged 7 charges ~ 20 M net charge. = 1.2×10 22 cm -3. liquid Water is 55 M solid NaCl is 37 M. +. +. +. +. +. -. -. -. -. Selectivity Filters and Gates of Ion Channels are Active Sites.

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slide2

Active Sites of Proteins are Very Charged

7 charges ~ 20M net charge

= 1.2×1022 cm-3

liquidWater is 55 Msolid NaCl is 37 M

+

+

+

+

+

-

-

-

-

Selectivity Filters and Gates of Ion Channels

are

Active Sites

Physical basis of function

OmpF Porin

Hard Spheres

Na+

Ions are Crowded

K+

Ca2+

Na+

Induced Fit of Side Chains

K+

4 Å

Figure adapted from Tilman Schirmer

crowded active sites in 573 enzymes

Crowded Active Sitesin 573 Enzymes

Jimenez-Morales,Liang, Eisenberg

slide4

Example:

UDP-N-ACETYLGLUCOSAMINE ENOLPYRUVYL TRANSFERASE (PDB:1UAE)

Functional Pocket Molecular Surface Volume: 1462.40 A3

Density : 19.3 Molar (11.3 M+. 8 M-)

EC2: TRANSFERASESAverage Ionizable Density: 19.8 Molar

Crowded

Green: Functional pocket residues

Blue: Basic = Probably Positive = R+K+H

Red: Acid = Probably Negative = E + Q

Brown URIDINE-DIPHOSPHATE-N-

ACETYLGLUCOSAMINE

Jimenez-Morales, Liang, Eisenberg