Table of Contents
PROTEIN MODELING & COMPUTATIONAL CHEMISTRY
STRUCTURES
COMPARING DIFFERENT STRUCTURES
Typically, ..../A>
Comparison of Experimental Interleukin-1? Structures*
Comparison of X-ray, NMR and Homology Modeled Structures of Pyrococcus furiosus rubredoxin*
HOMOLOGY MODELING
The 5 X-ray Structures of Rubredoxin
HOMOLOGY MODELING APPROACH
Then...
more homology modeling...
D. baculatus (Norway 4) Cytochrome c3 with homologies to D. vulgaris (Miyazaki) c3 marked in RED.
D. baculatus (Norway 4) Cytochrome c3 and D. vulgaris (Miyazaki) c3 ribbon structures.
Why so similar? D. baculatus (Norway 4) Cytochrome c3 and D. vulgaris (Miyazaki) c3 hemes.
What describes a Structure?
X, Y, Z positions of atoms
Size of atoms (extent) What defines it?*
Are atoms symmetric?*
Are all like atoms the same?
Electronic configuration
The concepts of Atom Identification
Protein Data Bank Position ID's
COMPUTATIONAL PROCEDURES
Molecular Mechanics (cont.)....
The MM description
CALCULATIONS FROM THE COORDINATES
CALCULATIONS FROM COORDINATES, CHARACTERISTICS & PREFERENCES
Molecular surfaces
A contact surface
Coulombic potential
Dot surface colored by potential
Field vector
C3 Heme field vectors
? FORCE FIELD POTENTIAL FUNCTIONS
FOR PROTEIN MODELING
Ë A Survey of Programs Available
AMBER and AMBER Related
YETI
CHARMm
ECEPP/2
Tripos 5.2
A Survey & Comparison of Functions
BONDED INTERACTIONS
Bond potential
Bond potentials
Bond angle
Angle calculation
MM2 stretch
Torsion angle
Cross product calculation
AMBER torsion
CHARMm torsion
Other Geometrical Constraints
NON-BONDING INTERACTIONS
MM2, non-bonded
Parameters for "Soft" and "Hard" vdW potentials are typically very different
Electrostatic interactions.
Note on CHARMm
Empirical solvent screening
MM2: dipole-dipole potential
Hydrogen Bonding.
AMBER & H-bond
CHARMm & H-bond
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