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THE STRUCTURES WERE CALCULATED WITH X-PLOR, V. 3.851 (BRUNGER, 1992) USING A DISTANCE GEOMETRY/SIMULATED ANNEALING PROTOCOL (NILGES ET AL., FEBS LETT. 229, 317 (1988)). THE 3D STRUCTURE OF MYRISTOYLATED HIV-1 NEF ANCHOR
DOMAIN (MYR-2-57) SOLVED BY TWO-DIMENSIONAL HOMONUCLEAR NMR SPECTROSCOPY IS BASED ON 540 EXPERIMENTAL RESTRAINTS:
332 INTRARESIDUAL, 156 SEQUENTIAL AND MEDIUM RANGE (1<=|I-J|<=4), AND 10 LONG RANGE (|I-J|>=5) INTERPROTON
DISTANCE RESTRAINTS; 42 TORSION ANGLE RESTRAINTS (PHI). NO RESTRAINTS FOR HYDROGEN BONDS WERE ADDED.
X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
TWO STRUCTURES WITH LOW TOTAL ENERGY WERE SELECTED SHOWING THE CONFORMATIONAL VARIETY OF THE FLEXIBLE DOMAIN
Conformers Calculated Total Number
400
Conformers Submitted Total Number
2
Representative Model
1 (n/a)
Additional NMR Experimental Information
Details
THE COORDINATES OF 2 SIMULATED ANNEALING STRUCTURES ARE PRESENTED IN THIS ENTRY. THE STRUCTURE OF THE
MYRISTOYLATED HIV-1 NEF ANCHOR DOMAIN IS HIGHLY FLEXIBLE AND NOT WELL DEFINED BY NMR RESTRAINTS. ONLY TWO
SECONDARY STRUCTURE ELEMENTS CAN BE OBSERVED: A FIRST HELIX IN THE POSITIVE CLUSTER REGION FROM PRO14 TO ARG22
AND A SECOND HELICAL REGION FROM ALA33 TO GLY41. ADDITIONALLY, THE N-TERMINAL MYRISTIC ACID RESIDUE
CLOSELY INTERACTS WITH THE SIDE CHAIN OF TRP5 AND THEREBY FORMS A LOOP WITH GLY2, GLY3 AND LYS4 IN THE
KINK REGION. TWO MODELS ARE PRESENTED TO DEMONSTRATE THE CONFORMATIONAL VARIETY OF THE STRUCTURES CALCULATED.