Relationship between conformation and geometry as evidenced by molecular dynamics simulation of C^a,a dialkylated glycines
Cirilli M, Coiro VM, Di Nola A, Mazza F
BIOPOLYMERS
46 (4): 239-244 OCT 5 1998

FULL TEXT

Abstract:

The relationship between the local backbone conformation and bond angles at C-alpha of symmetrically substituted C-alpha,C-alpha-dialkylated glycines (C-alpha,C-alpha-dimethylglycine or alpha-aminoisobutyric acid Aib; C-alpha,C-alpha-diethylglycine, Deg; C-alpha,C-alpha-di-n-propylglycine, Dpg) has been investigated by molecular dynamics (MD) simulation adopting pat bottom harmonic potentials, instead of the usual harmonic restraints, for the C-alpha bond angles. The MD simulations show that the C-alpha bond angles are related to the local backbone conformation, irrespectively of the side-chain length of Aib, Deg, and Dpg residues. Moreover, the N-C-alpha-C' (tau) angle is the most sensitive conformational parameter and, in the folded form, is always larger and more flexible than in the extended one.

Author Keywords:

C-alpha,C-alpha-dialkylated glycines, molecular dynamics, geometry and conformation

KeyWords Plus:

ALPHA-AMINO-ACIDS, BACKBONE BOND DISTANCES, X-RAY-DIFFRACTION, FIRST PRINCIPLES, STRUCTURAL VERSATILITY, DIALKYLATED GLYCINES, AMINOISOBUTYRIC-ACID, EXTENDED STRUCTURES, ENERGY COMPUTATION, CRYSTAL-STRUCTURES

Addresses:

Mazza F, CNR, Ist Strutturist Chim, CP 10, I-00016 Monterotondo Stn, Rome, Italy
CNR, Ist Strutturist Chim, I-00016 Monterotondo Stn, Rome, Italy
Univ La Sapienza, Dipartimento Chim, I-00185 Rome, Italy
Univ Aquila, Dipartimento Chim Ingn Chim & Mat, I-67010 Laquila, Italy