title: Computational design of thermostabilizing D-amino acid substitutions.
abstract: Judicious incorporation of D-amino acids in engineered proteins confers many advantages such as preventing degradation by endogenous proteases and promoting novel structures and functions not accessible to homochiral polypeptides. Glycine to D-alanine substitutions at the carboxy termini can stabilize α-helices by reducing conformational entropy. Beyond alanine, we propose additional side chain effects on the degree of stabilization conferred by D-amino acid substitutions. A detailed, molecular understanding of backbone and side chain interactions is important for developing rational, broadly applicable strategies in using D-amino acids to increase protein thermostability. Insight from structural bioinformatics combined with computational protein design can successfully guide the selection of stabilizing D-amino acid mutations. Substituting a key glycine in the Trp-cage miniprotein with D-Gln dramatically stabilizes the fold without altering the protein backbone. Stabilities of individual substitutions can be understood in terms of the balance of intramolecular forces both at the α-helix C-terminus and throughout the protein.
authors: Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey (UMDNJ) and Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, USA.
authors: Agustina
authors: A
authors: Rodriguez-Granillo
authors: Srinivas
authors: S
authors: Annavarapu
authors: Lei
authors: L
authors: Zhang
authors: Ronald L
authors: RL
authors: Koder
authors: Vikas
authors: V
authors: Nanda
mesh_terms: D019943:Amino Acid Substitution; D000596:Amino Acids / Q000737:chemistry*; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D013696:Temperature; D013816:Thermodynamics
chemical_list: D000596:Amino Acids