protein structure

Driving force for formation of alpha-helices in solution

Maximization of hydrogen bonding (between carbonyl oxygen and amide hydrogen four residues apart), minimization of steric clashes, and the hydrophobic effect contributing by burying nonpolar side chains.

Evolution's role in maintaining protein function and structure

Conserves sequences critical for structural integrity (e.g., alpha-helices, beta-sheets) and functional sites; deleterious mutations are removed while allowing functional divergence through conserved folds.

Amino acid sequence of calmodulin

Acidic residues (glutamate/aspartate) bind Ca²⁺; flexible linker allows conformational changes; its alpha-helical dumbbell structure exposes hydrophobic patches for target protein regulation upon Ca²⁺ binding.

Secondary structure motifs as building blocks

Stable, versatile units (e.g., alpha-helices, beta-sheets), which can be recombined by evolution (e.g., TIM barrel, Greek key) to create new functions while retaining structural efficiency.

Recognizing secondary structure motifs from structure

Alpha-helices are spirals with 4-residue hydrogen bonding; beta-sheets are pleated strands with inter-strand H-bonds; Greek key has antiparallel beta-sheet topology; TIM barrel features 8 beta-strands surrounded by 8 alpha-helices.

Recognizing secondary structure motifs from primary sequence

Alpha-helices are rich in alanine, leucine, glutamate; beta-sheets show alternating hydrophobic/hydrophilic residues; turns/loops are characterized by glycine/proline disrupting regular structures.