Structure-based engineering of internal cavities in coiled-coil peptides.
Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins.
Yadav
Maneesh K
MK
Department of Chemistry, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
Redman
James E
JE
Leman
Luke J
LJ
Alvarez-Gutiérrez
Julietta M
JM
Zhang
Yanming
Y
Stout
C David
CD
Ghadiri
M Reza
MR
D000595:Amino Acid Sequence; D001665:Binding Sites; D002942:Circular Dichroism; D003460:Crystallization; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D007462:Iodobenzenes / Q000737:chemistry; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry*; D015202:Protein Engineering / Q000379:methods; D011494:Protein Kinases / Q000737:chemistry; D017433:Protein Structure, Secondary; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D012996:Solutions; D013329:Structure-Activity Relationship
D004268:DNA-Binding Proteins; D007462:Iodobenzenes; D010455:Peptides; D029701:Saccharomyces cerevisiae Proteins; D012996:Solutions; C031905:iodobenzene; D011494:Protein Kinases