Understanding the mechanism of β‐sheet folding from a chemical and biological perspective

Abstract

Perturbing the structure of the Pin1 WW domain, a 34-residue protein comprised of three beta-strands and two intervening loops has provided significant insight into the structural and energetic basis of beta-sheet folding. We will review our current perspective on how structure acquisition is influenced by the sequence, which determines local conformational propensities and mediates the hydrophobic effect, hydrogen bonding, and analogous intramolecular interactions. We have utilized both traditional site-directed mutagenesis and backbone mutagenesis approaches to alter the primary structure of this beta-sheet protein. Traditional site-directed mutagenesis experiments are excellent for altering side-chain structure, whereas amide-to-ester backbone mutagenesis experiments modify backbone-backbone hydrogen bonding capacity. The transition state structure associated with the folding of the Pin1 WW domain features a partially H-bonded, near-native reverse turn secondary structure in loop 1 that has little influence on thermodynamic stability. The thermodynamic stability of the Pin1 WW domain is largely determined by the formation of a small hydrophobic core and by the formation of desolvated backbone-backbone H-bonds enveloped by this hydrophobic core. Loop 1 engineering to the consensus five-residue beta-bulge-turn found in most WW domains or a four-residue beta-turn found in most beta-hairpins accelerates folding substantially relative to the six-residue turn found in the wild type Pin1 WW domain. Furthermore, the more efficient five- and four-residue reverse turns now contribute to the stability of the three-stranded beta-sheet. These insights have allowed the design of Pin1 WW domains that fold at rates that approach the theoretical speed limit of folding.

WW domain-binding protein 2: an adaptor protein closely linked to the development of breast cancer

“…Through the screening of synthesized WW domain libraries, WW domain has been identified as being involved in modulating the size of developing organs [14] in the Hippo signaling pathway Salvador–Warts–Hippo (or simply Hippo) by the identification of protein folding events [15–17]. Thus, this proline-rich peptide determines the biological and structural function and size of organs or in protein folding studies [18–20].…”

Chemical and Biological Approaches for Adapting Proteostasis to Ameliorate Protein Misfolding and Aggregation Diseases-Progress and Prognosis

“…On folding, multiple polypeptide chain reversals allow proteins to adopt compact structures stabilized by thousands of weak intramolecular electrostatic and hydrophobic interactions (Jager et al 2001(Jager et al , 2008Deechongkit et al 2004). These interactions stabilize the folded ensemble-the conformationally related family of structures that comprise the functional or native state of nearly all proteins.…”

Preventing fibril formation of a protein by selective mutation

“…1N), has been shown to fold with biphasic kinetics exhibiting intermediates during folding (3,5,6,(11)(12)(13)(14)(15)(16). We address this problem here with the design of new FBP28 WW domain mutants and by examining their structural properties and folding kinetics.Because of the small size, fast folding kinetics, and biological importance, the formation of intermolecular β-sheets is thought to be a crucial event in the initiation and propagation of amyloid diseases, such as Alzheimer's disease, and spongiform encephalopathy, FBP28, and other WW domain proteins (e.g., Pin1 and FiP35) have been the subjects of extensive experimental (4,11,(17)(18)(19)(20)(21)(22)(23) and theoretical (3,5,6,(12)(13)(14)(15)(16)(24)(25)(26)(27) studies. However, a folding mechanism of the FBP28 was debatable for a long time because of its complexity.…”