Rigidity of protein structure revealed by incoherent neutron scattering

• Published in: Biochimica et biophysica acta. General subjects Vol. 1864; no. 4; p. 129536
• Main Authors: Nakagawa, Hiroshi, Kataoka, Mikio
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.04.2020
• Subjects: Boson peak; Dynamical heterogeneity; Dynamical transition; environmental factors; Force constant; hardness; hydrogen bonding; Incoherent neutron scattering; molecular dynamics; neutron diffraction; Protein dynamics; protein structure; protein-protein interactions; temperature; Force constant; Boson peak; Dynamical transition; Protein dynamics; Incoherent neutron scattering; Dynamical heterogeneity
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2020.129536

The rigidity and flexibility of a protein is reflected in its structural dynamics. Studies on protein dynamics often focus on flexibility and softness; this review focuses on protein structural rigidity. The extent of rigidity can be assessed experimentally with incoherent neutron scattering; a method that is complementary to molecular dynamics simulation. This experimental technique can provide information about protein dynamics in timescales of pico- to nanoseconds and at spatial scales of nanometers; these dynamics can help quantify the rigidity of a protein by indices such as force constant, Boson peak, dynamical transition, and dynamical heterogeneity. These indicators also reflect the rigidity of a protein's secondary and tertiary structures. In addition, the indices reveal how rigidity is influenced by different environmental parameters, such as hydration, temperature, pressure, and protein-protein interactions. Hydration affects both rigidity and softness more than other environmental factors. Interestingly, hydration affects harmonic and anharmonic motions in opposite ways. This difference is probably due to the protein's dynamic coupling with water molecules via hydrogen bonding. •Protein has two different dynamical features, rigidity and flexibility.•Protein rigidity is required for its specific function.•Protein rigidity is evaluated with incoherent neutron scattering.•Boson peak and protein dynamical transition are good indicators of protein rigidity.•Structural state and hydration control protein rigidity.