pH-Dependent Picosecond Structural Dynamics in the Distal Pocket of Nitrophorin 4 Investigated by 2D IR Spectroscopy

• Published in: The journal of physical chemistry. B 2013-12, Vol.117 (49), p.15804-15811
• Main Authors: Cheng, Mark, Brookes, Jennifer F, Montfort, William R, Khalil, Munira
• Format: Article
• Language: English
• Subjects: Crystallography, X-Ray; Dynamic structural analysis; Dynamics; Fluctuation; Hemeproteins - chemistry; Hemeproteins - genetics; Hemeproteins - metabolism; Hydrogen-Ion Concentration; Infrared spectroscopy; Molecular Dynamics Simulation; Nitric Oxide - chemistry; Nitric Oxide - metabolism; Nitrosyls; Protein Structure, Tertiary; Recombinant Proteins - biosynthesis; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Salivary Proteins and Peptides - chemistry; Salivary Proteins and Peptides - genetics; Salivary Proteins and Peptides - metabolism; Spectrophotometry, Infrared; Temperature; Time; Two dimensional
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp407052a

Nitrophorin 4 (NP4) belongs to a family of pH-sensitive, nitric oxide (NO) transporter proteins that undergo a large structural change from a closed to an open conformation at high pH to allow for NO delivery. Measuring the pH-dependent structural dynamics in NP4–NO around the ligand binding site is crucial for developing a mechanistic understanding of NO binding and release. In this study, we use coherent two-dimensional infrared (2D IR) spectroscopy to measure picosecond structural dynamics sampled by the nitrosyl stretch in NP4–NO as a function of pH at room temperature. Our results show that both the closed and open conformers of the protein are present at low (pD 5.1) and high (pD 7.9) pH conditions. The closed and open conformers are characterized by two frequencies of the nitrosyl stretching vibration labeled A0 and A1, respectively. Analysis of the 2D IR line shapes reveals that at pD 5.1, the closed conformer experiences structural fluctuations arising from solvation dynamics on a ∼3 ps time scale. At pD 7.9, both the open and closed conformers exhibit fluctuations on a ∼1 ps time scale. At both pD conditions, the closed conformers maintain a static distribution of structures within the experimental time window of 100 ps. This is in contrast to the open conformer, which is able to interconvert among its substates on a ∼100 ps time scale. Our results directly measure the time scales of solvation dynamics in the distal pocket, the flexibility of the open conformation at high pH, and the rigidity of the closed conformers at both pH conditions. We discuss how the pH-dependent equilibrium structural fluctuations of the nitrosyl ligand measured in this study are related to the uptake and delivery of nitric oxide in NP4.