Observation of the cascaded atomic-to-global length scales driving protein motion

Abstract

Model studies of the ligand photodissociation process of carboxymyoglobin have been conducted by using amplified few-cycle laser pulses short enough in duration (<10 fs) to capture the phase of the induced nuclear motions. The reaction-driven modes are observed directly in real time and depict the pathway by which energy liberated in the localized reaction site is efficiently channeled to functionally relevant mesoscale motions of the protein. Principles of chemistry and biology merge at the active or receptor sites of proteins. The initial reaction forces that are harnessed in biological processes are subjected to atomic-length scale fluctuations that ultimately must manifest their effect over the mesoscale dimensions of the biological complex. In one extreme, the system is subject to quantum effects, and in the other limit there are enough degrees of freedom that a continuum or classical description is appropriate. Nature seamlessly bridges the quantum and classical limits of force transduction. Exactly how biological systems transcend the quantum to continuum limits of mechanics is an open issue. Given the enormous number of superfluous degrees of freedom in biological molecules, there must exist efficient pathways by which conformational potential energy is transmitted from a localized chemical reaction site to the relevant functional degrees of freedom. The process by which this energy channeling occurs is one of the central mysteries in understanding biomechanics. Here we observe the photodissociation process of carboxymyoglobin (MbCO) using visible, few-cycle-duration light pulses to probe very fast nuclear motions in this system. The phase and amplitude of the reaction-driven modes give direct insight into the pathway by which initially localized reaction forces become spatially distributed and ultimately couple to the protein's functionally relevant motions.Myoglobin serves as a model system for the tertiary protein motions that form the basis for the molecular cooperativity exhibited by hemoglobin in the transport of oxygen. In the oxymyoglobin tertiary structure, the iron porphyrin plane defining the oxygen-binding site is planar. The deoxymyoglobin (deoxyMb) tertiary structure (pentavalent iron) is distinctly different. The iron is displaced 0.3 Å to the proximal side from the plane, the heme porphyrin puckers slightly, and there are long-range correlated motions of the surrounding globin (1-3). The most pronounced motion involves the E-F helix, in closest contact with the iron through the proximal histidine, and defines the primary allosteric motions controlling molecular cooperativity. The force for this motion is thought to be derived from the iron out-of-plane displacement and heme puckering: the socalled heme-doming coordinate. This before-and-after picture defines a transition-state process in which the initially localized reaction forces of the FeOligand (O 2 ) bond seem to act normal to the heme plane and ultimately displace the E-F helix and associated helices. How do these initially localiz...

Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins

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Investigations of Low-Frequency Vibrational Dynamics and Ligand Binding Kinetics of Cystathionine β-Synthase

“…Under such conditions, a coherent mode, coupled to a heme with a homogeneous Soret band absorbing near 428 nm, would exhibit an intensity dip near 428 nm and a phase difference of ~π for blue- and red-side excitation. The rapid exchange of energy between the heme and the protein could also potentially lead to a coherent protein response in this very low frequency region47–49. This possibility is of particular interest since calculations 50;51 have found a peak in the protein density-of-states near 20 cm −1 .…”

Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy — Observation of a candidate promoting vibration

“…The FPPS technique (alternatively called ‘impulsive coherent vibrational spectroscopy’) has successfully been applied for observing vibrational modes in other metalloproteins such as blue copper proteins [35–39] and heme proteins [40–42], and it was previously used by some of the authors to characterize the isolated N 2 ase cofactor, ‘FeMo-co’ [43] (the cluster that can be extracted into NMF solvent upon denaturing the MoFe protein). Here, we compare the FPPS results with the data from NRVS and Resonance Raman (RR) spectroscopies.…”