Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering

Yang, Cheolhee; Choi, Minseo; Kim, Jong Goo; Kim, Hanui; Muniyappan, Srinivasan; Nozawa, Shiro; Adachi, Shin‐ichi; Henning, Robert; Kosheleva, Irina; Ihee, Hyotcherl

doi:10.3390/ijms19113633

Cited by 8 publications

(11 citation statements)

References 86 publications

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“…† We note that the intermediates of K30D have two substrates of the fully photolyzed and partially photolyzed forms, which are structurally indistinguishable from each other. The same was revealed from previous laser power dependency studies on WT and other mutants, [35][36][37][38] which provided direct evidence that the partially photolyzed dimer subunit undergoes the same structural evolution as the fully photolyzed subunit, directly demonstrating the allosteric regulation of HbI.…”

supporting

confidence: 74%

“…For the data analysis, we removed the thermal heating contribution using a well-established method. [35][36][37][38] During the experiment, the temperature was maintained at 25 C by a stream of cold nitrogen gas (Oxford Cryostream).…”

Section: Data Acquisitionmentioning

confidence: 99%

“…The data exhibit oscillatory features along the q-axis due to protein structural changes. To extract kinetic information of intermediates and their structures from DS(q, t), we followed the well-established procedure [35][36][37][38] which had been applied in previous TRXSS studies on WT and various mutants of HbI, consisting of kinetic analysis using singular value decomposition (SVD) and principal component analysis (PCA). As detailed in the ESI, † SVD and the global t of le singular vectors (lSVs) show that the kinetics involves four structurally distinct intermediates and ve time constants of 4.6 (AE0.7) ns, 47 (AE13) ns, 588 (AE81) ns, 616 (AE109) ms, and 5.34 (AE5.22) ms.…”

Section: Kinetic Analysis Of Time-resolved Difference Solution Scattering Curvesmentioning

confidence: 99%

“…To distinguish the intermediates of WT and K30D, we labeled I 1 , I 2 , and I 3 of WT as I WT 1 , I WT 2 , and I WT 3 , respectively, and likewise labeled the intermediates of K30D as I K30D transition, as in WT and other mutants, with time constants of 47 ns and 588 ns, which are smaller than those of WT (730 ns and 5.6 ms) by factors of 15.5 and 9.5, respectively, indicating acceleration with respect to WT. According to TRXSS studies on WT and mutants, [35][36][37][38] this I WT 2 -to-I WT 3 transition accounts for the quaternary structural change where both the rotation angle and the heme-heme distance signicantly changes. Thus, the accelerated rates mean that either (i) these structural changes occur more rapidly or (ii) different structural changes are involved in K30D.…”

Section: Kinetic Analysis Of Time-resolved Difference Solution Scattering Curvesmentioning

confidence: 99%

“…To extract key structural parameters of each intermediate structure, we performed structure renement applied with a rigid-body modeling approach using crystallographic structures as template structures, which is established in our previous study on WT. [35][36][37][38] In the case of K30D, since its crystallographic structures were not reported, we made the template structures for the structural analysis by modifying the crystallographic structures of WT (see the ESI † for details). From the structure renement, the rened candidate structures for the intermediates were obtained, and their theoretical scattering curves show excellent agreement with the experimental SADSs (Fig.…”

Section: Structural Analysis Of Intermediatesmentioning

confidence: 99%

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Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics

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supporting

confidence: 74%

Section: Data Acquisitionmentioning

confidence: 99%

Section: Kinetic Analysis Of Time-resolved Difference Solution Scattering Curvesmentioning

confidence: 99%

Section: Kinetic Analysis Of Time-resolved Difference Solution Scattering Curvesmentioning

confidence: 99%

Section: Structural Analysis Of Intermediatesmentioning

confidence: 99%

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Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics

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Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction

Lee

Kim

et al. 2021

Cell Reports Physical Science

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Spectrally Silent Protein Reaction Dynamics Revealed by Time-Resolved Thermodynamics and Diffusion Techniques

Terazima

2021

Acc. Chem. Res.

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Conspectus Biological functions essentially consist of a series of chemical reactions, including intermolecular interactions, and also involve the cooperation of a number of biological molecules performing these reactions. To understand this function at the molecular level, all steps of the reactions must be elucidated. However, since the biosystems including the surrounding environment are notably large, the reactions have to be elucidated from several different approaches. A variety of techniques have been developed to obtain structural information, and the knowledge of the three-dimensional structure of biomolecules has increased dramatically. Contrarily, the current information on reaction dynamics, which is essential for understanding reactions, is still not enough. Although frequently used techniques, such as spectroscopy, have revealed several important processes of reactions, there are various hidden dynamics that are not detected by these methods (silent dynamics). For example, although water molecules are essential for bioreactions, dynamics of the protein–water interaction are very difficult to trace and spectrally silent. Transient association/dissociations of proteins with partner proteins are difficult to observe. Another important property to understand the reaction of proteins is fluctuations, which are random movements that do not change the average structure and energy. The importance of fluctuations has been pointed out in order to explain enzymatic activity; however, it is extremely difficult to detect changes in fluctuation during a reaction. In this Account, unique time-resolved methods, time-resolved thermodynamics, and time-resolved diffusion methods, both of which are able to detect silent dynamics in solution at physiological temperature, are described. Thermodynamic properties are important for characterizing materials, in particular, macromolecules such as biomolecules. Therefore, the data available regarding these properties, for several stable proteins, is abundant. However, it is almost impossible to characterize short-lived intermediate species in irreversible reactions using traditional thermodynamic techniques. Similarly, although the translational diffusion coefficient is a useful property to determine the protein size and intermolecular interactions, there have been no reports revealing reaction dynamics. The transient grating (TG) method enables us to measure these quantities in a time-resolved manner for a variety of irreversible reactions. With this method, it is now possible to study biomolecule reactions from the viewpoint of thermodynamic properties and diffusion, and to elucidate reaction dynamics that cannot be detected by other spectroscopic methods. Here, the principles of the methodologies used, their characteristic advantages, and their applications to protein reactions are described. The TG measurements of octopus rhodopsin revealed a spectrally hidden intermediate and determined an energetic profile along the reaction coordinate. This emphasizes that the measureme...

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Protein Structural Dynamics of Wild-Type and Mutant Homodimeric Hemoglobin Studied by Time-Resolved X-Ray Solution Scattering

Cited by 8 publications

References 86 publications

Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics

Effect of the abolition of intersubunit salt bridges on allosteric protein structural dynamics

Reversible molecular motional switch based on circular photoactive protein oligomers exhibits unexpected photo-induced contraction

Spectrally Silent Protein Reaction Dynamics Revealed by Time-Resolved Thermodynamics and Diffusion Techniques

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