Quaternary Speeding in Hemoglobin

Spiro, Thomas G.; Balakrishnan, Gurusamy

doi:10.1016/j.jmb.2010.05.056

Cited by 5 publications

(5 citation statements)

References 12 publications

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“…26) provide strong support for the two-step quaternary transition predicted by the calculations (see Fig. 2); in the R to T direction, the early large quaternary change Q2 would correspond to the 2-μs step, whereas the smaller late quaternary change Q1 and some tertiary changes would correspond to the 20-μs step.…”

Section: Discussionsupporting

confidence: 57%

“…The overall C2 symmetry of the αβ-dimers is preserved, but the α-and β-subunits behave very differently. These results provide an unsuspected pathway of the allosteric transition of hemoglobin and serve to explain some recent experiments on the R to T transition after photodissociation (23)(24)(25)(26). Although the calculations were essentially completed and most of the manuscript was written by 2000, a crucial experiment (23) validating the results was published only in 2010.…”

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confidence: 66%

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Unsuspected pathway of the allosteric transition in hemoglobin

Fischer

Olsen

Nam

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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Large conformational transitions play an essential role in the function of many proteins, but experiments do not provide the atomic details of the path followed in going from one end structure to the other. For the hemoglobin tetramer, the transition path between the unliganded (T) and tetraoxygenated (R) structures is not known, which limits our understanding of the cooperative mechanism in this classic allosteric system, where both tertiary and quaternary changes are involved. The conjugate peak refinement algorithm is used to compute an unbiased minimum energy path at atomic detail between the two end states. Although the results confirm some of the proposals of Perutz [Perutz MF (1970) Stereochemistry of cooperative effects in haemoglobin. Nature 228:726-734], the subunit motions do not follow the textbook description of a simple rotation of one αβ-dimer relative to the other. Instead, the path consists of two sequential quaternary rotations, each involving different subdomains and axes. The quaternary transitions are preceded and followed by phases of tertiary structural changes. The results explain the recent photodissociation measurements, which suggest that the quaternary transition has a fast (2 μs) as well as a slow (20 μs) component and provide a testable model for single molecule FRET experiments.conformational change | cooperativity | domain motion | protein hinges M any proteins undergo large conformational transitions that are essential for their functions (1-3). The transitions can occur in monomers such as the myosin molecular motor (4-6), in multisubunit complexes such as the chaperone GroEL (7), and in systems such as the flagellar motor of bacteria, which is composed of several hundred proteins (8). Probably the most studied example is the T (tense) to R (relaxed) transition in the vertebrate hemoglobin tetramer (Hb) (9-11), for which the conformational transition increases the efficiency of oxygen transport. Hemoglobin, which is composed of two identical α-and two identical β-subunits, is the paradigm for the development of models of cooperativity and allosteric regulation in proteins (9-13). Phenomenologically, the positive cooperativity involves the increase in the affinity for oxygen of unliganded subunits upon the successive binding of oxygen to other subunits. This is achieved by structural changes within subunits (tertiary changes) and between subunits (quaternary changes). Based on the superposition of the crystallographic structures for the deoxy unliganded T state and the fully liganded R state of the protein, the quaternary T → R transition has been described as involving primarily an approximately 15°rotation of one "dimer" (α 1 β 1 ) relative to the other (α 2 β 2 ) around a virtual axis (Fig. 1A) (9, 14). Together with a small relative translation of the αβ-dimers, this reduces the central cavity between the dimers (a channel along the C2 axis of symmetry), where the heterotropic effector 2,3-bisphosphoglycerate is bound in the T state. An important aspect of these structural ch...

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Section: Discussionsupporting

confidence: 57%

mentioning

confidence: 66%

Unsuspected pathway of the allosteric transition in hemoglobin

Fischer

Olsen

Nam

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…These have been called the "hinge" and "switch" contacts (Figure 1), the hinge involving a reorientation, and the switch involving an altered interdigitation of the contacting side chains. 4 Wide angle X-ray scattering (WAXS) measurements 27 indicate that the main structural rearrangement occurs during the first quaternary phase, at ∼2 μs (see ref 28 for a synopsis of these experimental developments). The finding of two quaternary steps strikingly supports a new computational result from Karplus and co-workers, 29 who applied the conjugate peak refinement (CPR) method 30 to find the minimum-energy pathway of the T-R transformation.…”

Section: ■ Introductionmentioning

confidence: 99%

Heme Reactivity is Uncoupled from Quaternary Structure in Gel-Encapsulated Hemoglobin: A Resonance Raman Spectroscopic Study

2012

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Encapsulation of hemoglobin (Hb) in silica gel preserves structure and function, but greatly slows protein motion, thereby providing access to intermediates along the allosteric pathway that are inaccessible in solution. Resonance Raman (RR) spectroscopy with visible and ultraviolet laser excitation provides probes of heme reactivity and of key tertiary and quaternary contacts. These probes were monitored in gels after deoxygenation of oxyHb and after CO binding to deoxyHb, which intiate conformational change in the R-T and T-R directions, respectively. The spectra establish that quaternary structure change in the gel takes a week or more, but that the evolution of heme reactivity, as monitored by the Fe-histidine stretching vibration, νFeHis, is completed within two days, and is therefore uncoupled from the quaternary structure. Within each quaternary structure, the evolving νFeHis frequencies span the full range of values between those previously associated with the high- and low-affinity end states, R and T. This result supports the tertiary two-state (TTS) model, in which the Hb subunits can adopt high- and low-affinity tertiary structures, r and t, within each quaternary state. The spectra also reveal different tertiary pathways, involving the breaking and re-formation of E and F inter-helical contacts in the R-T direction but not the T-R direction. In the latter, tertiary motions are restricted by the T quaternary contacts.

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“…The studies using TA spectroscopy in the 1970s and 1980s suggested that the decaying kinetics at several tens of ms is due to the R-T transition because the TA spectrum corresponding to that time scale is very similar to the difference spectrum between the absorption spectra of the R and T states. 4,11,12,20 According to this assignment, the hinge contact was made within a few ms and then the switch contact was formed within tens of ms. 2 Later, other studies using TA spectroscopy, singular value decomposition (SVD) and kinetic modelling suggested that the fast relaxation occurring within a few ms could also be related to the R-T transition although the slow dynamics at the tens of ms time scale was interpreted as the major quaternary structural change due to the R-T transition.…”

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confidence: 99%

“…On the other hand, in the studies using TR-UVRR spectroscopy, the biphasic structural changes of the hydrogen bonds in the dimer-dimer interface, which are known as the hinge contact and switch contact formations, respectively, were observed and assigned to the R-T transition. 4,11,12,20 According to this assignment, the hinge contact was made within a few ms and then the switch contact was formed within tens of ms. Recently, the studies using TR-WAXS technique, which can monitor the conformational changes of various biomolecules occurring in the solution phase, 5,6,15,[42][43][44][45][46][47][48][49][50][51][52][53][54] revealed that the significant scattering signal change was observed mainly at a few ms time scale and assigned to the R-T transition.…”

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confidence: 99%