Hironari Kamikubo

Low-barrier hydrogen bond in photoactive yellow protein

Low-barrier hydrogen bonds (LBHBs) have been proposed to play roles in protein functions, including enzymatic catalysis and proton transfer. Transient formation of LBHBs is expected to stabilize specific reaction intermediates. However, based on experimental results and theoretical considerations, arguments against the importance of LBHB in proteins have been raised. The discrepancy is caused by the absence of direct identification of the hydrogen atom position. Here, we show by high-resolution neutron crystallography of photoactive yellow protein (PYP) that a LBHB exists in a protein, even in the ground state. We identified ≈87% (819/942) of the hydrogen positions in PYP and demonstrated that the hydrogen bond between the chromophore and E46 is a LBHB. This LBHB stabilizes an isolated electric charge buried in the hydrophobic environment of the protein interior. We propose that in the excited state the fast relaxation of the LBHB into a normal hydrogen bond is the trigger for photo-signal propagation to the protein moiety. These results give insights into the novel roles of LBHBs and the mechanism of the formation of LBHBs.

Watching a Signaling Protein Function in Real Time Via 100-Ps Time-Resolved Laue Crystallography.

To understand how signaling proteins function, it is crucial to know the time-ordered sequence of events that lead to the signaling state. We recently developed on the BioCARS 14-IDB beamline at the Advanced Photon Source the infrastructure required to characterize structural changes in protein crystals with near-atomic spatial resolution and 150-ps time resolution, and have used this capability to track the reversible photocycle of photoactive yellow protein (PYP) following trans-to-cis photoisomerization of its p-coumaric acid (pCA) chromophore over 10 decades of time. The first of four major intermediates characterized in this study is highly contorted, with the pCA carbonyl rotated nearly 90° out of the plane of the phenolate. A hydrogen bond between the pCA carbonyl and the Cys69 backbone constrains the chromophore in this unusual twisted conformation. Density functional theory calculations confirm that this structure is chemically plausible and corresponds to a strained cis intermediate. This unique structure is short-lived (∼600 ps), has not been observed in prior cryocrystallography experiments, and is the progenitor of intermediates characterized in previous nanosecond time-resolved Laue crystallography studies. The structural transitions unveiled during the PYP photocycle include trans/cis isomerization, the breaking and making of hydrogen bonds, formation/relaxation of strain, and gated water penetration into the interior of the protein. This mechanistically detailed, near-atomic resolution description of the complete PYP photocycle provides a framework for understanding signal transduction in proteins, and for assessing and validating theoretical/computational approaches in protein biophysics.

Cytochrome c polymerization by successive domain swapping at the C-terminal helix.

Cytochrome c (cyt c) is a stable protein that functions in a monomeric state as an electron donor for cytochrome c oxidase. It is also released to the cytosol when permeabilization of the mitochondrial outer membrane occurs at the early stage of apoptosis. For nearly half a century, it has been known that cyt c forms polymers, but the polymerization mechanism remains unknown. We found that cyt c forms polymers by successive domain swapping, where the C-terminal helix is displaced from its original position in the monomer and Met-heme coordination is perturbed significantly. In the crystal structures of dimeric and trimeric cyt c, the C-terminal helices are replaced by the corresponding domain of other cyt c molecules and Met80 is dissociated from the heme. The solution structures of dimeric, trimeric, and tetrameric cyt c were linear based on small-angle X-ray scattering measurements, where the trimeric linear structure shifted toward the cyclic structure by addition of PEG and (NH4)2HPO4. The absorption and CD spectra of high-order oligomers (∼40 mer) were similar to those of dimeric and trimeric cyt c but different from those of monomeric cyt c. For dimeric, trimeric, and tetrameric cyt c, the ΔH of the oligomer dissociation to monomers was estimated to be about -20 kcal/mol per protomer unit, where Met-heme coordination appears to contribute largely to ΔH. The present results suggest that cyt c polymerization occurs by successive domain swapping, which may be a common mechanism of protein polymerization.

Molecular dissection of IZUMO1, a sperm protein essential for sperm-egg fusion

Although the membrane fusion of spermatozoon and egg cells is the central event of fertilization, the underlying molecular mechanism remains virtually unknown. Gene disruption studies have showed that IZUMO1 on spermatozoon and CD9 on oocyte are essential transmembrane proteins in sperm-egg fusion. In this study, we dissected IZUMO1 protein to determine the domains that were required for the function of sperm-egg fusion. We found that a fragment of the N terminus (Asp5 to Leu113) interacts with fertilization inhibitory antibodies. It also binds to the egg surface and effectively inhibits fusion in vitro. We named this fragment ‘IZUMO1 putative functional fragment (IZUMO1PFF)’. Surprisingly, IZUMO1PPF still maintains binding ability on the egg surface of Cd9-/- eggs. A series of biophysical measurements using circular dichroism, sedimentation equilibrium and small angle X-ray scattering revealed that IZUMO1PFF is composed of an N-terminal unfolded structure and a C-terminal ellipsoidal helix dimer. Egg binding and fusion inhibition were not observed in the IZUMO1PFF derivative, which was incapable of helix formation. These findings suggest that the formation of a helical dimer at the N-terminal region of IZUMO1 is required for its function. Cos-7 cells expressing the whole IZUMO1 molecule bound to eggs, and IZUMO1 accumulated at the interface between the two cells, but fusion was not observed. These observations suggest that IZUMO1 alone cannot promote sperm-egg membrane fusion, but it works as a factor that is related to the cellular surface interaction, such as the tethering of the membranes by a helical region corresponding to IZUMO1PFF-core.

Concentration-Dependent Tetramerization of Bovine Visual Arrestin

The oligomeric states of bovine visual arrestin in solution were studied by small-angle x-ray scattering. The Guinier plot of arrestin at the concentration ranging from 0.4 mg/ml to 11.1 mg/ml was approximated with a straight line, and the apparent molecular weight was evaluated by the concentration-normalized intensity at zero angle (I(0)/conc). Using ovalbumin as a molecular weight standard, it was found that arrestin varied from monomer to tetramer depending on the concentration. The I(0)/conc decreased at high-salt concentration, but was independent of temperature. The simulation analysis of the concentration-dependent increase of I(0)/conc demonstrated that the tetramerization is highly cooperative, and arrestin at the physiological concentration is virtually in the equilibrium between monomer and tetramer. The concentration of arrestin monomer, which is considered to be an active form, remains at an almost constant level even if the total concentration of arrestin fluctuates within the physiological range. The scattering profile of arrestin tetramer in solution was in good agreement with that in the crystal, indicating that the quaternary structure in solution is essentially identical to that in crystal. Small-angle x-ray scattering was applied to a binding assay of phosphorylated rhodopsin and arrestin in the detergent system, and we directly observed their association as the increase of I(0)/conc.

Mechanism of induced folding: Both folding before binding and binding before folding can be realized in staphylococcal nuclease mutants

A considerable number of functional proteins are unstructured under physiological condition. These “intrinsically disordered” proteins exhibit induced folding when they bind their targets. The induced folding comprises two elementary processes: folding and binding. Two mechanisms are possible for the induced folding: either folding before binding or binding before folding. We found that these two mechanisms can be distinguished by the target‐concentration dependence of folding kinetics. We also created two types of mutants of staphylococcal nuclease showing the different inhibitor‐concentration dependence of induced folding kinetics. One mutant obeys the scheme of binding before folding, while the other the folding before binding. This is the first experimental evidence demonstrating that both mechanisms are realized for a single protein. Binding before folding is possible, when the protein lacks essential nonlocal interaction to stabilize the native conformation. The results cast light on the protein folding mechanism involved in the intrinsically disordered proteins. Proteins 2008.

Conformational change of helix G in the bacteriorhodopsin photocycle: investigation with heavy atom labeling and x-ray diffraction.

According to the current structural model of bacteriorhodopsin, Ile222 is located at the cytoplasmic end of helix G. We labeled the single cysteine of the site-directed mutant Ile222 --> Cys with p-chloromercuribenzoic acid and determined the position of the labeled mercury by x-ray diffraction in the unphotolyzed state, and in the MN photointermediate accumulated in the presence of guanidine hydrochloride at pH 9.5. According to the difference Fourier maps between the MN intermediate and the unphotolyzed state, the structural change in the MN intermediate was not affected by mercury labeling. The difference Fourier map between the labeled and the unlabeled I222C gave the position of the mercury label. This information was obtained for both the unphotolyzed state and the MN intermediate. We found that the position of the mercury at residue 222 is shifted by 2.1 +/- 0.8 A in the MN intermediate. This agrees with earlier results that suggested a structural change in the G helix. The movement of the mercury label is so large that it must originate from a cooperative conformational change in the helix G at its cytoplasmic end, rather than from displacement of residue 222. Because Ile222 is located at the same level on the z coordinate as Asp96, the structural change in the G helix could have the functional role of perturbing the environment and therefore the pKa of this functionally important aspartate.

Structural basis for Arf6-MKLP1 complex formation on the Flemming body responsible for cytokinesis.

A small GTPase, Arf6, is involved in cytokinesis by localizing to the Flemming body (the midbody). However, it remains unknown how Arf6 contributes to cytokinesis. Here, we demonstrate that Arf6 directly interacts with mitotic kinesin‐like protein 1 (MKLP1), a Flemming body‐localizing protein essential for cytokinesis. The crystal structure of the Arf6–MKLP1 complex reveals that MKLP1 forms a homodimer flanked by two Arf6 molecules, forming a 2:2 heterotetramer containing an extended β‐sheet composed of 22 β‐strands that spans the entire heterotetramer, suitable for interaction with a concave membrane surface at the cleavage furrow. We show that, during cytokinesis, Arf6 is first accumulated around the cleavage furrow and, prior to abscission, recruited onto the Flemming body via interaction with MKLP1. We also show by structure‐based mutagenesis and siRNA‐mediated knockdowns that the complex formation is required for completion of cytokinesis. A model based on these results suggests that the Arf6–MKLP1 complex plays a crucial role in cytokinesis by connecting the microtubule bundle and membranes at the cleavage plane.

Pressure and temperature effects on the phase transition from a dense droplet to a lamellar structure in a ternary microemulsion

A small-angle x-ray scattering (SAXS) study of a ternary microemulsion composed of AOT [sodium bis(2-ethylhexyl) sulfosuccinate], water and n-decane was undertaken in order to clarify the phase behavior and the feature of the corresponding structural transition from a dense droplet to a lamellar structure with increasing pressure and temperature. The volume fractions of water and decane were fixed to be equal and the volume fraction of AOT against the whole volume (φs) was selected to be 0.209 and 0.230 in order to compare results with those obtained by small-angle neutron scattering (SANS). The pressure was varied between 1 and 800 bar under controlled temperature at 20, 25, 29, or 33 °C. Under all conditions applied, the phase transition from the droplet structure to the lamellar structure was observed. The results of analysis of the SAXS profiles indicated that the short-range adhesive potential between droplets becomes more intense with increasing pressure.

Role of C-terminal region of Staphylococcal nuclease for foldability, stability, and activity

The role of the C‐terminal region of Staphylococcal nuclease (SNase) was examined by deletion mutation. Deletions up to eight residues do not affect the structure and function. The structure and enzymatic activity were partially lost by deleting Ser141‐Asn149 (Δ141–149), and deletion of Trp140‐Asn149 (Δ140–149) resulted in further loss of structure and activity. A 13‐residue deletion showed the same effect as the 10‐residue deletion. Both Ser141Gln and Ser141Ala mutations for an eight‐residue deletion mutant did not alter properties as well as Ser141A1a for full‐length SNase. In contrast, Trp140Ala mutation for Δ141–149 shows the same effect as the deletion of Trp140. Trp140Ala mutation for full‐length SNase causes the loss of native structure. These observations indicate the significance of the 140th and the 141st residues. The side‐chain of the 140th residue is required to be tryptophan; however, the backbone of the 141st residue is solely critical for foldability, but the side‐chain information is not crucial. All of the mutants that take a non‐native conformation show enzymatic activity and inhibitor‐induced folding, suggesting that foldability is required for the activity. Proteins 2002;49:255–265.