Nanosecond crystallographic snapshots of protein structural changes

A molecule for all seasons: The heme

If life without heme-Fe were at all possible, it would definitely be different. Indeed this complex and versatile iron-porphyrin macrocycle upon binding to different “globins” yields hemeproteins crucial to sustain a variety of vital functions, generally classified, for convenience, in a limited number of functional families. Over-and-above the array of functions briefly outlined below, the spectacular progress in molecular genetics seen over the last 30 years led to the discovery of many hitherto unknown novel hemeproteins in prokaryotes and eukaryotes. Here, we highlight a few basic aspects of the chemistry of the hemeprotein universe, in particular those that are relevant to the control of heme-Fe reactivity and specialization, as sculpted by a variety of interactions with the protein moiety.

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.

Electronic polarization spectroscopy of metal phthalocyanine chloride compounds in superfluid helium droplets

We report the electronic polarization spectroscopy of two metal phthalocyanine chloride compounds (MPcCl, M=Al,Ga) embedded in superfluid helium droplets and oriented in a dc electric field. For both compounds, the laser induced fluorescence spectra show preference for perpendicular excitation relative to the orientation field. This result indicates that the permanent dipoles of both compounds are predominantly perpendicular to the transition dipole. Since the permanent dipole derives from the metal chloride, while the transition dipole derives from the phthalocyanine chromophore, in the plane of phthalocyanine, this qualitative result is not surprising. However, quantitative modeling reveals that this intuitive model is inadequate and that the transition dipole might have tilted away from the molecular plane of phthalocyanine. The out of plane component of the transition dipole amounts to approximately 10% if the permanent dipole is assumed to be approximately 4 debye. The origin for this tilt is puzzling, and we tentatively attribute it to the transition of nonbonding orbitals, either from the chlorine atom or from the bridge nitrogen atom, to the pi* orbitals of the phthalocyanine chromophore. On the other hand, although unlikely, we cannot completely exclude the possibility that both our high level density functional theory calculation and ab initio results severely deviate from reality. The droplet matrix induces redshifts in the origin of the electronic transition and produces discrete phonon wings. Nevertheless, in dc electric fields, all phonon wings and the zero phonon line demonstrate the same dependence on the polarization direction of the excitation laser. Although electronic excitation does couple to the superfluid helium matrix and the resulting phonon wings add complications to the electronic spectrum, this coupling does not affect the direction of the electronic transition dipole. Electronic polarization spectroscopy in superfluid helium droplets is thus still informative in revealing the permanent dipole and its relation relative to the transition dipole.

Rotational spectra of the van der Waals complexes of molecular hydrogen and OCS

The a- and b-type rotational transitions of the weakly bound complexes formed by molecular hydrogen and OCS, para-H2-OCS, ortho-H2-OCS, HD-OCS, para-D2-OCS, and ortho-D2-OCS, have been measured by Fourier transform microwave spectroscopy. All five species have ground rotational states with total rotational angular momentum J=0, regardless of whether the hydrogen rotational angular momentum is j=0 as in para-H2, ortho-D2, and HD or j=1 as in ortho-H2 and para-D2. This indicates quenching of the hydrogen angular momentum for the ortho-H2 and para-D2 species by the anisotropy of the intermolecular potential. The ground states of these complexes are slightly asymmetric prolate tops, with the hydrogen center of mass located on the side of the OCS, giving a planar T-shaped molecular geometry. The hydrogen spatial distribution is spherical in the three j=0 species, while it is bilobal and oriented nearly parallel to the OCS in the ground state of the two j=1 species. The j=1 species show strong Coriolis coupling with unobserved low-lying excited states. The abundance of para-H2-OCS relative to ortho-H2-OCS increases exponentially with decreasing normal H2 component in H2He gas mixtures, making the observation of para-H2-OCS in the presence of the more strongly bound ortho-H2-OCS dependent on using lower concentrations of H2. The determined rotational constants are A=22 401.889(4) MHz, B=5993.774(2) MHz, and C=4602.038(2) MHz for para-H2-OCS; A=22 942.218(6) MHz, B=5675.156(7) MHz, and C=4542.960(7) MHz for ortho-H2-OCS; A=15 970.010(3) MHz, B=5847.595(1) MHz, and C=4177.699(1) MHz for HD-OCS; A=12 829.2875(9) MHz, B=5671.3573(7) MHz, and C=3846.7041(6) MHz for ortho-D2-OCS; and A=13 046.800(3) MHz, B=5454.612(2) MHz, and C=3834.590(2) MHz for para-D2-OCS.

Rydberg states of small NaArn* clusters

The 4s and 5s Rydberg excited states of NaAr(n)* clusters are investigated using a pseudopotential quantum-classical method. While NaAr(n) clusters in their ground state are known to be weakly bound van der Waals complexes with Na lying at the surface of the argon cluster, isomers in 4s or 5s electronically excited states of small NaAr(n)* clusters (n< or =10) are found to be stable versus dissociation. The relationship between electronic excitation and cluster geometry is analyzed as a function of cluster size. For both 4s and 5s states, the stable exciplex isomers essentially appear as sodium-centered structures with similar topologies, converging towards those of the related NaAr(n)+ positive ions when the excitation level is increased. This is consistent with a Rydberg-type picture for the electronically excited cluster, described by a central sodium ion solvated by an argon shell, and an outer diffuse electron orbiting around this NaAr(n)+ cluster core.

Conformational identification of tryptamine embedded in superfluid helium droplets using electronic polarization spectroscopy

We report electronic polarization spectroscopy of tryptamine embedded in superfluid helium droplets. In a dc electric field, dependence of laser induced fluorescence from tryptamine on the polarization direction of the excitation laser is measured. Among the three observed major conformers A, D, and E, conformers D and E display preference for perpendicular excitation relative to the orientation field, while conformer A is insensitive to the polarization direction of the excitation laser. We attribute the behavior of conformer A to the fact that the angle between the permanent dipole and the transition dipole is close to the magic angle. Using a linear variation method, we can reproduce the polarization preference of the three conformers and determine the angle between the transition dipole and the permanent dipole. Since the side chain exerts small effect on the direction of the transition dipole in the frame of the indole chromophore, all three conformers have a common transition dipole more or less in the indole plane at an angle of approximately 60 degrees relative to the long axis of the chromophore. The orientation of the side chain, on the other hand, determines the size and direction of the permanent dipole, thereby affecting the angle between the permanent dipole and the transition dipole. For conformer D in the droplet, our results agree with the Anti(ph) structure, rather than the Anti(py) structure. Our work demonstrates that polarization spectroscopy is effective in conformational identification for molecules that contain a known chromophore. Although coupling of the electronic transition with the helium matrix is not negligible, it does not affect the direction of the transition dipole.

Quantum solvation dynamics of HCN in a helium-4 droplet

Ultracold nanodroplets of helium-4, containing several thousands of He atoms, offer considerable promise as microscopic cryogenic chambers. Potential applications include the creation of tailor-made chemical or biomolecular complexes and studies of superfluidity in nanoscale systems. Recent experiments have succeeded in interrogating droplets of quantum solvent which consist of as few as 1-20 helium-4 atoms and which contain a single solute molecule. This allows the transition from a floppy, but essentially molecular, complex to a dissolved molecule to be followed and, surprisingly, the transition is found to occur quite rapidly, in some cases for as few as N = 7-20 solvent atoms. For example, in experiments on helium-4 droplets seeded with CO molecules [Tang and McKellar, J. Chem. Phys. 119, 754 (2003)], two series of transitions are observed which correlate with the a-type (Delta K = 0) and b-type (Delta K = +/-1) lines of the binary complex, CO-He (K is the quantum number associated with the projection of the total angular momentum onto the vector connecting the atom and the molecular center of mass). The a-type series, which evolves from the end-over-end rotational motion of the CO-He binary complex, saturates to the nanodroplet limit for as few as 10-15 helium-4 atoms, i.e., the effective moment of inertia of the molecule converges to its asymptotic (solvated) value quite rapidly. In contrast, the b-type series, which evolves from the free-molecule rotational mode, disappears altogether for N approximately 7 atoms. Similar behavior is observed in recent computational studies of HCN(4He)N droplets [Paolini et al., J. Chem. Phys. 123, 114306 (2005)]. In this article the quantum solvation of HCN in small helium-4 droplets is studied using a new fixed-node diffusion Monte Carlo (DMC) procedure. In this approach a Born-Oppenheimer-type separation of radial and angular motions is introduced as a means of computing nodal surfaces of the many-body wave functions which are required in the fixed-node DMC method. Excited rotational energies are calculated for HCN(4He)N droplets with N = 1-20: the adiabatic node approach also allows concrete physical mechanisms to be proposed for the predicted disappearance of the b-type series as well as the rapid convergence of the a-type series to the nanodroplet limit with increasing N. The behavior of the a-type series is traced directly to the mechanics of angular momentum coupling-and decoupling-between identical bosons and the molecular rotor. For very small values of N there exists significant angular momentum coupling between the molecule and the helium atoms: at N approximately 10 solvation appears to be complete as evidenced by significant decoupling of the molecule and solvent angular momenta. The vanishing of the b-type series is predicted to be a result of increasing He-He repulsion as the number of solvent atoms increases.

Infrared intensity in small ammonia and water clusters

Helium droplet technique has been used in order to measure the strength of the infrared absorption in small ammonia and water clusters as a function of size. Hydrogen bonding in ammonia and water dimers causes an enhancement of the intensity of the hydrogen stretching bands by a factor of four and three, respectively. Two types of the hydrogen bonded clusters show different size dependence of the infrared intensity per hydrogen bond. In ammonia (NH3)2 and (NH3)3 it is close to the crystal value. In water clusters, it increases monotonically with cluster size being in tetramers, a factor of two smaller than in the ice. The measured infrared intensity in water clusters is found to be a factor of two to three smaller as compared to the results of numerical calculations.

Fluorescence spectroscopy monitoring of the conformational restraint of formaldehyde- and glutaraldehyde-treated infectious bursal disease virus proteins

Interaction of native proteinaceous antigens during the recognition and the effector phases of an immune response leads to antigenic conformational modifications which may elicit additional specific immune response. Protein cross-linking and conformation restraining formaldehyde and glutaraldehyde have been extensively used in vaccine preparation, but the relative efficiencies of conformational restraint at concentrations similar to those used in vaccine preparation have not been investigated. We addressed this issue by comparing the extent of conformational restraint of virus proteins in formaldehyde- and glutaraldehyde-treated virus preparations by monitoring the fluorescence intensities (I320) of infectious bursal disease virus preparations (IBDV) and those of untreated virus during thermal denaturation. Formaldehyde was found to cause no detectable conformational restraint at 0.01% and only very weak restraint at 1%, while glutaraldehyde caused very strong conformational restraint at 0.01%. It is proposed how conformational restraint of proteinaceous antigens may alter ensuing immunity.

New results using Laue diffraction and time-resolved crystallography

Several time-resolved crystallographic structures were determined over the past year, using a variety of trapping protocols and several data collection methods. A significant theme of recent time-resolved work is the importance of parallel comparative studies on the same protein, using different experimental protocols, in order to fully characterize the structural variation of the intermediates formed in the reaction pathway.

Synchrotron radiation applications to macromolecular crystallography

Progress has been rapid in the development and application of four different types of macromolecular crystallographic experiment at synchrotron hard X-ray sources: multiwavelength anomalous diffraction; studies of crystals with very large unit cell dimensions; structure determination at atomic or near-atomic resolution; and time-resolved studies. The results illustrate the interplay between the advanced technical capabilities available at new beamlines and more challenging scientific issues.

Laue crystallography: Lights! Camera! action!

Recent advances in the Laue method of X-ray data collection from protein crystals have allowed very short-lived reaction intermediates to be observed successfully.