Expression, purification and crystallization of CTB-MPR, a candidate mucosal vaccine component against HIV-1.

CTB-MPR is a fusion protein between the B subunit of cholera toxin (CTB) and the membrane-proximal region of gp41 (MPR), the transmembrane envelope protein of Human immunodeficiency virus 1 (HIV-1), and has previously been shown to induce the production of anti-HIV-1 antibodies with antiviral functions. To further improve the design of this candidate vaccine, X-ray crystallography experiments were performed to obtain structural information about this fusion protein. Several variants of CTB-MPR were designed, constructed and recombinantly expressed in Escherichia coli.

Time-resolved protein nanocrystallography using an X-ray free-electron laser.

We demonstrate the use of an X-ray free electron laser synchronized with an optical pump laser to obtain X-ray diffraction snapshots from the photoactivated states of large membrane protein complexes in the form of nanocrystals flowing in a liquid jet. Light-induced changes of Photosystem I-Ferredoxin co-crystals were observed at time delays of 5 to 10 µs after excitation. The result correlates with the microsecond kinetics of electron transfer from Photosystem I to ferredoxin.

Signal, noise, and resolution in correlated fluctuations from snapshot small-angle x-ray scattering.

It has been suggested that the three-dimensional structure of one particle may be reconstructed using the scattering from many identical, randomly oriented copies ab initio, without modeling or a priori information. This may be possible if these particles are frozen in either space or time, so that the conventional two-dimensional small-angle x-ray scattering (SAXS) distribution contains fluctuations and is no longer isotropic. We consider the magnitude of the correlated fluctuation SAXS (CFSAXS) signal for typical x-ray free-electron laser (XFEL) beam conditions and compare this against the errors derived with the inclusion of Poisson photon counting statistics.

Phasing of coherent femtosecond X-ray diffraction from size-varying nanocrystals.

The scattering between Bragg reflections from nanocrystals is used to aid solution of the phase problem. We describe a method for reconstructing the charge density of a typical molecule within a single unit cell, if sufficiently finely-sampled "snap-shot" diffraction data (as provided a free-electron X-ray laser) are available from many nanocrystals of different sizes lying in random orientations. By using information on the particle-size distribution within the patterns, this digital method succeeds, using all the data, without knowledge of the distribution of particle size or requiring atomic-resolution data.

Structure-factor analysis of femtosecond microdiffraction patterns from protein nanocrystals.

A complete set of structure factors has been extracted from hundreds of thousands of femtosecond single-shot X-ray microdiffraction patterns taken from randomly oriented nanocrystals. The method of Monte Carlo integration over crystallite size and orientation was applied to experimental data from Photosystem I nanocrystals. This arrives at structure factors from many partial reflections without prior knowledge of the particle-size distribution.

Femtosecond X-ray protein nanocrystallography.

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells.

Femtosecond protein nanocrystallography-data analysis methods.

X-ray diffraction patterns may be obtained from individual submicron protein nanocrystals using a femtosecond pulse from a free-electron X-ray laser. Many "single-shot" patterns are read out every second from a stream of nanocrystals lying in random orientations. The short pulse terminates before significant atomic (or electronic) motion commences, minimizing radiation damage.

Quantum Monte Carlo calculations of symmetric nuclear matter.

We present an accurate numerical study of the equation of state of nuclear matter based on realistic nucleon-nucleon interactions by means of auxiliary field diffusion Monte Carlo (AFDMC) calculations. The AFDMC method samples the spin and isospin degrees of freedom allowing for quantum simulations of large nucleonic systems and represents an important step forward towards a quantitative understanding of problems in nuclear structure and astrophysics.

1S0 Superfluid phase transition in neutron matter with realistic nuclear potentials and modern many-body theories.

The 1S0 pairing in neutron matter is studied using realistic two- and three-nucleon interactions. The auxiliary field diffusion Monte Carlo method and correlated basis function theory are employed to get quantitative and reliable estimates of the gap. The two methods are in good agreement up to the maximum gap density and both point to a slight reduction with respect to the standard BCS value.

Structure, rotational dynamics, and superfluidity of small OCS-doped He clusters.

The structural and dynamical properties of carbonyl sulfide (OCS) molecules solvated in helium clusters are studied using reptation quantum Monte Carlo, for cluster sizes n=3-20 He atoms. Computer simulations allow us to establish a relation between the rotational spectrum of the solvated molecule and the structure of the He solvent, and of both with the onset of superfluidity. Our results agree with a recent spectroscopic study of this system and provide a more complex and detailed microscopic picture of this system than inferred from experiments.

HF dimer in small helium clusters: interchange-tunneling dynamics in a quantum environment.

We present diffusion quantum Monte Carlo calculations of the interchange tunneling splitting of (4)He(n)(HF)(2) clusters, n = 1-10. The tunneling splitting decreases rapidly for n = 1-4 clusters, and much more slowly for n>4. The decrease calculated for (4)He(n)(HF)(2) represents 74% of the reduction in the tunneling splitting measured recently for HF dimer in nanodroplets of more than 2000 He atoms.