Robert M. Glaeser

From words to literature in structural proteomics.

Technical advances on several frontiers have expanded the applicability of existing methods in structural biology and helped close the resolution gaps between them. As a result, we are now poised to integrate structural information gathered at multiple levels of the biological hierarchy — from atoms to cells — into a common framework. The goal is a comprehensive description of the multitude of interactions between molecular entities, which in turn is a prerequisite for the discovery of general structural principles that underlie all cellular processes.

What can x-ray scattering tell us about the radial distribution functions of water?

We present an analysis of the Advanced Light Source (ALS) x-ray scattering experiment on pure liquid water at ambient temperature and pressure described in the preceding article. The present study discusses the extraction of radial distribution functions from the x-ray scattering of molecular fluids. It is proposed that the atomic scattering factors used to model water be modified to include the changes in the intramolecular electron distribution caused by chemical bonding effects. Based on this analysis we present a gOO(r) for water consistent with our recent experimental data gathered at the ALS, which differs in some aspects from the gOO(r) reported by other x-ray and neutron scattering experiments. Our gOO(r) exhibits a taller and sharper first peak, and systematic shifts in all peak positions to smaller r. Based on experimental uncertainties, we discuss what features of gOO(r) should be reproduced by classical simulations of nonpolarizable and polarizable water models, as well as ab initio simulation...

Electron Diffraction of Frozen, Hydrated Protein Crystals

High-resolution electron diffraction patterns have been obtained from frozen, hydrated catalase crystals to demonstrate the feasibility of using a frozen specimen hydration technique. The use of frozen specimens to maintain the hydration of complex biological structures has certain advantages over previously developed liquid hydration techniques.

Limitations to significant information in biological electron microscopy as a result of radiation damage

Quantitative measurements of radiation damage in crystalline specimens of l-valine, adenosine, and catalase (uranyl acetate stained) have been made by observing the loss of the electron diffraction pattern. Reciprocity of specimen lifetime and current density at the specimen demonstrates the absence of any dose-rate effect, such as specimen heating, as a cause of specimen damage within the range 10−3 to 10−5 amperes/cm2 current density at the specimen. Specimen lifetimes at high voltages are about two and a half times greater than at conventional voltages, and it is shown that this is consistent with the dependence of linear energy loss upon accelerating voltage. The limiting resolution for meaningful observation is considered in terms of the statistics of observation at partticle fluxes that are specified from the specimen lifetime data. The best values are probably not better than 50 A for l-valine, 20 A for adenosine, and 15 A for catalase.

A high-quality x-ray scattering experiment on liquid water at ambient conditions

We report a new, high-quality x-ray scattering experiment on pure ambient water using a synchrotron beam line at the Advanced Light Source at Lawrence Berkeley National Laboratory. Several factors contribute to the improved quality of our intensity curves including use of a highly monochromatic source, a well-characterized polarization correction, a Compton scattering correction that includes electron correlation, and more accurate intensities using a modern charge coupled device (CCD) detector. We provide a comprehensive description of the data processing that we have used for correcting systematic errors, and we provide an estimate of our remaining random errors. The resulting error estimates of our data are smaller then the discrepancies between data sets collected in past x-ray experiments. We find that the older x-ray curves support a family of gOO(r)’s that exhibit a smaller first peak (∼2.2), while the current data is better fit with a family of gOO(r)’s with a first peak height of 2.8, and systema...

Electron microscopy of frozen hydrated biological specimens

The use of frozen hydrated specimens for molecular structure determination is limited primarily by radiation damage. The radiation damage effect in frozen hydrated catalase crystals has been measured in terms of the loss of electron diffraction. The results show an improvement for this type of specimen relative to wet hydrated or to glucose embedded catalase crystals at room temperature. Bright field images of unstained, frozen hydrated catalase crystals extend to a resolution of 11.5 A. The image resolution is presently limited by design problems with the liquid nitrogen cooled specimen stage. Rather high contrast is present in these images of unstained biological material, presumably due to the 30% difference in mass density between ice and protein. The improved resistance to radiation damage also makes it possible to give better statistical definition to the image, thereby making the image features easier to see.

Radiation damage relative to transmission electron microscopy of biological specimens at low temperature: a review.

When biological specimens are irradiated by the electron beam in the electron microscope, the specimen structure is damaged as a result of molecular excitation, ionization, and subsequent chemical reactions. The radiation damage that occurs in the normal process of electron microscopy is known to present severe limitations for imaging high resolution detail in biological specimens. The question of radiation damage at low temperatures has therefore been investigated with the view in mind of reducing somewhat the rate at which damage occurs. The radiation damage protection found for small molecule (anhydrous) organic compounds is generally rather limited or even non‐existent. However, large molecule, hydrated materials show as much as a 10‐fold reduction at low temperature in the rate at which radiation damage occurs, relative to the damage rate at room temperature. In the case of hydrated specimens, therefore, low temperature electron microscopy offers an important advantage as part of the overall effort required in obtaining high resolution images of complex biological structures.

The relevance of dose-fractionation in tomography of radiation-sensitive specimens

It is commonly assumed that the number of projections required for single-axis tomography precludes its application to most beam-labile specimens. However, Hegerl and Hoppe have pointed out that the total dose required to achieve statistical significance for each voxel of a computed 3D reconstruction is the same as that required to obtain a single 2D image of that isolated voxel, at the same level of statistical significance. Thus a statistically significant 3D image can be computed from statistically insignificant projections, as long as the total dose that is distributed among these projections is high enough that it would have resulted in a statistically significant projection, if applied to only one image. We have tested this critical theorem by simulating the tomographic reconstruction of a realistic 3D model created from an electron micrograph. The simulations verify the basic conclusions of the theorem and extend its validity to the experimentally more realistic conditions of high absorption, signal-dependent noise, varying specimen contrast and missing angular range. Individual projections in the series of fractionated-dose images could be aligned by cross-correlation because they contained significant information derived from the summation of features from different depths in the structure. This latter information is generally not useful for structural interpretation prior to 3D reconstruction, owing to the complexity of most specimens investigated by single-axis tomography. These results demonstrate that it is feasible to use single-axis tomography with soft X-ray and electron microscopy of frozen-hydrated specimens.

Structure of an Early Intermediate in the M-State Phase of the Bacteriorhodopsin Photocycle

The structure of an early M-intermediate of the wild-type bacteriorhodopsin photocycle formed by actinic illumination at 230 K has been determined by x-ray crystallography to a resolution of 2.0 A. Three-dimensional crystals were trapped by illuminating with actinic light at 230 K, followed by quenching in liquid nitrogen. Amide I, amide II, and other infrared absorption bands, recorded from single bacteriorhodopsin crystals, confirm that the M-substate formed represents a structure that occurs early after deprotonation of the Schiff base. Rotation about the retinal C13-C14 double bond appears to be complete, but a relatively large torsion angle of 26 degrees is still seen for the C14-C15 bond. The intramolecular stress associated with the isomerization of retinal and the subsequent deprotonation of the Schiff base generates numerous small but experimentally measurable structural changes within the protein. Many of the residues that are displaced during the formation of the late M (M(N)) substate formed by three-dimensional crystals of the D96N mutant (Luecke et al., 1999b) are positioned, in early M, between their resting-state locations and the ones which they will adopt at the end of the M phase. The relatively small magnitude of atomic displacements observed in this intermediate, and the well-defined positions adopted by nearly all of the atoms in the structure, may make the formation of this structure favorable to model (simulate) by molecular dynamics.

Peptide-chain secondary structure of bacteriorhodopsin.

Ultraviolet circular dichroism spectroscopy in the interval from 190 to 240 nm and infrared spectroscopy in the region of the amide I band (1,600 cm-1 to 1,700 cm-1) has been used to estimate the alpha-helix content and the beta-sheet content of bacteriorhodopsin. Circular dichroism spectroscopy strongly suggests that the alpha-helix content is sufficient for only five helices, if each helix is composed of 20 or more residues. It also suggests that there is substantial beta-sheet conformation in bacteriorhodopsin. The presence of beta-sheet secondary structure is further suggested by the presence of a 1,639 cm-1 shoulder on the amide I band in the infrared spectrum. Although a structural model consisting of seven alpha-helical rods has been generally accepted up to this point, the spectroscopic data are more consistent with a model consisting of five alpha-helices and four strands of beta-sheet. We note that the primary amino acid sequence can be assigned to segments of alpha-helix and beta-sheet in a way that does not require burying more than two charged groups in the hydrophobic membrane interior, contrary to the situation for any seven-helix model.