Computational Structural Biology 
Axel T. Briinger, Ph.D. — Assistant Investigator 
Dr. Briinger is also Assistant Professor in the Department of Molecular Biophysics and Biochemistry at 
Yale University. He was born in Leipzig, Germany. He received his diploma in physics at the University of 
Hamburg and his Ph.D. degree from the Technical University of Munich. He held a NATO postdoctoral 
fellowship and subsequently became a research associate with Martin Karplus in the Department of 
Chemistry at Harvard University. His research has focused on molecular dynamics studies of protein 
structure and function and on methods in protein crystallography and nuclear magnetic resonance 
spectroscopy. 
OUR research lies at the interface between 
theory and experiment in the area of struc- 
tural biophysics. The research tools are sim- 
ulation methods of computational chemistry 
adapted to the requirements of macromolecular 
systems. Macromolecular simulations are an im- 
portant addition to the arsenal of methods avail- 
able to structural biologists working with x-ray 
crystallographic or nuclear magnetic resonance 
(NMR) spectroscopic data. In one set of projects 
we are trying to understand the detailed micro- 
scopic interactions that govern stability and rec- 
ognition in biological systems and to test the reli- 
ability of the theoretical methods as tools for this 
purpose. We are also directly combining macro- 
molecular simulation with experimental data to 
make data analysis possible or more efficient. 
Generalizing Molecular Replacement 
in X-ray Crystallography 
In macromolecular crystallography, the deter- 
mination of initial phases is the major obstacle to 
determining the structure of the crystallized mol- 
ecule. This is because the observable x-ray dif- 
fraction information from a single crystal com- 
prises only the amplitudes but not the phases of 
the reflections. Although this "phase problem" 
has been solved in the case of small molecules 
(up to a few hundred atoms in the unit cell) 
through the development of direct methods by 
Hauptman and Karle, the application of these meth- 
ods to macromolecules has so far been unsuccessful, 
and one has to resort to time-consuming and some- 
times difficult experimental methods. 
The initial determination of phases by molecu- 
lar replacement is often attempted if the struc- 
ture of a similar or homologous protein is known. 
Molecular replacement involves the placement 
(i.e., rotation and translation) of the known 
structure in the unit cell of the target crystal in 
order to obtain the best agreement between cal- 
culated model diffraction data and the observed 
diffraction data. Recent progress in obtaining ap- 
proximate three-dimensional models of macro- 
molecules from information other than x-ray 
crystallography suggests an increased use of mo- 
lecular replacement. For instance, the database of 
known protein sequences is growing rapidly. 
Techniques for aligning sequences, such as con- 
sensus templates, have been developed to recog- 
nize distantly related proteins or protein domains 
and to carry out model building on the basis of 
the several hundred known protein structures. 
Molecular replacement often fails if the search 
model is too inaccurate — that is, if the differ- 
ences in atomic positions between the search 
model and the crystal structure are more than 1 A. 
In this case we proposed to vary the orientations 
and positions of domains, or structural subunits, 
of the search model in a neighborhood around 
the initial positions . We developed a new molecu- 
lar replacement strategy. First a conventional ro- 
tation search is carried out. Then the rotation 
search is "filtered" by employing refinement of 
the domain orientations and positions against the 
Patterson correlation coefficient. Finally, the re- 
fined search models with the highest correlation 
coefficients are used for conventional translation 
searches. Computer model studies have already 
suggested the usefulness of the new method. Re- 
cently we obtained phases for six crystal struc- 
tures that previously could not be solved, includ- 
ing several monoclonal antibody Fab fragments. 
Presently, the molecular replacement strategy 
is extended by applying modern techniques 
of nonlinear optimization, such as simulated 
annealing. 
Predictions of Helix-Helix Association and 
Stability in Proteins: Leucine Zipper and 
Membrane Proteins 
Prediction of the three-dimensional structure 
of proteins based on their sequence has up to 
now been impossible. This fundamental problem 
of structural biology (the "folding problem") re- 
mains unsolved, despite improvements in com- 
putational techniques for macromolecular simu- 
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