Biology Department Biology Department  


Alexei S. Soares

Brookhaven National Laboratory
Bldg. 463 - P.O. Box 5000
Upton, NY 11973-5000

Phone: (631) 344-7306
Fax: (631) 344-2741
The Group:
Rick Jackimowicz (631) 344-7401
Chris Roessler (631) 344-7401

Alexei Soares is a beam line scientist in the Macromolecular Crystallography Research Resource (PXRR) which provides facilities and support at the National Synchrotron Light Source for the benefit of outside and in-house investigators.   The PXRR is supported by the NIH's National Center for Research Resources and the DOE Office of Biological and Environmental Research in its mission to create optimal facilities and environments for macromolecular structure determination by synchrotron X-ray diffraction.   With a staff of about 24, the PXRR innovates new access modes such as FedEx crystallography, builds new facilities, currently on the X25 undulator, advances automation, develops remote participation software, collaborates with outside groups, teaches novice users, and supports visting investigators with 7day, 20 hours staff coverage.

Research Interests

Using highly accurate triplet phases measured with the three-beam method to test and improve crystallographic data collection and refinement methods.

Developing methods to measure multiple triplet phases simultaneously, while still maintaining sufficient accuracy for phasing structures after conventional phasing methods have failed. An accurate "one at a time" triplet phase data set was designed to be sensitive to the correctness of the insulin solvent, and we invite collaborators to evaluate models against this hydration probe.

Investigating protein hydration and the role of water in protein function by solving protein structures at high-resolution and on an absolute electron density scale, as well as by applying high-pressure crystallographic methods currently under development.


Click on above image to view the
3-Beam Diffractometer in action.


Institutional Responsibilities

Mail-In Crystallography:   As part of the mail-in crystallography team of the PXRR - along with Annie Héroux and Howard Robinson - I carry out extensive crystal screening and data collection efforts for the benefit of remotely participating crystallographers. When collaborations can be established with these groups, concentrated efforts are made to derive initial structure solutions.

Automounters:   To augment the mail-in program, and particularly the scouting for the best-in-the-lot crystal in these projects, I promote the use of our cryogenic specimen automounters. I work with visiting and mail-in crystallographers in carrying out robot-based data collections using the combined capabilities of the bending magnet beam line X12B and the undulator beam line X29. I develop and test methods for remote data collection based on the dna-suite of programs.

User Program:   In addition, I assist outside investigators in efficient data collection and structure solving at beam line X12B which I manage jointly with D. Schneider. To further augment PXRR capabilities I embarked in building a program and facilities for the high-pressure freezing of crystals. Encouraging diffraction measurements on cubic and hexagonal insulin crystals frozen at high pressures at McChess and measured at BNL, indicate the significant reduction in mosaic disorder that can be achieved by this strikingly simple, but tecnologically challenging technique.


Selected Publications

  • Podzelinska K., He S., Soares A., Zechel D., Hove-Jensen B. and Jia Z.
    Expression, purification and preliminary diffraction studies of PhnP.
    Acta Crystallographica Section F: Structural Biology and Crystallization Communications, F64(Pt 6):554-557 (2008).
  • Salameh M., Soares A., Hockla A. and Radisky E.
    Structural basis for accelerated cleavage of bovine pancreatic trypsin inhibitor (BPTI) by human mesotrypsin.
    J Biol Chem., 283(7):4115-23 (2008).  PubMed
  • Soares A.S., Schneider D.K., Skinner J.M., Cowan M., Buono R., Robinson H.H., Heroux A., Carlucci-Dayton M., Saxena A., and Sweet R.M.
    Remote access to the PXRR macromolecular crystallography facilities at the NSLS.
    Synchrotron Radiation News, 21(5):17-23 (September, 2008).
  • Zhao X., Copeland D., Soares A. and West A.
    Crystal structure of a complex between the phosphorelay protein YPD1 and the response regulator domain of SLN1 bound to a phosphoryl analog.
    J. Mol. Biol., 375(4):1141-1151 (2008).  PubMed
  • Carra J.H., McHugh C.A., Mulligan S., Machiesky L.M., Soares A.S. and Millard C.B.
    Fragment-based identification of determinants of conformational and spectroscopic change at the ricin active site.
    BMC Struct. Biol., 7:72 (2007).  PubMed
  • Hewitson K.S., Lienard B.M., McDonough M.A., Clifton I.J., Butler D., Soares A.S., Oldham N.J., McNeill L.A. and Schofield C.J.
    Structural and mechanistic studies on the inhibition of the hypoxia-inducible transcription factor hydroxylases by tricarboxylic acid cycle intermediates.
    J. Biol. Chem., 282(5):3293-3301 (2007).  PubMed
  • Soares A.S., Carlucci-Dayton M., Robinson H., Sweet, R. and Schneider D.
    Automation program for macromolecular crystallography at the NSLS.
    American Crystallography Association Annual Meeting, Salt Lake City, (2007).
  • Copeland D.M., Soares A.S., West A.H. and Richter-Addo G.B.
    Crystal structures of the nitrite and nitric oxide complexes of horse heart myoglobin.
    J. Inorg. Biochem., 100(8):1413-1425 (2006).  PubMed
  • Robinson H., Soares A.S., Becker M., Sweet R. and Heroux A.
    Mail-in crystallography program at Brookhaven National Laboratory's National Synchrotron Light Source.
    Acta Cryst., D62(11):1336-1339 (2006).   PubMed   Full Text
  • Skinner J.M., Cowan M., Buono R., Nolan W., Bosshard H., Robinson H.H., Heroux A., Soares A.S., Schneider D.K. and Sweet R.M.
    Integrated software for macromolecular crystallography synchrotron beamlines II: revision, robots and a database
    Acta Cryst., D62(11):1340-1347 (2006).   PubMed   Full Text
  • Soares A.S. and Y. Vekhter.
    Experimental methods for measuring accurate high-amplitude phases and their importance in isomorphous replacement experiments.
    Acta Cryst., D61(11):1521-1527 (2005).   PubMed   Full Text
  • Lovelace J., Soares A., Bellamy H., Sweet R., Snell E. and Borgstahl G.
    First results of digital topography applied to macromolecular crystals.
    J Appl Cryst., 37:481-485 (2004).
  • Makowski L. and Soares A.
    Estimating the diversity of peptide populations from limited sequence data.
    Bioinformatics, 19(4):483-489 (2003).   PubMed   Full Text
  • Soares A.S., Caspar D.L.D., Weckert E., Héroux A., Hölzer K., Schroer K., Zellner J., Schneider D., Nolan W. and Sweet R.M.
    Three beam interference is a sensitive measure of the efficacy of macromolecular refinement techniques.
    Acta Cryst., D59(10):1716-1724 (2003).   PubMed   Full Text
  • Rodi D.J., Soares A.S. and Makowski L.
    Quantitative assessment of peptide sequence diversity in M13 combinatorial peptide phage display libraries.
    J Mol Biol., 322:1039-1052 (2002).   PubMed


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Last Modified: September 15, 2011
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