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Alexei S. Soares
Assistant Biophysicist
Ph.D. in Molecular Biophysics Florida State University, 2001
Biology Department, 463
tel: (631) 344-7306 The Group:
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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.
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| Research Interests: |
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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 imageto view the 3-Beam Diffractometer in action. |
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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. |
| Publications: |
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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. Feb 15;283(7):4115-23 (2008). PubMed |
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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 |
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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 |
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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 |
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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). |
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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 |
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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 |
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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 |
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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 |
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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). |
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Makowski L. and Soares A. Estimating the diversity of peptide populations from limited sequence data. Bioinformatics 19(4), 483-489 (2003). PbMed Full Text |
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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). PbMed Full Text |
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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). PbMed |
| In Preparation: |
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Soares AS, and Caspar DLD. X-ray diffraction measurement of cosolvent accessible volume in rhombohedral insulin crystals. In preparation for submission to Biophysical Journal. |
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Soares AS, Weckert E, and Sweet RM. Choosing optimal parameters for modeling and refinement of water molecules against x-ray data. In preparation for submission to Acta Cryst. D. |
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Soares AS, Héroux A, and Sweet RM. Optimal data truncation at I/sigma = 1.5 reduces the incidence of 'ghost' water molecules. In preparation for submission to Acta Cryst. D. |
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| Updated Feb. 12, 2008 |
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