Ariel Fernandez
- Visiting Professor
- Department of Computer Science
Contact Information
KARL F. HASSELMANN CHAIR IN ENGINEERING,
PROFESSOR OF BIOENGINEERING, RICE UNIVERSITY
Department of Bioengineering
Rice University
Houston, TX 77005
Adjunct Professor of Molecular Therapy, M. D. Anderson Cancer Center
Adjunct Professor of Computer Science, The University of Chicago
Department of Computer Science
Ryerson Hall # 258
The University of Chicago
Chicago, Illinois 60637
E-mail: ariel@uchicago.edu
Office: 258 Ryerson Hall
Phone: 317 278 9219
Fax: 317 278 9217
ariel@uchicago.edu
Personal Homepage
http://www.owlnet.rice.edu/~arifer/
Research
Prof. Ariel Fernández (born April 8, 1957) is interested in cooperativity and many body problems associated with biopolymer folding and interactions. He introduced the concept of structural wrapping and established its importance in the realms of protein interactivity, network centrality, molecular disease and drug discovery. The implications of the wrapping concept for biotechnology are sketched in the following contributions:Ariel Fernández: "Keeping Dry and Crossing Membranes". Nature Biotechnology 22, 1081-1084 (2004).
Ariel Fernández et al.:"An anticancer C-Kit inhibitor is re-engineered to make it more active and less cardiotoxic". Journal of Clinical Investigation 117, 4044-4054 (2007).
His current research interests are centered in understanding how proteins may enhance their interactive versatility while their fold remains conserved. In this regard, his contributions to systems biology stem from his biostructural physico-chemical background. His most recent publications along these lines are:
Ariel Fernández: "Functionality of wrapping defects in soluble proteins: What cannot be kept dry must be conserved". Journal of Molecular Biology 337, 477-484 (2004)
Ariel Fernández, L. Ridgway Scott and R. Stephen Berry: "The nonconserved wrapping of conserved folds reveals a trend towards increasing connectivity in proteomic networks". Proceedings of the National Academy of Sciences, USA 101, 2823-2827 (2004)
Ariel Fernández and R. Stephen Berry: "Molecular dimension explored in evolution to promote proteomic complexity". Proceedings of the National Academy of Sciences, USA 101, 13460-13465 (2004)
Florin Despa, Ariel Fernández and R. Stephen Berry: “Dielectric modulation of biological water”. Physical Review Letters 93, 228104 (4 pages) (2004); Featured in Nature (News and Views) 432, 688 (2004)
Ariel Fernández has also introduced the paradigm of "inhibitor as a wrapper of packing defects in proteins", a concept of paramount importance in drug discovery. One of his recent contributions in this realm is:
Ariel Fernández, Kristina Rogale, Ridgway Scott and Harold A. Scheraga: "Inhibitor design by wrapping packing defects in HIV-1 proteins", Proceedings of the National Academy of Sciences USA 101, 11640-11645 (2004).
Grant support for 2005
NIH Grant Award 1R01 GM072614-01A1 from the National Institute of General Medical Sciences (NIGMS).
PI: Ariel Fernandez.
Title: “Protein packing defects as functional markers and drug targets”.
Amount of Award: $1.4 million direct costs over a four-year period.
Publications for 2005
1. Ariel Fernández: “Direct nanoscale dehydration of hydrogen bonds”. Journal of Physics D, Applied Physics 38, 2928-2932 (2005).
2. Vladimir N. Uversky, Ariel Fernández and Anthony L. Fink. “Structural and conformational prerequisites of amyloidogenesis”. In: Protein Misfolding, Aggregation and Conformational Diseases. Vol. I: Protein Aggregation and Conformational Diseases (Uversky V.N., Fink A.L., Eds.) Kluwer Academic/Plenum Publishers, New York, USA, in press (2005).
3. Ariel Fernández: “Protein function with concurrent promiscuity”, Opinions and Commentary, Journal of Biomolecular Structure & Dynamics 22, 615-624 (2005).
4. Ariel Fernández: “Incomplete protein packing as a selectivity filter in drug design”. Structure 13, 1829-1836(2005).
5. Ariel Fernández: “The integrated development of network complexity modulates the diverse evolutionary mutation rates of individual proteins”, FEBS Letters (Fed. Eur. Biochem. Soc.) 579, 5718-5722 (2005).
6. Ariel Fernández: “What factor drives the fibrillogenic association of beta-sheets? FEBS Letters (Fed. Eur. Biochem. Soc.) 579, 6635-6640 (2005).
Education
M. Sc., M. Phil., Ph. D., Yale University, 1982-1984 (fastest awarded Ph. D. in Yale history).
Sr. Research Scientist, Max-Planck-Institut fuer biophysikalische Chemie, Abteilung Manfred Eigen, Goettingen, Germany, 1986-1989.
Research Associate (1985-1987), Visiting Senior Research Scientist (1994-1996), Princeton University.
Licenciado en Matematica (1980), Quimico (1979), Universidad Nacional del Sur, Argentina.
Ariel Fernández has contributed to a wide spectrum of research areas: Algebra, Representation Theory, Statistical Mechanics, Chemical Physics, Polymer Physics, Dissipative Systems, Molecular Biophysics, Interactive Proteomics and Integrative Biology. He has also perfomed and reported experimental work.
Awards and Appointments
Elected Fellow, American Institute for Medical and Biological Engineering (2006)
Camille and Henry Dreyfus Teacher-Scholar Awardee, 1991
Camille and Henry Dreyfus Distinguished New Faculty Awardee, 1989
John S. Guggenheim Memorial Foundation Fellow, 1995-1996
Consultant to U.S. Federal Government, NIH, Special Panel on Centers of Excellence in Systems Biology, 2003-
Visiting Senior Researcher, Max-Planck-Institut fuer Biochemie, Abteilung Robert Huber, Martinsried, Germany, 2000-
Visiting Senior Scientist, Institute for Nonlinear Science, University of California at San Diego, 1989
Editorial Board Member, Journal of Biological Physics and Chemistry, Basel, Switzerland, 2000-
Guest Professor, Institute for Protein Research, Osaka University, Japan, 2003
Fulbright Scholar, US Information Agency, 1999 and Fulbright Fellow, 1981
McKnight Fellow, USA, 1989
Alexander von Humboldt and Max Planck Society Scholar, Goettingen, Germany (1987-1989)
Feinberg Fellow, Israel, 1984-1985
Full Professor and Principal Investigator, UNS and Natl. Res. Council of Argentina, 1994-
Associate Professor, Department of Chemistry, Coral Gables Campus and Department of Biochemistry and Molecular Biology, University of Miami Medical School, 1989-1994
Medal "State of Buenos Aires" to the best graduate, Argentina, 1980
Deputy Governor, American Biographical Institute, 1998-
Co-organizer and Proceedings Editor of the Miami Bio/Technology Winter Symposium, Nature-sponsored, 1993.
Additional
Selected recent publicationsAriel Fernandez has published 302 research articles.
1.Ariel Fernandez: "Keeping Dry and Crossing Membranes". Nature Biotechnology 22, 1081-1084 (2004).
2.Ariel Fernandez: "Functionality of wrapping defects in soluble proteins: What cannot be kept dry must be conserved". Journal of Molecular Biology 337, 477-483 (2004).
3.Ariel Fernandez, L. Ridgway Scott and R. Stephen Berry: "The nonconserved wrapping of conserved folds reveals a trend towards increasing connectivity in proteomic networks". Proceedings of the National Academy of Sciences, USA 101, 2823-2827 (2004).
4.Ariel Fernandez, Kristina Rogale, L. Ridgway Scott and Harold A. Scheraga: "Inhibitor design by wrapping packing defects in HIV-1 proteins". Proceedings of the National Academy of Sciences, USA 101, 11640-11645 (2004).
5.Ariel Fernandez and Harold A. Scheraga: "Insufficiently dehydrated hydrogen bonds as determinants for protein interactions", Proceedings of the National Academy of Sciences, USA 100, 113-118 (2003).
6.Ariel Fernandez and R. Stephen Berry: "Proteins with hydrogen-bond packing defects are highly interactive with lipid bilayers: Implications for amyloidogenesis", Proceedings of the National Academy of Sciences, USA 100, 2391-2396 (2003).
7.Ariel Fernandez and Ridgway Scott: "Adherence of packing defects in soluble proteins", Physical Review Letters 91, 018102, 4 pages (2003).
8.Ariel Fernandez, Jozsef Kardos, Ridgway Scott, Yuji Goto and R. Stephen Berry: "Structural defects and the diagnosis of amyloidogenic propensity", Proceedings of the National Academy of Sciences,USA 100, 6446-6451 (2003).
Some Lectures
Ariel Fernández has been an invited speaker at numerous leading institutions of learning and research: Yale U. (1988); U. of Chicago (2001); Cornell U. (2002); Burroughs-Wellcome Lecturer, Univ. of Chicago (2002); Argonne Natl. Labs. (2001); Max-Planck-Institut fuer Biochemie (1999-) MPI biophysikalische Chemie (1988); Universitaet Zurich (1988); Universitaet Goettingen, Germany (1988); Universities of Tokyo, Kobe and Osaka, Japan (June-August, 2002); Japan Atomic Energy Research Institute (Kizu-Minami/Nara, July, 2002); Physics Department/Computations in Science Seminar, University of Chicago (August 20, 2003), etc.
Most recent lectures
Osaka University, Institute for Protein Research, August, 2002; Unilever lecture at the University of Cambridge (UK), Chemical Laboratory, Biophysics Colloquia, December 10, 2003; lecture seminar at Eli Lilly Corporation, on January 27, 2004; presentation at the Dean’s Council meeting, IUPUI/Interactive Intelligence Co., Indianapolis, April 30, 2004; lecture at the Center for Genomics and Bioinformatics, Indiana University/Bloomington, on May 19, 2004; Charles University, Prague, Czech Republic, June, 2004; NIH / National Cancer Institute, Frederick, Maryland, June, 2004; Indiana University, Bloomington, Indiana, Chemistry Department, September, 2004; State University of New York, Chemistry and Biological Sciences; Albany, 2005, 14th Conversation (6/05).
Projects
Laboratories
List of Publications
Available in PDF.