Pulling proteins on a computer

Prof. Hernandez's group is using molecular dynamics simulations—a kind of numerical experiment—to help uncover the pathways and chararacterize the energetics for specific proteins. More specifically, they have calculated the work (or energy) to break a protein apart.

A driving force in the field of proteomics is the determination of structure and function. Although structure affects function, a protein’s function often takes place under nonequilibrium conditions in which the protein structure may be differ from its native form by a little or even a lot. The determination of protein function therefore requires an understanding of the possible confirmations of the protein and how it moves between them. Such motions are driven by forces and energetics. Theoretical and computational methods can reveal these motions by way of determining the energetics along typical protein pathways. Unfortunately, this problem is not so easy because proteins and the solvent molecules that surround them are made up of a large number of atoms that need to be tracked. Our group is using molecular dynamics simulations—a kind of numerical experiment—to help uncover the pathways and characterize the energetics for specific proteins. More specifically, we have calculated the work (or energy) to break a protein apart. This energetic work—called the potential of mean force (PMF)—has been obtained for two different proteins thus far: decaalanine and neuropeptide Y (NPY). Decaalanine is a small peptide with only 10 residues that takes on a helical structure. It presents a useful test of our methods—adaptive steered molecular dynamics (ASMD)—because its PMF in the gas phase is known. In addition, we were able to obtain the PMF in water. In so doing, we learned the degree to which the hydrogen bonding to water affects the restructuring of the protein. A lot! We will discuss the energetics and pathways of these and other proteins.

Dr. Rigoberto Hernandez

Gompf Family Professor Department of Chemistry, Johns Hopkins University & Director of the Open Chemistry Collaborative in Diversity Equity (OXIDE)

Dr. Rigoberto Hernandez

Dr. Rigoberto Hernandez is the Gompf Family Professor in the Department of Chemistry at the Johns Hopkins University as of July 2016, and remains as the Director of the Open Chemistry Collaborative in Diversity Equity (OXIDE) since 2011. Before Hopkins, he was a Professor in the School of Chemistry and Biochemistry at Georgia Tech, and Co-Director of the Center for Computational Molecular Science and Technology he co-founded. He holds a B.S.E. in Chemical Engineering and Mathematics from Princeton University (1989), and a Ph.D. in Chemistry from the University of California, Berkeley (1993).  (Hernandez was born in Güinez, Havana, Cuba but was raised and educated in the United States of America since he was in primary school. He is a U.S. citizen by birthright.)

Dr. Hernandez is the recipient of a National Science Foundation (NSF) CAREER Award (1997), Research Corporation Cottrell Scholar Award (1999), the Alfred P. Sloan Fellow Award (2000), a Humboldt Research Fellowship (2006-07), the ACS Award for Encouraging Disadvantaged Students into Careers in the Chemical Sciences (2014), the CCR Diversity Award (2015), and the RCSA Transformative Research and Exceptional Education (TREE) Award (2016).  He is a Fellow of the American Association for the Advancement of Science (AAAS, 2004), the American Chemical Society (ACS, 2010), and the American Physical Society (APS, 2011). In 2015-2016, he was a Phi Beta Kappa Visiting Scholar. At Georgia Tech, he served as the first Blanchard Assistant Professor of Chemistry (1999-2001), the first Goizueta Foundation Junior Rotating Faculty Chair (2002-07) and a Vasser Woolley Faculty Fellow (2011-13). His recent board memberships include the National Academies Panel within the Army Research Laboratory Technical Assessment Board (2005-2011), the National Academies Board on Chemical Sciences and Technology (2007-2010), the Telluride Summer Research Conference Board of Directors (2007-09), the NIH Study Section on Molecular Structure and Function B (MSFB, 2009-2013), the Research Corporation Cottrell Scholars Advisory Committee (member 2011-15, and chair 2016-17), the DOE Committee of Visitors (Division of Chemical Sciences, Geosciences and Bio-sciences, 2014) and the American Chemical Society Board of Directors (2014-2019).

Dr.Hernandez's research programs are currently funded by the NSF through a single-investigator grant and the CCI Center for Sustainable Nanomaterials. The OXIDE effort is cofunded by the NSF, DOE and NIH.

Research Interests

Dr. Hernandez’s research area can be broadly classified as the theoretical and computational chemistry of systems far from equilibrium.  This includes a focus on microscopic reaction dynamics and their effects on macroscopic chemical reaction rates in arbitrary solvent environments.  His current projects involve questions pertaining to the diffusion of mesogens in colloidal suspensions and liquid crystals, the structure and dynamics of assemblies of Janus and other patchy particles, fundamental advances in transition state theory, design principles for sustainable nanotechnologies and the dynamics of protein folding and rearrangement.