12 research outputs found
Conservation and Variation of Structural Flexibility in Protein Families
In this issue, Raimondi et al. (2010) obtained interesting insights concerning structural flexibilities in the Ras superfamily that are essential to both function retention and specialization by analyzing the deformation patterns from physical models of protein structure and from crystal structures of homologous proteins
Protein structural variation in computational models and crystallographic data
Normal mode analysis offers an efficient way of modeling the conformational
flexibility of protein structures. Simple models defined by contact topology,
known as elastic network models, have been used to model a variety of systems,
but the validation is typically limited to individual modes for a single
protein. We use anisotropic displacement parameters from crystallography to
test the quality of prediction of both the magnitude and directionality of
conformational variance. Normal modes from four simple elastic network model
potentials and from the CHARMM forcefield are calculated for a data set of 83
diverse, ultrahigh resolution crystal structures. While all five potentials
provide good predictions of the magnitude of flexibility, the methods that
consider all atoms have a clear edge at prediction of directionality, and the
CHARMM potential produces the best agreement. The low-frequency modes from
different potentials are similar, but those computed from the CHARMM potential
show the greatest difference from the elastic network models. This was
illustrated by computing the dynamic correlation matrices from different
potentials for a PDZ domain structure. Comparison of normal mode results with
anisotropic temperature factors opens the possibility of using ultrahigh
resolution crystallographic data as a quantitative measure of molecular
flexibility. The comprehensive evaluation demonstrates the costs and benefits
of using normal mode potentials of varying complexity. Comparison of the
dynamic correlation matrices suggests that a combination of topological and
chemical potentials may help identify residues in which chemical forces make
large contributions to intramolecular coupling.Comment: 17 pages, 4 figure
A Departmental Focus on High Impact Undergraduate Research Experiences
Undergraduate research experiences have become an integral part of the Hamilton College chemistry experience. The major premise of the chemistry department’s curriculum is that research is a powerful teaching tool. Curricular offerings have been developed and implemented to better prepare students for the independence required for successful undergraduate research experiences offered during the academic year and the summer. Administrative support has played a critical role in our ability to initiate and sustain scholarly research programs for all faculty members in the department. The research-rich curriculum is built directly upon or derived from the scholarly research agendas of our faculty members. The combined strengths and synergies of our curriculum and summer research program have allowed us to pursue several programmatic initiatives
Role of Secondary Sialic Acid Binding Sites in Influenza N1 Neuraminidase
Role of Secondary Sialic Acid Binding Sites in Influenza N1 Neuraminidas
Synthesis, Characterization, and Computational Modeling of N-(1-Ethoxyvinyl)pyridinium Triflates, an Unusual Class of Pyridinium Salts
N-Substituted pyridinium salts constitute one of the most valuable reagent classes in organic synthesis, due to their versatility and ease of use. Herein we report a preliminary synthesis and detailed structural analysis of several N-(1-ethoxyvinyl)pyridinium triflates, an unusual class of pyridinium salts with potentially broad use as a reagent in organic synthesis. Treatment of pyridines with trifluoromethane sulfonic acid and ethoxyacetylene generates stable, isolable adducts which have been extensively characterized, due to their novelty. Three-dimensional structural stability is perpetuated by an array of C–H•••O hydrogen bonds involving oxygen atoms from the –SO3 groups of the triflate anion, and hydrogen atoms from the aromatic ring and vinyl group of the pyridinium cation. Predictions from density functional theory calculations of the energy landscape for rotation about the exocyclic C–N bond of 2-chloro-1-(1-ethoxyvinyl)pyridine-1-ium trifluoromethanesulfonate (7) and 1-(1-ethoxyvinyl)pyridine-1-ium trifluoromethanesulfonate (16) are also reported. Notably, the predicted global energy minimum of 7 was nearly identical to that found within the crystal structure
A Departmental Focus on High Impact Undergraduate Research Experiences
Undergraduate research experiences have become an integral part of the Hamilton College chemistry experience. The major premise of the chemistry department\u27s curriculum is that research is a powerful teaching tool. Curricular offerings have been developed and implemented to better prepare students for the independence required for successful undergraduate research experiences offered during the academic year and the summer. Administrative support has played a critical role in our ability to initiate and sustain scholarly research programs for all faculty members in the department. The research-rich curriculum is built directly upon or derived from the scholarly research agendas of our faculty members. The combined strengths and synergies of our curriculum and summer research program have allowed us to pursue several programmatic initiatives