TitleMacromolecular association equilibria
NameLapelosa, Mauro (author), Levy, Ron M (chair), Arnold, Eddy (internal member), Gallicchio, Emilio (internal member), Bromberg, Yana (outside member), Rutgers University, Graduate School - New Brunswick,
SubjectComputational Biology and Molecular Biophysics,
HIV (Viruses) ,
DescriptionProteins are dynamical entities and they can be studied exploring statistical ensembles of conformations rather than discrete states. The dynamics of proteins can be investigated using advanced sampling techniques such as Replica Exchange Molecular Dynamics (REMD). We have used REMD to study the population of ensembles of ELDKWA epitopes coming from the membrane proximal region (MPER) of gp41, which is a protein of the human immunodeficiency virus (HIV). The epitope has been inserted onto a surface loop of a rhinovirus (HRV), the common cold virus, and the design work was aimed at finding chimeric constructs able to present the epitope in an optimal conformation which would increase the antigenic characteristics of the chimeric HRV for 2F5, a broadly neutralizing antibody of HIV. Indeed, this was carried out in an attempt to build a chimeric construct able to trigger an immune response against HIV-1. The experimental part followed the computational design and led to good binding affinities for chimeric HRVs designed in silico. Computational and experimental results were in general agreement. This is relevant because it is a well designed use of molecular dynamics for protein design in order to develop vaccine constructs able to bind to a HIV broadly neutralizing antibody such as 2F5. From the epitope-antibody interactions we started to develop ideas about free energy in molecular associations and we moved our attention to free energy calculation methods. This led to the development of a binding energy distribution analysis method (BEDAM) to calculate the standard binding free energy. BEDAM was tested on a T4 lysozyme protein. The calculations were performed with a set of known binders and non-binders of the L99A and L99A/M102Q mutants of T4 lysozyme receptor. We also studied the dependence of binding volume on the free energy calculated by BEDAM and we showed that the free energy converged at an optimal value of the binding volume. The method was able to discriminate without error binders from non-binders, and the computed standard binding free energies of the binders are found to be in good agreement with experimental measurements. Finally, we also carried out BEDAM calculations on a pharmaceutical target, the FKBP12 protein, and we analyzed binding energies distributions and transitions from unbound to bound states.
NoteIncludes bibliographical references
Noteby Mauro Lapelosa
CollectionGraduate School - New Brunswick Electronic Theses and Dissertations
Organization NameRutgers, The State University of New Jersey
RightsThe author owns the copyright to this work.