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The Cramer Lab

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        Molecular Bioprocessing Research

 

      Research

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chromatography

Chromatography

Batch and column chromatography are used extensively in our laboratory to generate isotherm parameters and protein retention models for a variety of chromatographic resins including ion exchange, hydrophobic interaction, hydroxyapatite, and multimodal resins. High-throughput batch chromatography experiments have been used to screen protein binding interactions and selectivity with a variety of resin libraries and fluid phase binding and elution conditions. We employ both isocratic and gradient elution modes in our column chromatography studies in order to develop predictive models of protein retention behavior. Chromatographic studies have been carried out using diverse protein libraries as well as homologous series of proteins.

 

NMR

Nuclear Magnetic Resonance (NMR)

Nuclear magnetic resonance is widely employed for protein structure determination and protein-target interactions. In our studies, two-dimensional heteronuclear single quantum correlation experiments are employed to study the interactions of proteins with ion exchange and multimodal chromatographic ligands in solution. This technique makes it possible to identify the ligand interaction sites on a protein surface and the apparent binding affinities for each amino acid residue. Saturation transfer difference (STD) NMR experiments are routinely used for examining protein-ligand binding in solution and this technique is often used as an initial screening technique for evaluating the chemical moieties involved in binding.

 

md

Molecular Simulations

With the exponential increase in computing power in the last decade, computer simulations have become a very important tool to study molecular phenomena. Our lab employs Molecular Dynamics (MD) simulations to evaluate the binding behavior of multimodal ligands with proteins. The major goal of these studies is to provide a fundamental understanding of interactions between multimodal ligands and proteins. The two major thrust areas are the investigation of synergism present in multimodal systems and the role of fluid phase modifiers in modulating the interactions between proteins and multimodal ligands. 

 

colmod

Column Modeling

Column modeling has been a major area of research of the Cramer group. We have worked on modeling ion exchange, displacement, immobilized metal affinity and hydrophobic interaction chromatography.  The ability to effectively model chromatographic profiles can give many insights into the fundamentals and mechanisms of the chromatographic process as well as being used as a powerful predictive tool. It can also help to explore experimental conditions much faster than experimental methods without the need for large quantities of materials mechanisms of the particular process. 

 

QSAR

Quantitative Structure Property Relationships (QSPR)

QSPR is powerful analytical method for breaking down a molecule into a series of numerical values describing its relevant chemical and physical properties (e.g. charge density, hydrophobic surface area, etc.). By calculating these numerical descriptors for ligands and/or their protein targets, we use machine-learning methods to generate models that have predicted the retention of proteins on a variety of chromatography systems (ion-exchange, hydrophobic interaction, hydroxyapatite). Currently, we are developing a novel set of descriptors, based on the insights gained from MD simulations, to predict retention behavior of proteins in multimodal systems. Using the descriptors generated in our group, we are also generating machine-learning models to predict the binding affinity for novel peptides generating using high-thoughput systems.

 

Smart Biopolymer Affinity Precipitation Systems (with Wilfred Chen, UDel)

Development of an ELP based smart biopolymer fusion protein affinity precipitation systems for purification of antibodies and new classes of biopharmaceuticals. Our aim is to determine the robustness and scalability of these purification systems. We employ robotic HTS techniques to investigate the effect of a variety of operating conditions on antibody yield, purity and quality at various stages of the process. Additionally, various microscopy techniques are used to characterize the PSDs of the precipitates.

 

 

QSAR

Other techniques

We have employed several other techniques, including Atomic Force Microscopy (AFM), Quartz Crystal Microbalance (QCM), Isothermal Titration Calorimetry (ITC) and Surface Plasmon Resonance (SPR), to study the thermodynamics and kinetics of protein interactions with chromtographic ligands under various conditions.

 

 

 

Rensselaer Polytechnic Institute | Troy, NY 12180-3590