Computational Biomolecular Physics for Studies of Intermolecular Interactions

The binding sites of the carcinogen BPDE to the K-ras onco-gene have been determined at the CBMP facility via computational methods. [Deligkaris and Rodriguez, PCCP (2014)] The binding sites of the carcinogen BPDE to the K-ras onco-gene have been determined at the CBMP facility via computational methods. [Deligkaris and Rodriguez, PCCP (2014)]

The Biophysical Analysis Laboratory (BAL) includes, among others, instrumentation for isothermal titration calorimetry (ITC). In addition to its core experimental approaches, BAL partners with Purdue’s Computational Biomolecular & Mesoscopic Physics (CBMP) group to further investigate intermolecular interactions via computational methods. High performance computation performed by the CBMP group, in coordination with BAL, can provide insight at the atomistic and molecular levels about the physico-chemical origins of biomolecular interactions. Microscopic interpretation of thermodynamic (ITC) data can be obtained by complementary semiempirical  and ab-initio calculations at the atomistic and molecular levels. The CBMP and BAL facilities also have interest in linking biophysical and quantum chemical computation to surface plasmon resonance (SPR) and bio-layer interferometry (BLI).  For additional information on computational studies relevant to BAL’s work on biochemical and life sciences please visit the CBMP at:

The BAL and CBMP facilities aim to collaborate with Bindley users and researchers to analyze experimental data using the latest biophysical and biochemical computational models. For further information please contact Dr. Jia Ma at BAL ( or Prof. Jorge H. Rodriguez at CBMP (

Protocols for Analytical Ultracentrifugation Sample Preparation

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  1. Provide recipe of buffer used and protein sequence to
  2. Prior to the analytical ultracentrifuge runs, the sample MUST be dialyzed overnight. Submitted sample volume should be 500 μl. The last dialysis buffer will be your reference for the experiments. Please provide 15 ml of dialysis buffer.
  3. For accurate determination of molecular weight, oligomeric state and interactions, provide three (3) different concentrations for each sample. For example, a concentration series is 0.25 mg/mL, 0.50 mg/mL, and 1.00 mg/mL. Ensure that the absorbance at 280nm (or whatever wavelength desired) is not less than 0.25 at the lowest concentration, and does not exceed 1.00 at the highest concentration.
  4. Interference optics along with absorbance at 280 nm will be used to collect the data. The interference optics is extremely sensitive to mismatched buffers.
  5. DTT, 2-mercaptoethanol, protease inhibitors and detergents will interfere with the analysis; please try to avoid. If DTT is absolutely required to maintain sample stability, then do not exceed ~ 0.5 - 1 mM concentration. When detergents and lipids are needed, please contact me before you bring in the samples.
  6. Samples will be stored at 4 C and run at 20 C, unless otherwise specified.
  7. A general sample preparation protocol from Dr. Peter Schuck's Lab is available.
Protocol for Mass Spectometry Sample Preparation

Protocols for Analytical Ultracentrifugation Sample Preparation:

Analytical Ultracentrifugation



Jia Ma
Biophysical Analysis Laboratory Facility Director
Phone: (765) 496-6533

Purdue University, 610 Purdue Mall, West Lafayette, IN 47907, (765) 494-4600

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