Re: [ccp4bb] Assays for protein-ligand interaction?

2014-01-13 Thread Lorenzo Finci
Ho Jun Lee, Have you thought about differential scanning fluorimetry (Thermofluor)? With this biophysical technique you can characterize protein-ligand interactions and screen a wide variety of ligands using minimal concentration of ligand and protein. All you need is a quantitative PCR

Re: [ccp4bb] How to slow down crystallization? Need hep!

2013-02-25 Thread Lorenzo Finci
Feng Lei, I would personally recommend slowing down the process of nucleation either by lowering the temperature of crystallization or by utilizing Al's oil. These are two powerful ways to slow the overall kinetics of crystallization. Here is a relevant reference for you:

[ccp4bb] Postdoctoral Position in Structural Immunology at Harvard Medical School

2012-11-12 Thread Lorenzo Finci
Dear All, On behalf of Dr. Jia-huai Wang, I post this message. For inquiries please contact Dr. Wang directly at jw...@red.dfci.harvard.edu Postdoctoral Position in Structural Biology of Immune Receptors: There is an immediate opening for a postdoctoral position in protein crystallography at

Re: [ccp4bb] calculation of cavities within crystal protein

2012-08-10 Thread Dr. Lorenzo Finci
On Thu, 9 Aug 2012 10:05:19 -0400, Dr. Lorenzo Finci lfi...@hotmail.com wrote: Danilo, The protein cavity can be analyzed utilizing the program Voidoo ( Kleywegt GJ, 1994). This program uses an atomic-flattening algorithm based on a 3-dimensional grid to locate and delineate different

Re: [ccp4bb] calculation of cavities within crystal protein

2012-08-09 Thread Dr. Lorenzo Finci
Danilo, The protein cavity can be analyzed utilizing the program Voidoo ( Kleywegt GJ, 1994). This program uses an atomic-flattening algorithm based on a 3-dimensional grid to locate and delineate different cavities. A Van Der Waals cavity can further be generated with a probe radius with a

[ccp4bb] Protein-Protein Interactions

2012-08-02 Thread Dr. Lorenzo Finci
Dear Colleagues, I have a question for all of you bioinformatics oriented structural biologists: How do I predict the sites of protein-protein interactions between two receptors that have been proven to interact biochemically but lack specific details regarding proximity. This is not a

Re: [ccp4bb] off topic Thermal shift assay

2012-07-20 Thread Dr. Lorenzo Finci
. Lorenzo Finci wrote:

Re: [ccp4bb] off topic Thermal shift assay

2012-07-19 Thread Dr. Lorenzo Finci
Anita, In terms of the basics:Thermodynamic stability of a protein is related to Gibbs Free Energy of unfolding. The Gibbs Free Energy is made of temperature, enthalpy and entropy (Delta G = Delta H - T Delta S). At Delta G equivalent to zero, the concentration of folded protein is equivalent

Re: [ccp4bb] Disulphide bonds and closed conformation

2012-07-11 Thread Dr. Lorenzo Finci
Jan, I agree that the DTNB assay (Ellman's Reagent) can be used to quantify exposed Cysteines. Alternatively, you could do site directed mutagenesis and mutate significant amino acids responsible for the conformational change from the open to the closed state, with hopes to lock the protein

Re: [ccp4bb] recommendations_on_purification

2012-03-26 Thread Lorenzo Finci
Petros, It has indeed been speculated that high concentrations of Magnesium and/or other metals present in the cell lysate effect the binding of the Histidine-tag, and thus specific conditions for binding and elution need to be optimized for specific elution of your target protein. I believe

Re: [ccp4bb] recommendations_on_purification

2012-03-26 Thread Lorenzo Finci
Etros, It has indeed been speculated that high concentrations of Magnesium and/or other metals present in the cell lysate effect the binding of the Histidine-tag, and thus specific conditions for binding and elution need to be optimized for specific elution of your target protein. I believe

[ccp4bb] Protein Biochemist - Peking University Beijing, China

2012-03-20 Thread Lorenzo Finci, Ph.D.
Protein Biochemist Position in Structural Neuroscience There is an immediate opening for an enthusiastic and experienced protein biochemist to join the international structural biology laboratory of Jia-Huai Wang based at Peking University in Beijing, China. The research is focused on the