[ccp4bb] pKa and electrostatic affinity

Dear colleagues: I was wondering if you could kindly share your thoughts and help me understand the relationship between pKa and affinity of a protein for a ligand. Are these two properties related? Specifically, does a lysine with a pKa of 8.5 have a greater affinity for a negatively charged

[ccp4bb] Summary on Aspartate pKa increase and catalysis

to predict protein ionization http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2578799/ 8. Fap1_BBRC.pdf Apologies if I missed out on any reference or critical point/s raised in the discussion. Thank you. Deepak Oswal

[ccp4bb] On pKa of Aspartic acid

irrespective of whether the pKa is 3.8 or 6.44; isn’t that true? d) Have similar increase in pKa values observed for aspartic acids before? I would be grateful if anybody could explain or comment on the above queries. Deepak Oswal

[ccp4bb] activation of thiol group

Dear colleagues: We have a 1.4 Angstrom structure of an enzyme showing a water molecule enclosed in a triangular pocket formed by the hydroxyl oxygens of 2 serine residues and a sulfhydryl group of an essential cysteine. The water molecule is forming a 2.8 Angstrom hydrogen bond with each of the

[ccp4bb] Structure-function analysis

Dear colleagues: I am trying to interpret the results of the substitution of a Methionine with Alanine. Following is the kinetic data on the mutation - 1. Km increased by 0.5 fold 2. Vmax decreased by 3.5 fold 3. Kcat decreased by 4 fold 4. Kcat/Km decreased by 10 fold. 5. Activity at saturating

Re: [ccp4bb] Structure-function analysis

, at 10:43 AM, Deepak Oswal wrote: Dear colleagues: I am trying to interpret the results of the substitution of a Methionine with Alanine. Following is the kinetic data on the mutation - 1. Km increased by 0.5 fold 2. Vmax decreased by 3.5 fold 3. Kcat decreased by 4 fold 4. Kcat/Km decreased