Biological assembly from the asymmetric unit and using it for MD
Hi, very basic question here. I found ways to generate the tetramer biological assembly starting from the monomer asymmetric unit . (Downloading the BA directly from RCSB and alternatively using the BU function in Chimera's Model panel). The procedures are equivalent AFAIU. Now, this generated structure should be a valid starting point for molecular dynamics simulations? Does anybody have experience with that?. There are other structures showing the tetramer, but the resolution is too low. Thanks! David.
Hi David, The assemblies defined in the Protein Databank are the most valid information available, i.e., I can’t think of what else you would use. There may be limitations from the resolution of the structure, as well as what the authors believe to be the biological assembly, but that will always be the case. Also if you are going to invest computational time on MD, presumably you will read carefully any publication that describes the structure (see the page for that entry at the RCSB PDB website for the reference). If you are concerned about the inferred stoichiometry (e.g. dimer or a tetramer?) you can use programs like PISA or look in databases like 3DComplex and PiQSi: <http://www.ccp4.ac.uk/pisa/> <http://www.3dcomplex.org/> <http://www.piqsi.org/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2020, at 8:07 PM, David Sáez <davidsaez@udec.cl> wrote:
Hi, very basic question here. I found ways to generate the tetramer biological assembly starting from the monomer asymmetric unit . (Downloading the BA directly from RCSB and alternatively using the BU function in Chimera's Model panel). The procedures are equivalent AFAIU. Now, this generated structure should be a valid starting point for molecular dynamics simulations? Does anybody have experience with that?. There are other structures showing the tetramer, but the resolution is too low. Thanks! David.
Dear Elaine, Many thanks for your reply. I already read the articles and I am sure the stoichiometry is correct. My concern was more related to the possible issues raised from an asymmetric unit smaller than the biological assembly (I have never seen this case before). But I was doing some research and expanding my very limited knowledge about crystallograhy, after removing some clashing solvent molecules, the MD should run OK. Thanks again for your help. David. On Wed, Feb 26, 2020 at 2:29 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi David, The assemblies defined in the Protein Databank are the most valid information available, i.e., I can’t think of what else you would use. There may be limitations from the resolution of the structure, as well as what the authors believe to be the biological assembly, but that will always be the case. Also if you are going to invest computational time on MD, presumably you will read carefully any publication that describes the structure (see the page for that entry at the RCSB PDB website for the reference).
If you are concerned about the inferred stoichiometry (e.g. dimer or a tetramer?) you can use programs like PISA or look in databases like 3DComplex and PiQSi:
<http://www.ccp4.ac.uk/pisa/> <http://www.3dcomplex.org/> <http://www.piqsi.org/>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 25, 2020, at 8:07 PM, David Sáez <davidsaez@udec.cl> wrote:
Hi, very basic question here. I found ways to generate the tetramer biological assembly starting from the monomer asymmetric unit . (Downloading the BA directly from RCSB and alternatively using the BU function in Chimera's Model panel). The procedures are equivalent AFAIU. Now, this generated structure should be a valid starting point for molecular dynamics simulations? Does anybody have experience with that?. There are other structures showing the tetramer, but the resolution is too low. Thanks! David.
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David Sáez -
Elaine Meng