Re: [ccp4bb] [External] Re: [ccp4bb] protein DNA complex structure and extension of DNA structure
Dear Dhiraj, I believe the solution is using combination of our dnatco.datmos.org description of nucleic acid conformations (so called NtC) and the MMB (MacroMoleculeBuilder, the github version implements NtC modeling). Contact me if you need more details. best, JC On 01. 01. 22 18:38, Srivastava, Dhiraj wrote: Thank for the suggestion. I think I should have been more specific about the problem. The promoter has binding site for two different transcription factors which interacts with each other to affect the transcription in spatiotemporal manner. I solved the structure of one protein (not deposited in PDB yet) which shows DNA bending. I am curious to see how this DNA bending affect the conformation of DNA nearby thus potentially affecting the binding of other transcription factor through DNA mediated allosterism. Off-course I am going to do simulation after extending the DNA. Since DNA is bend, I can not simply extend it using ideal DNA double helix conformation. How can I extend it computationally? x3DNA will work but needs pdb id. Thanks Dhiraj From: Phoebe A. Rice <mailto:pr...@uchicago.edu> Sent: Saturday, January 1, 2022 11:01 AM To: Srivastava, Dhiraj <mailto:dhiraj-srivast...@uiowa.edu>; CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [External] Re: [ccp4bb] protein DNA complex structure and extension of DNA structure I would try the tools on this site - http://web.x3dna.org/index.php/protein From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of "Srivastava, Dhiraj" <mailto:dhiraj-srivast...@uiowa.edu> Reply-To: "Srivastava, Dhiraj" <mailto:dhiraj-srivast...@uiowa.edu> Date: Monday, December 27, 2021 at 8:32 PM To: "CCP4BB@JISCMAIL.AC.UK"<mailto:CCP4BB@JISCMAIL.AC.UK> <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] protein DNA complex structure and extension of DNA structure Hi I solved the structure of protein DNA complex where the DNA molecule is bent. I want to extend the DNA computationally so I can model two DNA binding proteins together on same DNA molecule. is there a way by which I can extend the DNA in both direction? its easy to do it with ideal DNA molecule but I don't know how to do it with bent DNA. Thank you Dhiraj To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 - Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [External] Re: [ccp4bb] protein DNA complex structure and extension of DNA structure
Thank for the suggestion. I think I should have been more specific about the problem. The promoter has binding site for two different transcription factors which interacts with each other to affect the transcription in spatiotemporal manner. I solved the structure of one protein (not deposited in PDB yet) which shows DNA bending. I am curious to see how this DNA bending affect the conformation of DNA nearby thus potentially affecting the binding of other transcription factor through DNA mediated allosterism. Off-course I am going to do simulation after extending the DNA. Since DNA is bend, I can not simply extend it using ideal DNA double helix conformation. How can I extend it computationally? x3DNA will work but needs pdb id. Thanks Dhiraj From: Phoebe A. Rice Sent: Saturday, January 1, 2022 11:01 AM To: Srivastava, Dhiraj ; CCP4BB@JISCMAIL.AC.UK Subject: [External] Re: [ccp4bb] protein DNA complex structure and extension of DNA structure I would try the tools on this site - http://web.x3dna.org/index.php/protein From: CCP4 bulletin board on behalf of "Srivastava, Dhiraj" Reply-To: "Srivastava, Dhiraj" Date: Monday, December 27, 2021 at 8:32 PM To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] protein DNA complex structure and extension of DNA structure Hi I solved the structure of protein DNA complex where the DNA molecule is bent. I want to extend the DNA computationally so I can model two DNA binding proteins together on same DNA molecule. is there a way by which I can extend the DNA in both direction? its easy to do it with ideal DNA molecule but I don't know how to do it with bent DNA. Thank you Dhiraj To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] protein DNA complex structure and extension of DNA structure
I would try the tools on this site - http://web.x3dna.org/index.php/protein From: CCP4 bulletin board on behalf of "Srivastava, Dhiraj" Reply-To: "Srivastava, Dhiraj" Date: Monday, December 27, 2021 at 8:32 PM To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] protein DNA complex structure and extension of DNA structure Hi I solved the structure of protein DNA complex where the DNA molecule is bent. I want to extend the DNA computationally so I can model two DNA binding proteins together on same DNA molecule. is there a way by which I can extend the DNA in both direction? its easy to do it with ideal DNA molecule but I don't know how to do it with bent DNA. Thank you Dhiraj To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] protein DNA complex structure and extension of DNA structure
Hi I solved the structure of protein DNA complex where the DNA molecule is bent. I want to extend the DNA computationally so I can model two DNA binding proteins together on same DNA molecule. is there a way by which I can extend the DNA in both direction? its easy to do it with ideal DNA molecule but I don't know how to do it with bent DNA. Thank you Dhiraj To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
