NDLI: Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation

Content Provider	Springer Nature Link
Author	Liu, Qianjun Hu, Guodong Cao, Zanxia Wang, Jihua Chen, Haifeng
Copyright Year	2015
Abstract	DSS1 is a small acidic intrinsically disordered protein (IDP) that can fold upon binding with PCID2 TREX-2. The resulting complex plays a key role in mRNA export. However, the binding mechanism between DSS1 and PCID2 is unsolved. Here, three independent 500-ns molecular dynamics (MD) simulations were performed to study the DSS1–PCID2 binding mechanism by comparing apo-PCID2 and bound PCID2. The results show that the conformational variation of bound PCID2 is smaller than that of apo-PCID2, especially in the binding domain of two helices (helix IV and VIII). The probability of coil formation between helix III and helix IV of bound PCID2 increases, and a short anti-parallel β-sheet forms upon DSS1 binding. The decomposition of binding free energy into protein and residue pairs suggests that electrostatic and hydrophobic interactions play key roles in the recognition between DSS1 and PCID2. There is a hydrophobic core of seven residues in DSS1 favorable to the binding of PCID2. These analytical methods can be used to reveal the recognition mechanisms of other IDPs and their partners. Figure Differences of second structure of PCID2 in bound and unbound states. The interaction surface between the helix VIII of PCID2 and helix of DSS1
Starting Page	1
Ending Page	9
Page Count	9
File Format	PDF
ISSN	16102940
Journal	Journal of Molecular Modeling
Volume Number	21
Issue Number	5
e-ISSN	09485023
Language	English
Publisher	Springer Berlin Heidelberg
Publisher Date	2015-04-26
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	PCID2 protein Molecular dynamics simulation Conformational changes Binding free energy Computer Applications in Chemistry Molecular Medicine Computer Application in Life Sciences Characterization and Evaluation of Materials Theoretical and Computational Chemistry
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Physical and Theoretical Chemistry Computational Theory and Mathematics Catalysis Inorganic Chemistry Computer Science Applications

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation

Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation

Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics

Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes

Role of pH in structural changes for Pin1 protein: an insight from molecular dynamics study

Entropy versus aromaticity in the conformational dynamics of aromatic rings

Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants

Molecular dynamics simulation of temperature induced unfolding of animal prion protein

Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation

Similar Documents

Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations

Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation

Insights into scFv:drug binding using the molecular dynamics simulation and free energy calculation

Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics

Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes

Role of pH in structural changes for Pin1 protein: an insight from molecular dynamics study

Entropy versus aromaticity in the conformational dynamics of aromatic rings

Conformational dynamics of threonine 195 and the S1 subsite in functional trypsin variants

Molecular dynamics simulation of temperature induced unfolding of animal prion protein

Conformational stability of PCID2 upon DSS1 binding with molecular dynamics simulation