NDLI: Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

Please wait, while we are loading the content...

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

HIV-1Lai genomic RNA: combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin

Plasmalemmal concentration and affinity of mouse vascular endothelial cadherin, VE-cadherin

Two processes lead to a stable all-trans and 13-cis isomer equilibrium in dark-adapted bacteriorhodopsin; effect of high pressure on bacteriorhodopsin, bacteriorhodopsin mutant D96N and fluoro-bacteriorhodopsin analogues

Evidence of quasi-linear gas transport through sperm whale myoglobin

Effects of membranotropic agents on mono- and multilayer structures of dipalmitoylphosphatidylcholine

Membrane water-penetration profiles from spin labels

European Biophysics Journal : Volume 31, Issue 6, October 2002

European Biophysics Journal : Volume 31, Issue 5, August 2002

European Biophysics Journal : Volume 31, Issue 4, July 2002

European Biophysics Journal : Volume 31, Issue 3, June 2002

European Biophysics Journal : Volume 31, Issue 2, May 2002

European Biophysics Journal : Volume 31, Issue 1, March 2002

European Biophysics Journal : Volume 30

European Biophysics Journal : Volume 29

European Biophysics Journal : Volume 28

European Biophysics Journal : Volume 27

European Biophysics Journal : Volume 26

European Biophysics Journal : Volume 25

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

Content Provider	Springer Nature Link
Author	Antes, Iris Thiel, Walter van Gunsteren, Wilfred F.
Copyright Year	2002
Abstract	Photoactive yellow protein (PYP) is a prototype of the PAS domain superfamily of signaling proteins. The signaling process is coupled to a three-state photocycle. After the photoinduced trans-cis isomerization of the chromophore, 4-hydroxycinnamic acid (pCA), an early intermediate (pR) is formed, which proceeds to a second intermediate state (pB) on a sub-millisecond time scale. The signaling process is thought to be connected to the conformational changes upon the formation of pB and its recovery to the ground state (pG), but the exact signaling mechanism is not known. Experimental studies of PYP by solution NMR and X-ray crystallography suggest a very flexible protein backbone in the ground as well as in the signaling state. The relaxation from the pR to the pB state is accompanied by the protonation of the chromophore's phenoxyl group. This was found to be of crucial importance for the relaxation process. With the goal of gaining a better understanding of these experimental observations on an atomistic level, we performed five MD simulations on the three different states of PYP: a 1 ns simulation of PYP in its ground state [pG(MD)], a 1 ns simulation of the pR state [pR(MD)], a 2 ns simulation of the pR state with the chromophore protonated (pRprot), a 2 ns simulation of the pR state with Glu46 exchanged by Gln (pRGln) and a 2 ns simulation of PYP in its signaling state [pB(MD)]. Comparison of the pG simulation results with X-ray and NMR data, and with the results obtained for the pB simulation, confirmed the experimental observations of a rather flexible protein backbone and conformational changes during the recovery of the pG from the pB state. The conformational changes in the region around the chromophore pocket in the pR state were found to be crucially dependent on the strength of the Glu46-pCA hydrogen bond, which restricts the mobility of the chromophore in its unprotonated form considerably. Both the mutation of Glu46 with Gln and the protonation of the chromophore weaken this hydrogen bond, leading to an increased mobility of pCA and large structural changes in its surroundings. These changes, however, differ considerably during the pRGln and pRprot simulations, providing an atomistic explanation for the enhancement of the rate constant in the Gln46 mutant.
Starting Page	504
Ending Page	520
Page Count	17
File Format	PDF
ISSN	01757571
Journal	European Biophysics Journal
Volume Number	31
Issue Number	7
e-ISSN	14321017
Language	English
Publisher	Springer-Verlag
Publisher Date	2002-10-18
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biophysics/Biomedical Physics Cell Biology Biochemistry Plant Physiology Animal Physiology Neurobiology
Content Type	Text
Resource Type	Article
Subject	Medicine Biophysics

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

Protonation/Deprotonation Reactions Triggered by Photoactivation of Photoactive Yellow Protein from Ectothiorhodospira halophila

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers

Engineering Photocycle Dynamics CRYSTAL STRUCTURES AND KINETICS OF THREE PHOTOACTIVE YELLOW PROTEIN HINGE-BENDING MUTANTS

Mimic of Photocycle by a Protein Folding Reaction in Photoactive Yellow Protein

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments

Photoactive Yellow Protein Terahertz Response: Hydration, Heating and Intermediate States

Molecular dynamics simulations and membrane protein structure quality

Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP)

The Two Photocycles of Photoactive Yellow Protein fromRhodobacter sphaeroides

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation

Similar Documents

Protonation/Deprotonation Reactions Triggered by Photoactivation of Photoactive Yellow Protein from Ectothiorhodospira halophila

Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers

Engineering Photocycle Dynamics CRYSTAL STRUCTURES AND KINETICS OF THREE PHOTOACTIVE YELLOW PROTEIN HINGE-BENDING MUTANTS

Mimic of Photocycle by a Protein Folding Reaction in Photoactive Yellow Protein

Acyl chain order parameter profiles in phospholipid bilayers: computation from molecular dynamics simulations and comparison with 2H NMR experiments

Photoactive Yellow Protein Terahertz Response: Hydration, Heating and Intermediate States

Molecular dynamics simulations and membrane protein structure quality

Neutron and X-ray structural studies of short hydrogen bonds in photoactive yellow protein (PYP)

The Two Photocycles of Photoactive Yellow Protein fromRhodobacter sphaeroides

Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation