Influence of the Methyl Groups on the Structure, Charge Distribution, and Proton Affinity of the Retinal Schiff Base

Tajkhorshid, Emad; Suhai, Sándor

doi:10.1021/jp983742b

Cited by 46 publications

(45 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The calculated interaction energies show that the water molecule binds stronger in NMB-water along NH side than the CH side. Further it can be seen in the Tables 1 and 2, the application of the DFT techniques result in the prediction of shorter single bonds and longer double bonds compared to HF method for these polyene Schiff base models, which confirms the results of Tajhorshid and Suhai [14] that the DFT calculations have overestimate the extend of the л-electronic delocalization in the polarized polyenes.…”

Section: Nmb-water Interaction: Geometries and Energeticssupporting

confidence: 81%

Structure, Stability and Interaction Studies on Schiff Base Analogue Systems

Kolandaivel

Kanakaraju²

2004

IJMS

View full text Add to dashboard Cite

Ab initio and density functional theory methods have been applied to study the molecular structure and interaction of water with N-methyl-2-propenylidenimine and Nmethyl-2-butenylidenimine molecules. The most possible reactive sites of the above molecules have been identified for the water interactions. The strength of the hydrogen bond is discussed using the atomic charges, which were calculated using the Mulliken population analysis and Natural population analysis schemes at MP2/6-31G* level of theory. The electron density (ρ) and laplacian of electron density (∇ 2 ρ) have been calculated for the possible existence of the hydrogen bonds with CH and CH3 groups of molecules using the "Atoms in molecules" approach. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed for the conformational stability of these molecules.

show abstract

Section: Nmb-water Interaction: Geometries and Energeticssupporting

confidence: 81%

Structure, Stability and Interaction Studies on Schiff Base Analogue Systems

Kolandaivel

Kanakaraju²

2004

IJMS

View full text Add to dashboard Cite

show abstract

“…The protein was embedded in a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membrane, surrounded by a water box, and neutralized by adding 150 mM NaCl. The system, comprising 55,708 atoms, was simulated at 310 K using a 2-fs timestep and NPT conditions with the CHARMM27 force field (40) and retinal parameters obtained from Hayashi et al (41)(42)(43)(44)(45). Long-range electrostatic forces were treated using the particle-mesh Ewald (PME) method.…”

Section: Methodsmentioning

confidence: 99%

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

Suomivuori

Gámiz‐Hernández

Sundholm

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na + pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521: [48][49][50][51][52][53]. To elucidate its molecular mechanism for Na + pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na + binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.bacterial ion pumps | bioenergetics | QM/MM | optogenetics | retinal P rimary biological energy conversion is based on the efficient capture and conversion of light and chemical energy into ion gradients across biological membranes (1, 2). The established gradients are used to thermodynamically drive energy-requiring processes, such as active transport and synthesis of adenosine triphosphate (ATP) (3, 4). The rhodopsin family of proteins catalyzes such reactions by harnessing the energy from retinal photoisomerization and deprotonation reactions, followed by conformational changes that further trigger the pumping of ions across the membrane (5). All previously known ion-pumping rhodopsins function either as inward chloride or outward proton pumps, but the structure of the first Na + pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2) (6), was recently resolved (7,8). In the absence of Na + ions, KR2 functions as an outward proton pump, similarly to bacteriorhodopsin (bR), but under physiological conditions, KR2 pumps Na + out of the cell (6, 9).KR2 shares the heptahelical transmembrane (7TM) structure common to all microbial rhodopsins (Fig. 1A) (5,7,8). In contrast to bR, however, where a highly conserved Asp-Thr-Asp (DTD) motif is used to pump protons, KR2 employs a unique NDQ motif comprising residues Asn112, Asp116, and Gln123 (6). In bR, Asp85 and Asp96 function as proton acceptors and donors for the protonated Schiff base (PSB), respectively, whereas in KR2, Asn112 and Gln123 occupy these positions, and Asp116 replaces Thr89. In analogy to bR, it has been suggested that Gln123 aids in capturing ions from the solvent and that Asn112 might be part of a Na + binding site (6,10).Similarly to other microbial rhodopsins, four photocycle intermediates have been spectroscopically identified in KR2 (Fig. 1B) (6)...

show abstract

“…Time-dependent protein dynamic simulations of 500-ps duration were performed using the chemical simulation software package GROMACS (47) with a time step of 1 fs. The Gromos-96 force field was used throughout (48) and was modified to include parameters for the retinal and Schiff base where partial charges for simulations (49) were kindly provided by E. Tajkhorshid, 2 and torsional displacements from planarity were subject to a harmonic energy penalty of ϳ320 kJ⅐mol Ϫ1 ⅐radian Ϫ2 . All protein C ␣ atoms were restrained to their crystal positions by a force constant of 100 kJ⅐mol⅐nm Ϫ1 .…”

Section: Methodsmentioning

confidence: 99%

Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin

Edman

Royant

Larsson

et al. 2004

Journal of Biological Chemistry

112

View full text Add to dashboard Cite

Light-driven vectorial proton translocation is basic to the mechanism of energy transduction by photosynthetic systems. Bacteriorhodopsin (bR)1 is the simplest known light-driven proton pump and has long served as a model system for understanding how protons may be transported "up hill" against a transmembrane proton motive potential. bR contains seven transmembrane ␣-helices that surround a proton translocation channel lined with strategically placed charged residues (3). Depending upon their protonation states, which change in a well orchestrated cascade as a proton is transported across the cell membrane, these charged residues can serve as either proton donors or proton acceptors. Light activation of the chromophore, an all-trans-retinal molecule covalently attached to Lys-216 in helix G via a protonated Schiff base (the primary proton donor) results in the 13-cis-retinal configuration with two-thirds quantum efficiency. Steric conflicts and mechanical stress resulting from photoisomerization initiate a sequence of conformational changes that can be characterized spectroscopically and that perturb the local environment of several key residues, strongly affecting their pK a values and creating transient pathways for proton transfer.The specific spectral intermediates of the bR photocycle have been well characterized, and a common reaction scheme is: bR 570 3 K 590 7 L 550 7 M 412 7 N 560 7 O 640 3 bR 570 (sub-

show abstract

Influence of the Methyl Groups on the Structure, Charge Distribution, and Proton Affinity of the Retinal Schiff Base

Cited by 46 publications

References 66 publications

Structure, Stability and Interaction Studies on Schiff Base Analogue Systems

Structure, Stability and Interaction Studies on Schiff Base Analogue Systems

Energetics and dynamics of a light-driven sodium-pumping rhodopsin

Deformation of Helix C in the Low Temperature L-intermediate of Bacteriorhodopsin

Contact Info

Product

Resources

About