IR spectra of protonated benzaldehyde clusters, C7H7O+–Ln (L=Ar,N2;n≤2): Ion-ligand binding motifs of the cis and trans oxonium isomers

2010 ◽  
Vol 133 (4) ◽  
pp. 044307 ◽  
Author(s):  
Shamik Chakraborty ◽  
Alexander Patzer ◽  
Otto Dopfer
Keyword(s):  
Ligand Binding ◽  
Ir Spectra ◽  
Binding Motifs ◽  
Cis And Trans

scholarly journals Cooperative Interaction of Nck and Lck Orchestrates Optimal TCR Signaling

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 834
Author(s):  
Frederike A. Hartl ◽  
Jatuporn Ngoenkam ◽  
Esmeralda Beck-Garcia ◽  
Liz Cerqueira ◽  
Piyamaporn Wipa ◽  
...  
Keyword(s):  
T Cell ◽  
Ligand Binding ◽  
T Cell Activation ◽  
Cell Activation ◽  
Adaptor Protein ◽  
Cooperative Interaction ◽  
Tcr Signaling ◽  
Binding Motifs ◽  
Adaptive Immune

The T cell antigen receptor (TCR) is expressed on T cells, which orchestrate adaptive immune responses. It is composed of the ligand-binding clonotypic TCRαβ heterodimer and the non-covalently bound invariant signal-transducing CD3 complex. Among the CD3 subunits, the CD3ε cytoplasmic tail contains binding motifs for the Src family kinase, Lck, and the adaptor protein, Nck. Lck binds to a receptor kinase (RK) motif and Nck binds to a proline-rich sequence (PRS). Both motifs only become accessible upon ligand binding to the TCR and facilitate the recruitment of Lck and Nck independently of phosphorylation of the TCR. Mutations in each of these motifs cause defects in TCR signaling and T cell activation. Here, we investigated the role of Nck in proximal TCR signaling by silencing both Nck isoforms, Nck1 and Nck2. In the absence of Nck, TCR phosphorylation, ZAP70 recruitment, and ZAP70 phosphorylation was impaired. Mechanistically, this is explained by loss of Lck recruitment to the stimulated TCR in cells lacking Nck. Hence, our data uncover a previously unknown cooperative interaction between Lck and Nck to promote optimal TCR signaling.

Vibrational spectra of solid cis- and trans-2-thioxohexahydroquinazolin-4(1H)-one and theoretical calculations towards the interpretation of its thermal reactivity

RSC Advances ◽  
2015 ◽  
Vol 5 (54) ◽  
pp. 43345-43352 ◽  
Author(s):  
A. G. Iriarte ◽  
W. J. Peláez ◽  
F. Fülöp ◽  
G. A. Argüello
Keyword(s):  
Ir Spectra ◽  
Vibrational Spectra ◽  
Solid Phase ◽  
Theoretical Calculations ◽  
Thermal Reactivity ◽  
Ft Ir ◽  
Cis And Trans ◽  
Ft Raman

FT-Raman and FT-IR spectra ofcisandtrans2-thioxohexahydroquinazolin-4(1H)-one are reported. Both compounds are dimers in the solid phase, withC2symmetry. This work contributes to the knowledge of data which are rather scarce for quinazolinones.

Classification of Vegetable Oils by FT-IR

1997 ◽  
Vol 51 (8) ◽  
pp. 1118-1124 ◽  
Author(s):  
Donald B. Dahlberg ◽  
Shawn M. Lee ◽  
Seth J. Wenger ◽  
Julie A. Vargo
Keyword(s):  
Ir Spectra ◽  
Principal Component ◽  
Fast Detection ◽  
Signal Correction ◽  
Ft Ir ◽  
Ir Detection ◽  
The Fourier Transform ◽  
Cooking Oils ◽  
Cis And Trans

The Fourier transform infrared (FT-IR) spectra of 27 brands of 10 types of cooking oils and margarines were measured without temperature control. Attempts to predict the vegetable source and physical properties of these oils failed until wavelength selection and multiplicative signal correction (MSC) were applied to the FT-IR spectra. After pretreatment of the data, principal component analysis (PCA) was totally successful at oil identification, and partial least-squares (PLS) models were able to predict both the refractive indices [standard error of estimation (SEE) 0.0002] and the viscosities (SEE 0.52 cP) of the oils. These models were based predominately on the FT-IR detection of the cis and trans double-bond content of the oils, as well as small amounts of defining impurities in sesame oils. Efforts to use selected wavelengths to discriminate oil sources were only partially successful. These results show the potential utility of FT-IR in the fast detection of substitution or adulteration of products like cooking oils.

Platinum(II) and magnesium(II) nucleotide complexes. Synthesis, FT-ir spectra, and structural properties

1983 ◽  
Vol 61 (8) ◽  
pp. 1813-1822 ◽  
Author(s):  
H. A. Tajmir-Riahi ◽  
T. Theophanides
Keyword(s):  
Water Molecule ◽  
Ir Spectra ◽  
Metal Ions ◽  
Structural Properties ◽  
Acidic Solution ◽  
Neutral Solution ◽  
Metal Bonding ◽  
Ft Ir ◽  
Cis And Trans ◽  
Chemical Evidence

Guanosine-5′-monophosphate (5′-GMP) reacts with Pt(II) and Mg(II) metal ions to give complexes of the type Pt(5′-GMP)nCl2•xH2O, cis- and trans-[Pt(NH3)2(5′-GMP)2]Cl2•xH2O and Mg(5'-GMP2)•xH2O, where n = 1, 2, 3, 4 and x = 4–10.Spectroscopic and chemical evidence showed marked similarities with those of the structurally known N7-bonded 5′-GMP complexes of Mn(II), Co(II), Ni(II), Cu(II), and Cd(II) metal ions. Therefore, Pt(II) and Mg(II) are also found to be N7-bonded in these series of nucleotide complexes.The direct phosphate coordination was observed in Mg(II) nucleotide complexes obtained from acidic solution, whereas Mg(II) complexes prepared from neutral solution showed no direct phosphate–Mg(II) interaction. Pt(II) complexes exhibited no direct phosphate metal bonding, while the possibility of an indirect Pt(II)–phosphate interaction through a hydrogen-bonded water molecule can be proposed here.

scholarly journals Vinblastine and vincristine as anticancer molecules stopping the tubulin dimers

2020 ◽  
Vol 9 (1) ◽  
pp. 870-874
Keyword(s):  
Tyrosine Kinase ◽  
Ligand Binding ◽  
Ir Spectra ◽  
Theoretical Calculations ◽  
Vinca Alkaloid ◽  
Dielectric Constants ◽  
Vibrational Modes ◽  
Cell Surfaces ◽  
Hydrophobic Domain ◽  
Chemical Analogue

Vinblastine is belonging to vinca alkaloid family which is a chemical analogue of vincristine molecules. It has a high potential for attaching to tubulin of microtubules, therefore inhibiting the assembly of that biomolecules. Human EGFRs receptors are cell surfaces receptors proteins including three different domains which are known extracellular ligand-binding domain, trans-membranes hydrophobic domain and cytoplasmic C-terminal domain with tyrosine kinase. The Chemical & physical vibrational spectral data obtained from NMR, NBO and IR spectra based on the results of the theoretical calculations using DFT and HF methods. The fundamental vibrational modes were characterized depending on the stabilities of Herceptin in different dielectric constants. Thus, the goal of this article is to evaluate and quantify and qualify of the mechanism in various solvents.

scholarly journals Elucidation of Novel Structural Scaffold in Rohu TLR2 and Its Binding Site Analysis with Peptidoglycan, Lipoteichoic Acid and Zymosan Ligands, and Downstream MyD88 Adaptor Protein

2013 ◽  
Vol 2013 ◽  
pp. 1-15 ◽  
Author(s):  
Bikash Ranjan Sahoo ◽  
Madhubanti Basu ◽  
Banikalyan Swain ◽  
Manas Ranjan Dikhit ◽  
Pallipuram Jayasankar ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Interleukin 1 ◽  
Adaptor Protein ◽  
Comparative Modeling ◽  
Lipoteichoic Acid ◽  
3D Models ◽  
Dynamics Simulation ◽  
Binding Motifs ◽  
Downstream Signaling ◽  
Binding Domains

Toll-like receptors (TLRs) play key roles in sensing wide array of microbial signatures and induction of innate immunity. TLR2 in fish resembles higher eukaryotes by sensing peptidoglycan (PGN) and lipoteichoic acid (LTA) of bacterial cell wall and zymosan of yeasts. However, in fish TLR2, no study yet describes the ligand binding motifs in the leucine rich repeat regions (LRRs) of the extracellular domain (ECD) and important amino acids in TLR2-TIR (toll/interleukin-1 receptor) domain that could be engaged in transmitting downstream signaling. We predicted these in a commercially important freshwater fish species rohu (Labeo rohita) by constructing 3D models of TLR2-ECD, TLR2-TIR, and MyD88-TIR by comparative modeling followed by 40 ns (nanosecond) molecular dynamics simulation (MDS) for TLR2-ECD and 20 ns MDS for TLR2-TIR and MyD88-TIR. Protein (TLR2-ECD)–ligands (PGN, LTA, and zymosan) docking in rohu by AutoDock4.0, FlexX2.1, and GOLD4.1 anticipated LRR16–19, LRR12–14, and LRR20-CT as the most important ligand binding motifs. Protein (TLR2-TIR)—protein (MyD88-TIR) interaction by HADDOCK and ZDOCK predicted BB loop,αB-helix,αC-helix, and CD loop in TLR2-TIR and BB loop,αB-helix, and CD loop in MyD88-TIR as the critical binding domains. This study provides ligands recognition and downstream signaling.

Realization of Unusual Ligand Binding Motifs in Metalated Container Molecules: Synthesis, Structures, and Magnetic Properties of the Complexes[(LMe)Ni2(μ-L′)]n+ with L′=NO3−, NO2−, N3−, N2H4, Pyridazine, Phthalazine, Pyrazolate, and Benzoate

2004 ◽  
Vol 10 (7) ◽  
pp. 1716-1728 ◽  
Author(s):  
Julia Hausmann ◽  
Marco H. Klingele ◽  
Vasile Lozan ◽  
Gunther Steinfeld ◽  
Dieter Siebert ◽  
...  
Keyword(s):  
Magnetic Properties ◽  
Ligand Binding ◽  
Binding Motifs

The Interpretation of the Infrared Spectra of Conjugated Polyenes in the 1000–900 cm−1 Region

1971 ◽  
Vol 25 (3) ◽  
pp. 368-371 ◽  
Author(s):  
N. B. Colthup
Keyword(s):  
Fatty Acids ◽  
Ir Spectra ◽  
Infrared Spectra ◽  
Conjugated Polyenes ◽  
Cis And Trans

The ir spectra of conjugated polyenes such as fatty acids and derivatives are known to have band patterns in the 1000–900 cm−1 region which are characteristic for various arrangements of cis and trans groups within the different polyenes. This paper presents an interpretation of these bands and also predicts absorption patterns for less commonly observed polyenes with cis or trans groups.

Mechanical Unfolding Studies on Single-Domain SUMO and Multi-Domain Periplasmic Binding Proteins

2017 ◽  
Vol 12 (01) ◽  
pp. 1-10 ◽  
Author(s):  
Hema Chandra Kotamarthi ◽  
Sri Rama Koti Ainavarapu
Keyword(s):  
Ligand Binding ◽  
Single Molecule ◽  
Binding Proteins ◽  
Mechanical Stability ◽  
Binding Motifs ◽  
Protein Mechanics ◽  
Cellular Processes ◽  
Residue Contacts ◽  
Periplasmic Binding Proteins ◽  
Single Molecule Studies

Protein mechanics is a key component of many cellular and sub-cellular processes. The current review focuses on recent studies from our laboratory that probe the effect of sequence on the mechanical stability of structurally similar proteins and the unfolding mechanisms of multi-domain periplasmic binding proteins. Ubiquitin and small ubiquitin-related modifiers (SUMOs) are structurally similar and possess different mechanical stabilities, ubiquitin being stronger than SUMOs as revealed from their unfolding forces. These differences are plausibly due to the variation in number of inter-residue contacts. The unfolding potential widths determined from the pulling speed-dependent studies revealed that SUMOs are mechanically more flexible than ubiquitin. This flexibility of SUMOs plays a role in ligand binding and our single-molecule studies on SUMO interaction with SUMO binding motifs (SBMs) have shown that ligand binding decreases the SUMO flexibility and increases its mechanical stability. Studies on multi-domain periplasmic binding proteins have revealed that the unfolding energy landscape of these proteins is complex and they follow kinetic partitioning between two-state and multiple three-state pathways.

Tetracyclosqualene and Its Bearing on the Structure of Cyclized Rubber

1964 ◽  
Vol 37 (2) ◽  
pp. 486-490 ◽  
Author(s):  
Morton A. Golub ◽  
Jorge Heller
Keyword(s):  
Double Bond ◽  
Ir Spectra ◽  
Nmr Spectra ◽  
Bicyclic Structure ◽  
Fused Ring ◽  
Ring Structures ◽  
Methylene Groups ◽  
Cis And Trans ◽  
Rule Out

Abstract Recently we reported that cyclized rubber consists of six-membered rings fused into predominantly bicyclic structures which are connected by methylene groups and/or uncyclized isoprene units. Each of the fused ring structures is presumed to contain a single tetra-, tri- or di-substituted double bond, the relative amounts of which are in the order, tetra- > tri- > di-substituted. The predominantly bicyclic structure was not rigorously established, but it was considered reasonable on the basis of a comparison of the nmr spectra of cyclized cis-polyisoprene and cyclized cis-poly (2-methyl-d3-1,3-butadiene-1,1-d2). However, although a predominantly monocyclic structure was clearly excluded, it was not possible to rule out a structure in which the average number of rings per fused segment (“cyclicity”) exceeds two and may even be as high as three. In an effort to determine this cyclicity more accurately, we now compare the nmr and ir spectra of cyclized cis- and trans-polyisoprenes with the corresponding spectra of tetracyclosqualene (TCS). The latter is known to have a structure consisting of two bicyclic segments connected by two methylene groups.

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