scholarly journals Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding

2012 ◽  
Vol 28 (18) ◽  
pp. i423-i430 ◽  
Author(s):  
F. Gaudreault ◽  
M. Chartier ◽  
R. Najmanovich
Keyword(s):  
Hydrogen Bonding ◽  
Ligand Binding ◽  
Side Chain

scholarly journals Side-Chain to Main-Chain Hydrogen Bonding Controls the Intrinsic Backbone Dynamics of the Amyloid Precursor Protein Transmembrane Helix

2014 ◽  
Vol 106 (6) ◽  
pp. 1318-1326 ◽  
Author(s):  
Christina Scharnagl ◽  
Oxana Pester ◽  
Philipp Hornburg ◽  
Daniel Hornburg ◽  
Alexander Götz ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Amyloid Precursor Protein ◽  
Main Chain ◽  
Transmembrane Helix ◽  
Precursor Protein ◽  
Backbone Dynamics ◽  
Side Chain

The significance of the Cα substituent in the selective inhibition of matrix metalloproteinases 1 and 9

2011 ◽  
Vol 392 (11) ◽  
Author(s):  
Riyad Domingo ◽  
Kelly Chibale ◽  
Edward D. Sturrock
Keyword(s):  
Hydrogen Bonding ◽  
Matrix Metalloproteinases ◽  
Active Sites ◽  
Unsaturated Compound ◽  
Selective Inhibition ◽  
Acid Group ◽  
Side Chain ◽  
Carboxylic Acid Group ◽  
Lead Compounds ◽  
Hydrogen Bonding Interactions

Abstract Matrix metalloproteinases (MMPs) cleave and degrade most components of the extracellular matrix, and unregulated MMP activity has been correlated to cancer and metastasis. Hence there is a burgeoning need to develop inhibitors that bind selectively to structurally similar MMPs. The inhibition profiles of peptidomimetics containing Cα substituents at the α,β unsaturated carbon were evaluated against the recombinant forms of ADAM17, MMP1, and MMP9. The dicarboxylic acid D2 and hydroxamate C2 inhibited MMP9 but not MMP1. The unsaturated compound E2 displayed selective inhibition for MMP1, compared with the saturated precursor C2, with an IC50 value of 3.91 μm. The molecular basis for this selectivity was further investigated by the molecular docking of E2 and D2 into the active sites of MMP1 and MMP9. These data demonstrate hydrogen-bonding interactions between the carbonyl group of the Cα substituent of E2 and the side chain of Asn180 present in the active site of MMP1. Conversely, the docked MMP9-D2 structure shows hydrophobic and hydrogen bonding between the ligand’s morpholine substituent and second carboxylic acid group with Leu187 and an amide, respectively. This study suggests that substituents other than P1′ and P2′ may confer selectivity among MMPs and may aid in the search for novel lead compounds.

Supramolecular Interactions in Aromatic Structures for Non-Optical and Optical Chemosensors of Explosive Chemicals

2021 ◽  
Vol 317 ◽  
pp. 202-207
Author(s):  
Juan Matmin ◽  
Nur Fatiha Ghazalli ◽  
Fazira Ilyana Abdul Razak ◽  
Hendrik O. Lintang ◽  
Mohamad Azani Jalani
Keyword(s):  
Hydrogen Bonding ◽  
High Performance ◽  
Molecular Design ◽  
Optical Sensing ◽  
Green Emission ◽  
Supramolecular Interactions ◽  
Side Chain ◽  
Optical Chemosensors ◽  
Random Aggregate ◽  
Metal Metal

The scientific investigation based on the molecular design of aromatic compounds for high-performance chemosensor is challenging. This is because their multiplex interactions at the molecular level should be precisely determined before the desired compounds can be successfully used as sensing materials. Herein, we report on the molecular design of chemosensors based on aromatic structures of benzene as the organic motif of benzene-1,3,5-tricarboxamides (BTA), as well as the benzene pyrazole complexes (BPz) side chain, respectively. In the case of BTA, the aromatic benzene acts as the centre to allow the formation of π–π stacking for one-dimensional materials having rod-like arrangements that are stabilized by threefold hydrogen bonding. We found that when nitrate was applied, the rod-like BTA spontaneously formed into a random aggregate due to the deformation of its hydrogen bonding to form inactive nitroso groups for non-optical sensing capability. For the optical chemosensor, the aromatic benzene is decorated as a side-chain of BPz to ensure that cage-shaped molecules make maximum use of their centre providing metal-metal interactions for fluorescence-based sensing materials. In particular, when exposed to benzene, Cu-BPz displayed a blue-shift of its original emission band from 616 to 572 nm (Δ = 44 nm) and emitted bright orange to green emission colours. We also observe a different mode of fluorescence-based sensing materials for Au-BPz, which shows a particular quenching mechanism resulting in 81% loss of its original intensity on benzene exposure to give less red-orange emission (λ = 612 nm). The BTA and BPz synthesized are promising high-performance supramolecular chemosensors based on the non-optical and optical sensing capability of a particular interest analyte.

Structure, stability and folding of the α-helix

2001 ◽  
Vol 68 ◽  
pp. 95-110 ◽  
Author(s):  
Andrew J. Doig ◽  
Charles D. Andrew ◽  
Duncan A. E. Cochran ◽  
Eleri Hughes ◽  
Simon Penel ◽  
...  
Keyword(s):  
Hydrogen Bonding ◽  
Hydrophobic Interactions ◽  
Data Bank ◽  
Site Directed Mutagenesis ◽  
Model Systems ◽  
Side Chain ◽  
Structure Stability ◽  
Helical Peptides ◽  
Vast Number ◽  
Α Helix

Pauling first described the α-helix nearly 50 years ago, yet new features of its structure continue to be discovered, using peptide model systems, site-directed mutagenesis, advances in theory, the expansion of the Protein Data Bank and new experimental techniques. Helical peptides in solution form a vast number of structures, including fully helical, fully coiled and partly helical. To interpret peptide results quantitatively it is essential to use a helix/coil model that includes the stabilities of all these conformations. Our models now include terms for helix interiors, capping, side-chain interactions, N-termini and 310-helices. The first three amino acids in a helix (N1, N2 and N3) and the preceding N-cap are unique, as their amide NH groups do not participate in backbone hydrogen bonding. We surveyed their structures in proteins and measured their amino acid preferences. The results are predominantly rationalized by hydrogen bonding to the free NH groups. Stabilizing side-chain-side-chain energies, including hydrophobic interactions, hydrogen bonding and polar/non-polar interactions, were measured accurately in helical peptides. Helices in proteins show a preference for having approximately an integral number of turns so that their N- and C-caps lie on the same side. There are also strong periodic trends in the likelihood of terminating a helix with a Schellman or αL C-cap motif. The kinetics of α-helix folding have been studied with stopped-flow deep ultraviolet circular dichroism using synchrotron radiation as the light source; this gives a far superior signal-to-noise ratio than a conventional instrument. We find that poly(Glu), poly(Lys) and alanine-based peptides fold in milliseconds, with longer peptides showing a transient overshoot in helix content.

The lack of intramolecular hydrogen bonding and the side chain effect in alanine conformers

2012 ◽  
Vol 1014 ◽  
pp. 12-16 ◽  
Author(s):  
Rodrigo A. Cormanich ◽  
Lucas C. Ducati ◽  
Roberto Rittner
Keyword(s):  
Hydrogen Bonding ◽  
Intramolecular Hydrogen Bonding ◽  
Side Chain ◽  
Intramolecular Hydrogen

scholarly journals A substrate selected by phage display exhibits enhanced side-chain hydrogen bonding to HIV-1 protease

2018 ◽  
Vol 74 (7) ◽  
pp. 690-694 ◽  
Author(s):  
Ian W. Windsor ◽  
Ronald T. Raines
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Molecular Recognition ◽  
Hydrogen Bonds ◽  
Phage Display ◽  
Directed Evolution ◽  
Side Chain ◽  
Endogenous Substrates ◽  
Hiv 1 ◽  
Additional Hydrogen

Crystal structures of inactive variants of HIV-1 protease bound to peptides have revealed how the enzyme recognizes its endogenous substrates. The best of the known substrates is, however, a nonnatural substrate that was identified by directed evolution. The crystal structure of the complex between this substrate and the D25N variant of the protease is reported at a resolution of 1.1 Å. The structure has several unprecedented features, especially the formation of additional hydrogen bonds between the enzyme and the substrate. This work expands the understanding of molecular recognition by HIV-1 protease and informs the design of new substrates and inhibitors.

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