scholarly journals Hydrogen Bonding in a l-Glutamine-Based Polyamidoamino Acid and its pH-Dependent Self-Ordered Coil Conformation

Polymers ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 881
Author(s):  
Federica Lazzari ◽  
Amedea Manfredi ◽  
Jenny Alongi ◽  
Fabio Ganazzoli ◽  
Francesca Vasile ◽  
...  

This paper reports on synthesis, acid–base properties, and self-structuring in water of a chiral polyamidoamino acid, M-l-Gln, obtained from the polyaddition of N,N′-methylenebisacrylamide with l-glutamine, with the potential of establishing hydrogen bonds through its prim-amide pendants. The M-l-Gln showed pH-responsive circular dichroism spectra, revealing ordered conformations. Structuring was nearly insensitive to ionic strength but sensitive to denaturing agents. The NMR diffusion studies were consistent with a population of unimolecular nanoparticles thus excluding aggregation. The M-l-Gln had the highest molecular weight and hydrodynamic radius among all polyamidoamino acids described. Possibly, transient hydrogen bonds between l-glutamine molecules and M-l-Gln growing chains facilitated the polyaddition reaction. Theoretical modeling showed that M-l-Gln assumed pH-dependent self-ordered coil conformations with main chain transoid arrangements reminiscent of the protein hairpin motif owing to intramolecular dipole moments and hydrogen bonds. The latter were most numerous at the isoelectric point (pH 4.5), where they mainly involved even topologically distant main chain amide N–H and side chain amide C=O brought to proximity by structuring. Hydrogen bonds at pH 4.5 were also suggested by variable temperature NMR. The 2D NOESY experiments at pH 4.5 confirmed the formation of compact structures through the analysis of the main chain/side chain hydrogen contacts, in line with MD simulations.

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Albert Escobedo ◽  
Busra Topal ◽  
Micha B. A. Kunze ◽  
Juan Aranda ◽  
Giulio Chiesa ◽  
...  

1998 ◽  
Vol 120 (45) ◽  
pp. 11558-11566 ◽  
Author(s):  
Wojciech M. Wolf ◽  
Marcin Stasiak ◽  
Miroslav T. Leplawy ◽  
Alberto Bianco ◽  
Fernando Formaggio ◽  
...  

2020 ◽  
Vol 118 (3) ◽  
pp. 369a-370a
Author(s):  
Albert Escobedo ◽  
Busra Topal ◽  
Micha Kunze ◽  
Juan Aranda ◽  
Giulio Chiesa ◽  
...  

2004 ◽  
Vol 856 ◽  
Author(s):  
Kirt A. Page ◽  
Robert B. Moore

ABSTRACTSeveral high temperature methods of processing Nafion® have been developed using various alkylammonium ion forms of the ionomer, and the choice of counterion has been shown to have a significant effect on the thermal and mechanical properties of this material. In particular, it has been shown that neutralization gives rises to two high-temperature mechanical relaxations as observed in dynamic mechanical analysis (DMA). While several studies in the literature have attempted to explain the molecular origins of these mechanical relaxations, the assignments were based primarily on limited DMA results and have at times been contradictory. The study presented here is a fundamental investigation into the molecular origins of the thermally induced morphological relaxations and dynamics of alkylammonium forms of Nafion® membranes as studied by variable temperature small-angle x-ray scattering (SAXS) and solid-state 19F NMR spectroscopy. The intensity of the small-angle ionomer peak at ca. q = 2 nm–1 was monitored as a function of temperature for each alkylammonium neutralized sample in unoriented and oriented states. In the case of the oriented samples, the degree of anisotropic scattering from the oriented ionomer morphology was quantified using the Hermann's orientation function and monitored as a function of temperature. Changes in intensity of the ionomer peak and the Hermann's parameter as a function of temperature were shown to correlate well with relaxations observed in DMA. Several variable temperature solid-state 19F NMR techniques (including spin diffusion, side-band analysis and T1ρ experiments) were used to investigate the dynamics of the Nafion® chains. Side band analysis indicated that the side-chain is more mobile than the main chain and that the mobility is greatly affected by the size of the counterion. Changes in side-band intensity as a function of temperature were shown to correlate well with DMA data. Results from T1ρ experiments show strong counterion dependence and suggest coupled main- and side-chain motions. A two-component relaxation process was also observed for the main-chain fluorines. The results of the NMR investigations, along with the SAXS data, have led to the development of a more detailed description of the dynamics of Nafion® and the molecular origins of the mechanical relaxations. With this information, the continuing goal to determine how the strength of the electrostatic interactions in perfluorosulfonate ionomers affects the chain dynamics and developing morphology may be realized for the purpose of controlling the morphology to create more efficient ionomeric membrane materials.


eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Han Han ◽  
Nicole Monroe ◽  
Wesley I Sundquist ◽  
Peter S Shen ◽  
Christopher P Hill

The hexameric AAA ATPase Vps4 drives membrane fission by remodeling and disassembling ESCRT-III filaments. Building upon our earlier 4.3 Å resolution cryo-EM structure (<xref ref-type="bibr" rid="bib29">Monroe et al., 2017</xref>), we now report a 3.2 Å structure of Vps4 bound to an ESCRT-III peptide substrate. The new structure reveals that the peptide approximates a β-strand conformation whose helical symmetry matches that of the five Vps4 subunits it contacts directly. Adjacent Vps4 subunits make equivalent interactions with successive substrate dipeptides through two distinct classes of side chain binding pockets formed primarily by Vps4 pore loop 1. These pockets accommodate a wide range of residues, while main chain hydrogen bonds may help dictate substrate-binding orientation. The structure supports a ‘conveyor belt’ model of translocation in which ATP binding allows a Vps4 subunit to join the growing end of the helix and engage the substrate, while hydrolysis and release promotes helix disassembly and substrate release at the lagging end.


2018 ◽  
Vol 74 (4) ◽  
pp. 264-278 ◽  
Author(s):  
Hakan Atakisi ◽  
David W. Moreau ◽  
Robert E. Thorne

The modulation of main-chain and side-chain conformational heterogeneity and solvent structure in monoclinic lysozyme crystals by dehydration (related to water activity) and temperature is examined. Decreasing the relative humidity (from 99 to 11%) and decreasing the temperature both lead to contraction of the unit cell, to an increased area of crystal contacts and to remodeling of primarily contact and solvent-exposed residues. Both lead to the depopulation of some minor side-chain conformers and to the generation of new conformations. Side-chain modifications and main-chain r.m.s.d.s associated with cooling from 298 to 100 K depend on relative humidity and are minimized at 85% relative humidity (r.h.). Dehydration from 99 to 93% r.h. and cooling from 298 to 100 K result in a comparable number of remodeled residues, with dehydration-induced remodeling somewhat more likely to arise from contact interactions. When scaled to equivalent temperatures based on unit-cell contraction, the evolution of side-chain order parameters with dehydration shows generally similar features to those observed on cooling toT= 100 K. These results illuminate the qualitative and quantitative similarities between structural perturbations induced by modest dehydration, which routinely occurs in samples prepared for 298 and 100 K data collection, and cryocooling. Differences between these perturbations in terms of energy landscapes and occupancies, and implications for variable-temperature crystallography between 180 and 298 K, are discussed. It is also noted that remodeling of a key lysozyme active-site residue by dehydration, which is associated with a radical decrease in the enzymatic activity of lysozyme powder, arises due to a steric clash with the residue of a symmetry mate.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Raghavendar Reddy Sanganna Gari ◽  
Joel José Montalvo‐Acosta ◽  
George R. Heath ◽  
Yining Jiang ◽  
Xiaolong Gao ◽  
...  

AbstractConformational changes in ion channels lead to gating of an ion-conductive pore. Ion flux has been measured with high temporal resolution by single-channel electrophysiology for decades. However, correlation between functional and conformational dynamics remained difficult, lacking experimental techniques to monitor sub-millisecond conformational changes. Here, we use the outer membrane protein G (OmpG) as a model system where loop-6 opens and closes the β-barrel pore like a lid in a pH-dependent manner. Functionally, single-channel electrophysiology shows that while closed states are favored at acidic pH and open states are favored at physiological pH, both states coexist and rapidly interchange in all conditions. Using HS-AFM height spectroscopy (HS-AFM-HS), we monitor sub-millisecond loop-6 conformational dynamics, and compare them to the functional dynamics from single-channel recordings, while MD simulations provide atomistic details and energy landscapes of the pH-dependent loop-6 fluctuations. HS-AFM-HS offers new opportunities to analyze conformational dynamics at timescales of domain and loop fluctuations.


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