scholarly journals Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

Polymers ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 885 ◽  
Author(s):  
Alina Asandei ◽  
Isabela Dragomir ◽  
Giovanni Di Muccio ◽  
Mauro Chinappi ◽  
Yoonkyung Park ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Molecule ◽  
Ionic Current ◽  
Ionic Currents ◽  
Time Discrimination ◽  
Voltage Dependent ◽  
Hydrophobic Amino Acids ◽  
Molecular Brake ◽  
Oppositely Charged ◽  
Molecule Dynamics

In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.

scholarly journals Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores

2018 ◽  
Author(s):  
Alina Asandei ◽  
Isabela S. Dragomir ◽  
Giovanni Di Muccio ◽  
Mauro Chinappi ◽  
Yoonkyung Park ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Molecule ◽  
Ionic Current ◽  
Ionic Currents ◽  
Alpha Hemolysin ◽  
Time Discrimination ◽  
Voltage Dependent ◽  
Hydrophobic Amino Acids ◽  
Molecular Brake ◽  
Oppositely Charged

In this work we demonstrate the proof-of-concept of real-time discrimination between patches of serine or isoleucine monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when hydrophilic serine or hydrophobic isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent ‘molecular brake’ on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of three serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL.

scholarly journals Uncharged S4 Residues and Cooperativity in Voltage-dependent Potassium Channel Activation

1998 ◽  
Vol 111 (3) ◽  
pp. 421-439 ◽  
Author(s):  
Catherine J. Smith-Maxwell ◽  
Jennifer L. Ledwell ◽  
Richard W. Aldrich
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Potassium Channel ◽  
Voltage Dependence ◽  
Channel Gating ◽  
Ionic Currents ◽  
Channel Activation ◽  
Functional Changes ◽  
Activation Pathway ◽  
Voltage Dependent

Substitution of the S4 of Shaw into Shaker alters cooperativity in channel activation by slowing a cooperative transition late in the activation pathway. To determine the amino acids responsible for the functional changes in Shaw S4, we created several mutants by substituting amino acids from Shaw S4 into Shaker. The S4 amino acid sequences of Shaker and Shaw S4 differ at 11 positions. Simultaneous substitution of just three noncharged residues from Shaw S4 into Shaker (V369I, I372L, S376T; ILT) reproduces the kinetic and voltage-dependent properties of Shaw S4 channel activation. These substitutions cause very small changes in the structural and chemical properties of the amino acid side chains. In contrast, substituting the positively charged basic residues in the S4 of Shaker with neutral or negative residues from the S4 of Shaw S4 does not reproduce the shallow voltage dependence or other properties of Shaw S4 opening. Macroscopic ionic currents for ILT could be fit by modifying a single set of transitions in a model for Shaker channel gating (Zagotta, W.N., T. Hoshi, and R.W. Aldrich. 1994. J. Gen. Physiol. 103:321–362). Changing the rate and voltage dependence of a final cooperative step in activation successfully reproduces the kinetic, steady state, and voltage-dependent properties of ILT ionic currents. Consistent with the model, ILT gating currents activate at negative voltages where the channel does not open and, at more positive voltages, they precede the ionic currents, confirming the existence of voltage-dependent transitions between closed states in the activation pathway. Of the three substitutions in ILT, the I372L substitution is primarily responsible for the changes in cooperativity and voltage dependence. These results suggest that noncharged residues in the S4 play a crucial role in Shaker potassium channel gating and that small steric changes in these residues can lead to large changes in cooperativity within the channel protein.

scholarly journals Development of natural and unnatural amino acid delivery systems against hookworm infection

2020 ◽  
Vol 3 (1) ◽  
pp. 471-482 ◽  
Author(s):  
Stacey Bartlett ◽  
Mariusz Skwarczynski ◽  
Xin Xie ◽  
Istvan Toth ◽  
Alex Loukas ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Cell Epitope ◽  
Unnatural Amino Acid ◽  
Nippostrongylus Brasiliensis ◽  
Peptide Fragments ◽  
Specific Pathogen ◽  
Hydrophobic Amino Acids ◽  
Natural Amino Acids

Peptide-based vaccines consist of short antigen fragments derived from a specific pathogen. Alone, these peptide fragments are poorly or non-immunogenic; however, when incorporated into a proper delivery system, they can trigger strong immune responses. To eliminate the need for toxic and often ineffective oral adjuvants, we designed single molecule-based self-adjuvating vaccines against hookworms using natural and unnatural hydrophobic amino acids. Two vaccine conjugates were synthesized, consisting of B-cell epitope p3, derived from the hookworm Na-APR-1 protein; universal T-helper peptide P25; and either double copies of unnatural lipoamino acid (2-amino-D,L-eicosanoic acid), or ten copies of the natural amino acid leucine. After challenge with the model hookworm, Nippostrongylus brasiliensis, mice orally immunized with the conjugates, but without adjuvant, generated antibody responses against the hookworm epitope, resulting in significantly reduced worm and egg burdens compared to control mice. We have demonstrated that vaccine nanoparticles composed exclusively of natural amino acids can be effective even when administered orally.

scholarly journals Extracellular Mg2+ Modulates Slow Gating Transitions and the Opening of Drosophila Ether-à-Go-Go Potassium Channels

2000 ◽  
Vol 115 (3) ◽  
pp. 319-338 ◽  
Author(s):  
Chih-Yung Tang ◽  
Francisco Bezanilla ◽  
Diane M. Papazian
Keyword(s):  
Time Course ◽  
Ionic Current ◽  
Ionic Currents ◽  
K Channel ◽  
Gating Currents ◽  
Gating Charge ◽  
Channel Opening ◽  
Voltage Dependent ◽  
Pore Opening ◽  
Sequential Activation

We have characterized the effects of prepulse hyperpolarization and extracellular Mg2+ on the ionic and gating currents of the Drosophila ether-à-go-go K+ channel (eag). Hyperpolarizing prepulses significantly slowed channel opening elicited by a subsequent depolarization, revealing rate-limiting transitions for activation of the ionic currents. Extracellular Mg2+ dramatically slowed activation of eag ionic currents evoked with or without prepulse hyperpolarization and regulated the kinetics of channel opening from a nearby closed state(s). These results suggest that Mg2+ modulates voltage-dependent gating and pore opening in eag channels. To investigate the mechanism of this modulation, eag gating currents were recorded using the cut-open oocyte voltage clamp. Prepulse hyperpolarization and extracellular Mg2+ slowed the time course of ON gating currents. These kinetic changes resembled the results at the ionic current level, but were much smaller in magnitude, suggesting that prepulse hyperpolarization and Mg2+ modulate gating transitions that occur slowly and/or move relatively little gating charge. To determine whether quantitatively different effects on ionic and gating currents could be obtained from a sequential activation pathway, computer simulations were performed. Simulations using a sequential model for activation reproduced the key features of eag ionic and gating currents and their modulation by prepulse hyperpolarization and extracellular Mg2+. We have also identified mutations in the S3–S4 loop that modify or eliminate the regulation of eag gating by prepulse hyperpolarization and Mg2+, indicating an important role for this region in the voltage-dependent activation of eag.

Changes in intracellular potentials and ionic currents of the mollusk and activity of Cl--channels under exposure to some inhibitory amino acids and new litium-containing compounds of them

2015 ◽  
Vol 13 (3) ◽  
pp. 39-47 ◽  
Author(s):  
Petr Dmitrievich Shabanov ◽  
Anatoliy Ivanovich Vislobokov ◽  
Georgiy Nolianovich Shilov ◽  
P M Bulay ◽  
A P Lugovskii
Keyword(s):  
Amino Acids ◽  
Chloride Channels ◽  
Impulse Activity ◽  
Ionic Current ◽  
Ionic Currents ◽  
Dependent Manner ◽  
Cl Channels ◽  
Ganglion Neurons ◽  
Inhibitory Amino Acids ◽  
Dose Dependent

The Changes of membrane rest potential (RP), action potential (AP), impulse activity (IA) as well as sodium, calcium and potassium ionic currents in neurons of isolated central nervous system of the Planorbarius corneus mollusk (pedal ganglia) under the extracellular action of inhibitory amino acids GABA, glycine and β-alanine and their litium-containing derivatives (LCD) in 0.1, 1 and 5 mM concentrations have been studied using a microelectrode technique. They induced the same dose-dependent and irreversible depolarization of neurons on 2-10 mV accompanied by increase of AP frequency, prolongation of their duration and decrease of summmerized ionic currents (dV/dt). According to degree of depolarization, the drugs were placed in the following range in decreasing activity: compound 3 > compound 2 > compound 1. In identified pedal ganglion neurons (PPed1), compound 3 in contrast to other compounds induced hyperpolarization by 2-10 mV and blocked impulse activity. The amplitude of sodium and calcium channels was decreased by 7-15 %, in the same degree after application of all compounds exposed in concentration of 5 mM. Efflux potassium ionic currents were increased in dose-dependent manner and irreversibly about by 3-7 % assessed on amplitude indexes without changes in kinetic parameters after application of LCD. Therefore, the decrease of ionic current amplitudes was due to both depolarization of neurons and direct action of LCD on ionic channels. Thus, LCD possess membranotropic activity and can modulate functional state of neurons. In the study of chloride channels in cells culture of rat glioma C6 in vitro by patch-clamp method, GABA, glycine, β-alanine and their LCD 10 µM/l activated chloride channels, shifting equiliblium membrane potential of glioma cells from -90… -70 mV to -55... -60 mV. All compounds (transmitters and LCD) were placed in the following range: glycine > GABA > β-alanine and compound 1 > compound 3 > compound 2 according to descending activity. Therefore, the most active compounds activating Cl--channels were glycine and compound 1 (LCD). Glycine was shown to be coagonist GABA receptors and its litium salt possessed significant membranotropic activity.

13C nuclear magnetic resonance study of cyclodipeptides containing 13C enriched hydrophobic amino acids

1980 ◽  
Vol 45 (2) ◽  
pp. 482-490 ◽  
Author(s):  
Jaroslav Vičar ◽  
François Piriou ◽  
Pierre Fromageot ◽  
Karel Bláha ◽  
Serge Fermandjian
Keyword(s):  
Amino Acids ◽  
Nuclear Magnetic Resonance ◽  
Nuclear Magnetic Resonance Study ◽  
Coupling Constants ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Magnetic Resonance Study ◽  
Side Chain Conformation ◽  
13C Nuclear Magnetic Resonance ◽  
Hydrophobic Amino Acids

The diastereoisomeric pairs of cyclodipeptides cis- and trans-cyclo(Ala-Ala), cyclo(Ala-Phe), cyclo(Val-Val) and cyclo(Leu-Leu) containing 85% 13C enriched amino-acid residues were synthesized and their 13C-13C coupling constants were measured. The combination of 13C-13C and 1H-1H coupling constants enabled to estimate unequivocally the side chain conformation of the valine and leucine residues.

Multidimensional Characterization of Single‐Molecule Dynamics in a Plasmonic Nanocavity

2021 ◽  
Author(s):  
Lucas Domulevicz ◽  
Hyunhak Jeong ◽  
Nayan K. Paul ◽  
Juan Sebastian Gomez-Diaz ◽  
Joshua Hihath
Keyword(s):  
Single Molecule ◽  
Single Molecule Dynamics ◽  
Molecule Dynamics

scholarly journals Functional consequences of alterations to hydrophobic amino acids located in the M4 transmembrane sector of the Ca(2+)-ATPase of sarcoplasmic reticulum.

1993 ◽  
Vol 268 (24) ◽  
pp. 18359-18364 ◽  
Author(s):  
D.M. Clarke ◽  
T.W. Loo ◽  
W.J. Rice ◽  
J.P. Andersen ◽  
B. Vilsen ◽  
...  
Keyword(s):  
Amino Acids ◽  
Sarcoplasmic Reticulum ◽  
Functional Consequences ◽  
Hydrophobic Amino Acids

scholarly journals Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

2021 ◽  
Vol 22 (3) ◽  
pp. 1018
Author(s):  
Hiroaki Yokota
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Amino Acid ◽  
Single Molecule ◽  
Underlying Mechanism ◽  
Amino Acid Sequences ◽  
E Coli ◽  
X Ray Crystallography ◽  
Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

Sign in / Sign up

Export Citation Format

Share Document