Cited Article: Hummer, G. Water conduction through the hydrophobic channel of a carbon nanotube
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Title:
Translocation events in a single-walled carbon nanotube
Authors:
He, J; Liu, H; Pang, P; Cao, D; Lindsay, S
Author Full Names:
He, Jin; Liu, Hao; Pang, Pei; Cao, Di; Lindsay, Stuart
Source:
JOURNAL OF PHYSICS-CONDENSED MATTER 22 (45): Art. No. 454112 NOV 17 2010
Language:
English
Document Type:
Article
KeyWords Plus:
MASS-TRANSPORT; STRANDED-DNA; WATER; MEMBRANES; CHANNEL; NANOFLUIDICS; MOLECULES; NANOPIPES; NANOPORES; PORE
Abstract:
Translocation of DNA oligomers through a single-walled carbon nanotube was demonstrated recently. Translocation events are accompanied by giant current pulses, the origin of which remains obscure. Here, we show that the introduction of a nucleotide, guanosine triphosphate, alone into the input reservoir of a carbon nanotube nanofluidic device also gives giant current pulses. Taken together with data on oligomer translocation, these new results suggest that the pulse width has a nonlinear, power-law dependence on the number of nucleotides in a DNA molecule. We have also measured the time for the onset of DNA translocation pulses after bias reversal, finding that the time for the onset of translocation is directly proportional to the period of the bias reversal.
Reprint Address:
He, J, Arizona State Univ, Biodesign Inst, Tempe, AZ 85287 USA.
Research Institution addresses:
[He, Jin; Lindsay, Stuart] Arizona State Univ, Biodesign Inst, Tempe, AZ 85287 USA; [Liu, Hao; Lindsay, Stuart] Arizona State Univ, Dept Chem & Biochem, Tempe, AZ 85287 USA; [Pang, Pei; Cao, Di; Lindsay, Stuart] Arizona State Univ, Dept Phys, Tempe, AZ 85287 USA
E-mail Address:
jinhe@asu.edu
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Cited Reference Count:
41
Times Cited:
0
Publisher:
IOP PUBLISHING LTD; DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND
Subject Category:
Physics, Condensed Matter
ISSN:
0953-8984
DOI:
10.1088/0953-8984/22/45/454112
IDS Number:
673HZ
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Title:
Hydration properties of mechanosensitive channel pores define the energetics of gating
Authors:
Anishkin, A; Akitake, B; Kamaraju, K; Chiang, CS; Sukharev, S
Author Full Names:
Anishkin, A.; Akitake, B.; Kamaraju, K.; Chiang, C-S; Sukharev, S.
Source:
JOURNAL OF PHYSICS-CONDENSED MATTER 22 (45): Art. No. 454120 NOV 17 2010
Language:
English
Document Type:
Article
KeyWords Plus:
MOLECULAR-DYNAMICS SIMULATIONS; ESCHERICHIA-COLI MSCS; CAPILLARY EVAPORATION; SMALL-CONDUCTANCE; ACETYLCHOLINE-RECEPTOR; HYDROPHOBIC SURFACES; ION CHANNELS; WATER; MECHANISM; PROTEIN
Abstract:
Opening of ion channels directly by tension in the surrounding membrane appears to be the most ancient and simple mechanism of gating. Bacterial mechanosensitive channels MscL and MscS are the best-studied tension-gated nanopores, yet the key physical factors that define their gating are still hotly debated. Here we present estimations, simulations and experimental results showing that hydration of the pore might be one of the major parameters defining the thermodynamics and kinetics of mechanosensitive channel gating. We associate closing of channel pores with complete dehydration of the hydrophobic gate (occlusion by 'vapor lock') and formation of two water-vapor interfaces above and below the constriction. The opening path is the expansion of these interfaces, ultimately leading to wetting of the hydrophobic pore, which does not appear to be the exact reverse of the closing path, thus producing hysteresis. We discuss specifically the role of polar groups (glycines) buried
in narrow closed conformations but exposed in the open states that change the wetting characteristics of the pore lining and stabilize conductive states of the channels.
Reprint Address:
Anishkin, A, Univ Maryland, Dept Biol, College Pk, MD 20742 USA.
Research Institution addresses:
[Anishkin, A.; Akitake, B.; Kamaraju, K.; Chiang, C-S; Sukharev, S.] Univ Maryland, Dept Biol, College Pk, MD 20742 USA
E-mail Address:
sukharev@umd.edu
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71
Times Cited:
0
Publisher:
IOP PUBLISHING LTD; DIRAC HOUSE, TEMPLE BACK, BRISTOL BS1 6BE, ENGLAND
Subject Category:
Physics, Condensed Matter
ISSN:
0953-8984
DOI:
10.1088/0953-8984/22/45/454120
IDS Number:
673HZ
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Title:
Exploring the Changes in the Structure of alpha-Helical Peptides Adsorbed onto a Single Walled Carbon Nanotube Using Classical Molecular Dynamics Simulation
Authors:
Balamurugan, K; Gopalakrishnan, R; Raman, SS; Subramanian, V
Author Full Names:
Balamurugan, K.; Gopalakrishnan, R.; Raman, S. Sundar; Subramanian, V.
Source:
JOURNAL OF PHYSICAL CHEMISTRY B 114 (44): 14048-14058 NOV 11 2010
Language:
English
Document Type:
Article
KeyWords Plus:
ALANINE-BASED PEPTIDES; FORCE-FIELD; SECONDARY STRUCTURE; WATER; PROTEINS; POLYPEPTIDES; ALGORITHMS; TRANSITION; ENERGETICS; MEMBRANES
Abstract:
Classical molecular dynamics (MD) simulation has been carried out in an explicit solvent environment to understand the interaction between the single walled carbon nanotube (SWCNT) and alpha-helix. A polyalanine peptide consisting of 40 alanine residues has been chosen as the model for the a-helix (PA(40)). Results reveal that the SWCNT induces conformational changes in PA(40). Furthermore, breakage of hydrogen bonds in the chosen model peptides has been observed, which leads to conformational transitions (alpha -> turns) in different parts of the PA(40). Owing to these transitions, regions of different structural and energetic stability are generated in PA(40) which enable the PA(40) to curl around the surface of the SWCNT. The overall observations obtained from the MD simulations are not significantly influenced by the starting geometry and the choice of the force field. Although the qualities of structural information obtained from the MD simulation using ff03 and OPLS are
different, the overall observation derived from the ff03 is similar to that of PLS. Results from the MD simulation on the interaction of the alpha-helical fragment of the SNARES protein with the SWCNT elicit that the amino acid composition influences the interaction pattern. The wrapping of the a-helical fragment of the SNARES onto the SWCNT is similar to that of PA(40). Overall, there is a considerable decrease in the helical content of peptides upon interaction with SWCNTs, in agreement with the experimental findings.
Reprint Address:
Subramanian, V, Cent Leather Res Inst, Chem Lab, Council Sci & Ind Res, Madras 600020, Tamil Nadu, India.
Research Institution addresses:
[Balamurugan, K.; Gopalakrishnan, R.; Raman, S. Sundar; Subramanian, V.] Cent Leather Res Inst, Chem Lab, Council Sci & Ind Res, Madras 600020, Tamil Nadu, India
E-mail Address:
subuchem@hotmail.com
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Cited Reference Count:
67
Times Cited:
0
Publisher:
AMER CHEMICAL SOC; 1155 16TH ST, NW, WASHINGTON, DC 20036 USA
Subject Category:
Chemistry, Physical
ISSN:
1520-6106
DOI:
10.1021/jp106177n
IDS Number:
673ZT
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