Abstract:
:The folding of short alanine-based peptides with different numbers of lysine residues is simulated at constant temperature (274 K) using the rigid-element Monte Carlo method. The solvent-referenced potential has prevented the multiple-minima problem in helix folding. From various initial structures, the peptides with three lysine residues fold into helix-dominated conformations with the calculated average helicity in the range of 60-80%. The peptide with six lysine residues shows only 8-14% helicity. These results agree well with experimental observations. The intramolecular electrostatic interaction of the charged lysine side chains and their electrostatic hydration destabilize the helical conformations of the peptide with six lysine residues, whereas these effects on the peptides with three lysine residues are small. The simulations provide insight into the helix-folding mechanism, including the beta-bend intermediate in helix initiation, the (i, i + 3) hydrogen bonds, the asymmetrical helix propagation, and the asymmetrical helicities in the N- and C-terminal regions. These findings are consistent with previous studies.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Sung SSdoi
10.1016/S0006-3495(95)80259-6subject
Has Abstractpub_date
1995-03-01 00:00:00pages
826-34issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(95)80259-6journal_volume
68pub_type
杂志文章abstract::The interpretation of phi-values has led to an understanding of the folding transition state ensemble of a variety of proteins. Although the main guidelines and equations for calculating phi are well established, there remains some controversy about the quality of the numerical values obtained. By analyzing a complete...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.113241
更新日期:2008-06-01 00:00:00
abstract::Orientational order parameters of two diphenylhexatriene (DPH)-based fluorescent probes, 2-(3-(diphenylhexatrienyl)propanoyl)-1-hexadecanoyl-sn-glycero-3-p hosphocholine (DPHpPC) and 1-(4-trimethylammoniumphenyl)-6-phenyl-1,3,5-hexatriene (TMA-DPH), in dipalmitoylphosphatidylcholine (DPPC) Langmuir-Blodgett monolayers...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78908-2
更新日期:1997-06-01 00:00:00
abstract::In an attempt to better define the parameters governing reconstitution and two-dimensional crystallization of membrane proteins, we have studied Ca2(+)-ATPase from rabbit sarcoplasmic reticulum. This ion pump forms vanadate-induced crystals in its native membrane and has previously been reconstituted at high lipid-to-...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78898-2
更新日期:1997-06-01 00:00:00
abstract::A simple theoretical analysis shows that specificity of double-stranded DNA (dsDNA) targeting by homopyrimidine peptide nucleic acids (hpyPNAs) is a kinetically controlled phenomenon. Our computations give the optimum conditions for sequence-specific targeting of dsDNA by hpyPNAs. The analysis shows that, in agreement...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78918-5
更新日期:1997-06-01 00:00:00
abstract::Crystallographic studies of insulin-protamine complexes, such as neutral protamine Hagedorn (NPH) insulin, have been hampered by high crystal solvent content, small crystal dimensions, and extensive disorder in the protamine molecules. We report herein in situ tapping mode atomic force microscopy (TMAFM) studies of cr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76609-4
更新日期:2000-01-01 00:00:00
abstract::Molecular motors are thought to generate force and directional motion via nonequilibrium switching between energy surfaces. Because all enzymes can undergo such switching, we hypothesized that the ability to generate rotary motion and torque is not unique to highly adapted biological motor proteins but is instead a co...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.02.008
更新日期:2018-05-08 00:00:00
abstract::We have worked out a procedure for covalent binding of native biomacromolecules on flat gold surfaces for scanning probe microscopy in aqueous buffer solutions and for other nanotechnological applications, such as the direct measurement of interaction forces between immobilized macromolecules, of their elastomechanica...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79810-7
更新日期:1996-05-01 00:00:00
abstract::By exploring a recent model in which DNA bending elasticity, described by the wormlike chain model, is coupled to basepair denaturation, we demonstrate that small denaturation bubbles lead to anomalies in the flexibility of DNA at the nanometric scale, when confined in two dimensions (2D), as reported in atomic-force ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.03.035
更新日期:2009-06-03 00:00:00
abstract::Molecular dynamics simulations have been performed of the sequence-symmetric cyclic decapeptide antibiotic gramicidin S (GS), in interaction with a hydrated dimyristoylphosphatidylcholine (DMPC) bilayer, and the results compared with a "control" simulation of the system in the absence of GS. Following experimental evi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76424-1
更新日期:2000-10-01 00:00:00
abstract::Connectin (titin) is a large filamentous protein (single peptide) with a molecular mass of approximately 3 MDa, contour length approximately 900 nm, and diameter approximately 4 nm, and resides in striated muscle. Connectin links the thick filaments to the Z-lines in a sarcomere and produces a passive elastic force wh...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81261-X
更新日期:1993-11-01 00:00:00
abstract::Skeletal muscle contraction is a canonical example of motor-driven force generation. Despite the long history of research in this topic, a mechanistic explanation of the collective myosin force generation is lacking. We present a theoretical model of muscle contraction based on the conformational movements of individu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.056846
更新日期:2005-06-01 00:00:00
abstract::The electrophysiological properties of the cation channel of the purified nicotinic acetylcholine receptor (AChR) reconstituted in planar lipid bilayers were characterized. Single-channel currents were activated by acetylcholine, carbamylcholine and suberyldicholine. The single channel conductance (28 pS in 0.3 M NaCl...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84145-4
更新日期:1984-01-01 00:00:00
abstract::The energetics of phospholipid aggregation depend on the apparent water-accessible apolar surface area (ASAap), ordering effects of the chains, and headgroup interactions. We quantify the enthalpy and entropy of these interactions separately. For that purpose, the thermodynamics of micelle formation of lysophosphatidy...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76012-2
更新日期:2001-01-01 00:00:00
abstract::A newly developed microscope using acousto-optic tunable filters (AOTFs) was used to generate in vivo hemoglobin saturation (SO2) and oxygen tension (PO2) maps in the cerebral cortex of mice. SO2 maps were generated from the spectral analysis of reflected absorbance images collected at different wavelengths, and PO2 m...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78155-4
更新日期:1997-09-01 00:00:00
abstract::Nuclear calcium is a key signal in the dialogue between synapse and nucleus that controls the genomic responses required for persistent adaptations, including memory and acquired neuroprotection. The amplitude and duration of nuclear calcium transients specify activity-induced transcriptional changes. However, the pre...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.10.044
更新日期:2010-12-15 00:00:00
abstract::The Ca(2+) permeability of N-methyl-D-aspartate receptor (NMDA-R) channels was studied in human embryonic kidney cells transfected with the NR1-NR2A subunit combination. To determine the fractional Ca(2+) current (P(f)), measurements of fura-2-based Ca(2+) influx and whole-cell currents were made in symmetrical monova...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79782-5
更新日期:1996-05-01 00:00:00
abstract::Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.127746
更新日期:2008-09-15 00:00:00
abstract::We describe a model that relates the maximum shortening velocity of a muscle fiber, Vm, to the kinetics of the dissociation of a myosin head from actin. At Vm, the positive work exerted by cross-bridges attached in the powerstroke must be balanced by cross-bridges that have been carried by movement of the filaments in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(94)80854-9
更新日期:1994-03-01 00:00:00
abstract::Ca(2+) ion effect on protoplasmic streaming in an internodal cell of Nitella has been investigated for various temperatures. We have found that the protoplasmic streaming at low temperature is remarkably affected by the Ca(2+) ions in the internodal cell but larger concentrations of the Ca(2+) ions are needed to suppr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81355-9
更新日期:1993-01-01 00:00:00
abstract::Fatty acid binding proteins play an important role in the transportation of fatty acids. Despite intensive studies, how fatty acids enter the protein cavity for binding is still controversial. Here, a gap-closed variant of human intestinal fatty acid binding protein was generated by mutagenesis, in which the gap is lo...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.12.005
更新日期:2020-01-21 00:00:00
abstract::Erythrocytes were electrofused with multiple rectangular voltage pulses to show an oscillatory movement, divided into swell phases and pump events. During each swell phase, which lasted from 0.5 s to more than 180 s, the fused cells' (doublets') volume increased by colloid osmotic swelling, and the membrane area was e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77094-3
更新日期:1999-11-01 00:00:00
abstract::A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000-000) has been used for computing the end-to-end distance distribut...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)74002-0
更新日期:1998-02-01 00:00:00
abstract::Voltage-dependent G-protein inhibition of N-type calcium channels reduces presynaptic calcium entry, sharply attenuating neurotransmitter release. Studies in neurons demonstrate that G-proteins have multiple modulatory effects on N-type channels. The observed changes may reflect genuine complexity in G-protein action ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79444-4
更新日期:1996-11-01 00:00:00
abstract::A long-standing question about membrane structure and function is the degree to which the physical properties of the inner and outer leaflets of a bilayer are coupled to one another. Using our recently developed methods to prepare asymmetric vesicles, coupling was investigated for vesicles containing phosphatidylcholi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.10.033
更新日期:2012-12-05 00:00:00
abstract::Sperm have generally been supposed to penetrate the zona pellucida surrounding the mammalian egg with the aid of a protease, acrosin. Difficulties associated with this view are discussed and an alternative, mechanical hypothesis introduced. The calculated force exerted by individual sperm is too small to permit the ru...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84207-1
更新日期:1984-04-01 00:00:00
abstract::In the studies of force-induced conformational transitions of biomolecules, the large timescale difference from experiments presents the challenge of obtaining convergent sampling for molecular dynamics simulations. To circumvent this fundamental problem, an approach combining the replica-exchange method and umbrella ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.11.004
更新日期:2010-02-17 00:00:00
abstract::The impedance measured in a strip of heart tissue from the moth Hyalophora cecropia is fitted by circuit models of several configurations. The circuits include: (a) a single R-C circuit (b) a double R-C circuit (c) terminated transmission lines, and (d) a pattern of cells with cell-to-cell transmission paths. The last...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(74)70001-7
更新日期:1974-02-01 00:00:00
abstract::The well-characterized integral membrane protein lactose (lac) permease from Escherichia coli was reconstituted together with trace amounts (molar fraction X = 0.005 of the total phospholipid) of different pyrene-labeled phospholipid analogs into 1-palmitoyl-2-oleoyl-sn-glycero-3-sn-glycero-3-phospho-rac'-glycerol (PO...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78771-X
更新日期:1997-03-01 00:00:00
abstract::The organization of filamentous actin and myosin II molecular motor contractility is known to modify the mechanical properties of the cell cortical actomyosin cytoskeleton. Here we describe a novel method, to our knowledge, for using force spectroscopy approach curves with tipless cantilevers to determine the actomyos...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.04.034
更新日期:2016-06-07 00:00:00
abstract::Presented here is a quantitative model of the wrapping and unwrapping of the DNA around the histone core of the nucleosome that suggests a mechanism by which this transition can be controlled: alteration of the charge state of the globular histone core. The mechanism is relevant to several classes of posttranslational...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.06.046
更新日期:2010-09-08 00:00:00