Abstract:
:Depending on the nucleotide sequence, the temperature, and other conditions, RNA hairpin-folding kinetics can be very complex. The complexity with a wide range of cooperative and noncooperative kinetic behaviors arises from the interplay between the formation of the loops, the disruption of the misfolded states, and the formation of the rate-limiting base stacks. With a rate constant model and a kinetic-cluster theory, we explore the broad landscape for RNA hairpin-folding kinetics. The model is validated through direct tests against several experimental measurements. The general kinetic folding mechanisms and the predicted great variety of folding kinetics are directly applicable and quantitatively testable in experiments. The results from this study suggest that 1), previous experimental findings based on the individual hairpins revealed only a small fraction of much broader and more complex RNA hairpin-folding landscapes; 2), even for structures as simple as hairpins, universal folding timescales and pathways do not exist; and 3), to treat the loop size as the sole factor to determine the hairpin-folding rate is an oversimplification.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Zhang W,Chen SJdoi
10.1529/biophysj.105.062935subject
Has Abstractpub_date
2006-02-01 00:00:00pages
765-77issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(06)72265-2journal_volume
90pub_type
杂志文章abstract::The active amplification of sound-induced vibrations in the cochlea, known to be crucial for auditory sensitivity and frequency selectivity, is not well understood. The outer hair cell (OHC) somatic electromotility is a potential mechanism for such amplification. Its effectiveness in vivo is putatively limited by the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.12.040
更新日期:2012-02-08 00:00:00
abstract::We aimed to investigate insulin amyloid fibril polymorphism caused by salt effects and heating temperature and to visualize the structural differences of the polymorphisms in situ using Raman imaging without labeling. The time course monitoring for amyloid formation was carried out in an acidic condition without any s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.04.031
更新日期:2020-06-16 00:00:00
abstract::The harmonic mode analysis method was used to characterize the conformational deformability of regular Watson-Crick paired, mismatch- and bulge-containing RNA. Good agreement between atomic Debye-Waller factors derived from x-ray crystallography of a regular RNA oligonucleotide and calculated atomic fluctuations was o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76798-1
更新日期:2000-05-01 00:00:00
abstract::The scattering and absorption coefficients of many homogeneous biological tissues such as muscle, skin, white matter in the brain, and dentin are often anisotropically oriented with respect to their bounding interface. In consequence the curves of equal intensity of re-emitted light on the surface of the slab will no ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.058305
更新日期:2005-05-01 00:00:00
abstract::A discrete multistate kinetic model for water-wire proton transport is constructed and analyzed using Monte Carlo simulations. In the model, each water molecule can be in one of three states: oxygen lone-pairs pointing leftward, pointing rightward, or protonated (H(3)O(+)). Specific rules for transitions among these s...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74335-0
更新日期:2004-05-01 00:00:00
abstract::Cells control organelle size with great precision and accuracy to maintain optimal physiology, but the mechanisms by which they do so are largely unknown. Cilia and flagella are simple organelles in which a single measurement, length, can represent size. Maintenance of flagellar length requires an active transport pro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.12.051
更新日期:2015-03-24 00:00:00
abstract::Using a combination of microelectrode measurements and high-power microscopy we have demonstrated that different Donnan potentials can be recorded from the A- and I-bands of glycerinated and chemically skinned muscles in rigor, so that the A-band fixed charge concentration exceeds the I-band fixed charge concentration...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83760-7
更新日期:1985-07-01 00:00:00
abstract::A 15-ns molecular dynamics (MD) simulation of the fully hydrated dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer in the liquid-crystalline state was carried out to investigate the effect of Chol on the hydrocarbon chain region of the bilayer. The last 8-ns fragment of the generated trajectory was used f...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75867-5
更新日期:2001-10-01 00:00:00
abstract::Many toxins and antimicrobial peptides permeabilize membrane vesicles by forming multimeric pores. Determination of the size of such pores is an important first step for understanding their structure and the mechanism of their self-assembly. We report a simple method for sizing pores in vesicles based on the different...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78822-2
更新日期:1997-04-01 00:00:00
abstract::The viral genome and replicative enzymes of the human immunodeficiency virus are encased in a shell consisting of assembled mature capsid protein (CA). The core shell is a stable, effective protective barrier, but is also poised for dissolution on cue to allow transmission of the viral genome into its new host. In thi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75725-6
更新日期:2001-07-01 00:00:00
abstract::Titin is a very large (>3 MDa) protein found in striated muscle where it is believed to participate in myogenesis and passive tension. A prominent feature in the A-band portion of titin is the presence of an 11-domain super-repeat of immunoglobulin superfamily and fibronectin-type-III-like domains. Seven overlapping c...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(01)75811-0
更新日期:2001-09-01 00:00:00
abstract::Rapid and robust methods are required to quantify the effect of hydrodynamic shear on protein conformation change. We evaluated such strategies in this work and found that the binding of the fluorescent probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) to hydrophobic pockets in the blood protein von ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.08.023
更新日期:2009-11-04 00:00:00
abstract::Scanning ion conductance microscopy (SICM) is a super-resolution live imaging technique that uses a glass nanopipette as an imaging probe to produce three-dimensional (3D) images of cell surface. SICM can be used to analyze cell morphology at nanoscale, follow membrane dynamics, precisely position an imaging nanopipet...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.04.017
更新日期:2016-05-24 00:00:00
abstract::We used high-resolution atomic force microscopy to image the compaction of linear and circular DNA by the yeast mitochondrial protein Abf2p, which plays a major role in packaging mitochondrial DNA. Atomic force microscopy images show that protein binding induces drastic bends in the DNA backbone for both linear and ci...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74231-9
更新日期:2004-03-01 00:00:00
abstract::The state of photosystem II core complex (PS II CC) in monolayer at the gas-water interface was investigated using in situ polarization-modulated infrared reflection absorption spectroscopy and x-ray reflectivity techniques. Two approaches for preparing and manipulating the monolayers were examined and compared. In th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77731-8
更新日期:1998-12-01 00:00:00
abstract::Disruption of the integrity of the plasma membrane by amyloidogenic proteins is linked to the pathogenesis of a number of common age-related diseases. Although accumulating evidence suggests that adverse environmental stressors such as unbalanced levels of metal ions may trigger amyloid-mediated membrane damage, many ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.11.3811
更新日期:2013-01-08 00:00:00
abstract::Imaging in any plane other than horizontal in a microscope typically requires a reconstruction from multiple optical slices that significantly decreases the spatial and temporal resolution that can be achieved. This can limit the precision with which molecular events can be detected, for example, at intercellular cont...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.143198
更新日期:2008-11-15 00:00:00
abstract::A triple mutant of sperm whale myoglobin (Mb) [Leu(B10) --> Tyr, His(E7) --> Gln, and Thr(E10) --> Arg, called Mb-YQR], investigated by stopped-flow, laser photolysis, crystallography, and molecular dynamics (MD) simulations, proved to be quite unusual. Rebinding of photodissociated NO, O2, and CO from within the prot...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(99)77289-9
更新日期:1999-03-01 00:00:00
abstract::The prediction of absolute ligand-receptor binding affinities is essential in a wide range of biophysical queries, from the study of protein-protein interactions to structure-based drug design. End-point free energy methods, such as the Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) model, have received ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74084-9
更新日期:2004-01-01 00:00:00
abstract::The force-extension curve of single myosin subfragment-1 molecules, interacting in the rigor state with an actin filament, has been investigated at low [ATP] by applying a slow triangle-wave movement to the optical traps holding a bead-actin-bead dumbbell. In combination with a measurement of the overall stiffness of ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.119396
更新日期:2008-03-15 00:00:00
abstract::Molecular interactions are often transient and might change within the window of observation, leading to changes in molecule movement. Therefore, accurate motion analysis often requires transient motion classification. Here we present an accurate and computationally efficient transient mobility analysis framework, ter...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.01.012
更新日期:2018-03-13 00:00:00
abstract::We have studied tubules formed from a polymerizable lipid in aqueous dispersion using freeze-fracture replication and transmission electron microscopy. The polymerizable diacetylenic lecithin 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine converts from liposomes to hollow cylinders, which we call tubules, o...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83852-2
更新日期:1985-12-01 00:00:00
abstract::The parameters of the immune response dynamics are usually estimated by the use of deterministic ordinary differential equations that relate data trends to parameter values. Since the physical basis of the response is stochastic, we are investigating the intensity of the data fluctuations resulting from the intrinsic ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.094508
更新日期:2007-05-15 00:00:00
abstract::The canonical mass balance relation derived for the central core model of the renal medulla is extended to medullary models in which an arbitrary assemblage of renal tubules and vascular capillaries exchange with each other both directly and via the medullary interstitium and in which not all of the vascular loops or ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(76)85773-6
更新日期:1976-11-01 00:00:00
abstract::Molecular dynamics simulations are performed on two hydrated dipalmitoylphosphatidylcholine bilayer systems: one with pure water and one with added NaCl. Due to the rugged nature of the membrane/electrolyte interface, ion binding to the membrane surface is characterized by the loss of ion hydration. Using this structu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75102-9
更新日期:2003-06-01 00:00:00
abstract::Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis of long molecules. So far, nevertheless, the exact determination of Tw in these models has been based on a computation of the writhe of the molecules (Wr) by ex...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.06.005
更新日期:2015-07-07 00:00:00
abstract::Deuterium and phosphorus nuclear magnetic resonance (NMR) has been used to investigate the dynamics of slow motional processes induced in bilayer cardiolipin upon binding with cytochrome c. 31P NMR line shapes suggest that protein binding induces less restricted, isotropic-like motions in the lipid phosphates within t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81048-8
更新日期:1993-07-01 00:00:00
abstract::Synchrotron radiation circular dichroism, Fourier transform infrared, and nuclear magnetic resonance spectroscopies, and small-angle x-ray scattering were used to monitor the reversible thermal unfolding of hen egg white lysozyme. The results were compared with crystal structures and high- and low-temperature structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.07.060
更新日期:2010-10-06 00:00:00
abstract::Phenotypic plasticity is posed to be a vital trait of cancer cells such as circulating tumor cells, allowing them to undergo reversible or irreversible switching between phenotypic states important for tumorigenesis and metastasis. While irreversible phenotypic switching can be detected by studying the genome, reversi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.02.012
更新日期:2017-03-28 00:00:00
abstract::Electrorotation of fixed red blood cells has been investigated in the frequency range between 16 Hz and 30 MHz. The rotation was studied as a function of electrolyte conductivity and surface charge density. Between 16 Hz and 1 kHz, fixed red blood cells undergo cofield rotation. The maximum of cofield rotation occurs ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77918-4
更新日期:1998-04-01 00:00:00