Abstract:
:A reduction in pH induces the release of iron from transferrin in a process that involves a conformational change in the protein from a closed to an open form. Experimental evidence suggests that there must be changes in the protonation states of certain, as yet not clearly identified, residues in the protein accompanying this conformational change. Such changes in protonation states of residues and the consequent changes in electrostatic interactions are assumed to play a large part in the mechanism of release of iron from transferrin. Using the x-ray crystal structures of human ferri- and apo-lactoferrin, we calculated the pKa values of the titratable residues in both the closed (iron-loaded) and open (iron-free) conformations with a continuum electrostatic model. With the knowledge of a residue's pKa value, its most probable protonation state at any specified pH may be determined. The preliminary results presented here are in good agreement with the experimental observation that the binding of ferric iron and the synergistic anion bicarbonate/carbonate results in the release of approximately three H+ ions. It is suggested that the release of these three H+ ions may be accounted for, in most part, by the deprotonation of the bicarbonate and residues Tyr-92, Lys-243, Lys-282, and Lys-285 together with the protonation of residues Asp-217 and Lys-277.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Lee DA,Goodfellow JMdoi
10.1016/S0006-3495(98)77983-4subject
Has Abstractpub_date
1998-06-01 00:00:00pages
2747-59issue
6eissn
0006-3495issn
1542-0086pii
S0006-3495(98)77983-4journal_volume
74pub_type
杂志文章abstract::The genetic map of T4 (and T2) bacteriophage is circular but the DNA molecule that is liberated by phenol extraction is a linear duplex of polynucleotide chains. If the genetic map is related to the physical structure of the DNA molecule, the problem arises as to how a linear molecule can give rise to a circular map. ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/s0006-3495(64)86771-0
更新日期:1964-03-01 00:00:00
abstract::The anisotropy of the spin-lattice relaxation time (T1) and the spin-spin relaxation times (T2) of water protons in skeletal muscle tissue have been studied by the spin-echo technique. Both T1 and T2 have been measured for the water protons of the tibialis anterior muscle of mature male rats for theta = 0, 55, and 90 ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85102-2
更新日期:1980-06-01 00:00:00
abstract::Previously, we discussed the calculation of the dipole moments of small proteins using the three-dimensional protein data-base. Our results demonstrate that the calculated dipole moments are in acceptable agreement with measured values. We, however, noted the difficulty of the calculation with larger proteins, in part...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81524-8
更新日期:1993-05-01 00:00:00
abstract::The AXH domain of protein Ataxin 1 is thought to play a key role in the misfolding and aggregation pathway responsible for Spinocerebellar ataxia 1. For this reason, a molecular level understanding of AXH oligomerization pathway is crucial to elucidate the aggregation mechanism, which is thought to trigger the disease...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.11.025
更新日期:2018-01-23 00:00:00
abstract::Keratin intermediate filaments form dynamic intracellular networks, which span the entire cytoplasm and provide mechanical strength to the cell. The mechanical resilience of the keratin intermediate filament network itself is determined by filament bundling. The bundling process can be reproduced in artificial conditi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.05.024
更新日期:2020-07-07 00:00:00
abstract::The cornea is the primary refractive lens in the eye and transmits >90% of incident visible light. It has been suggested that the development of postoperative corneal haze could be due to an increase in light scattering from activated corneal stromal cells. Quiescent keratocytes are thought to produce crystallins that...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.08.046
更新日期:2015-10-20 00:00:00
abstract::Solid phase amplification (SPA), a new method to amplify DNA, is characterized by the use of surface-bound primers. This limits the amplification to two-dimensional surfaces and therefore allows the easy parallelization of DNA amplification in a single system. SPA leads to the formation of small but dense DNA brushes,...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.051904
更新日期:2005-07-01 00:00:00
abstract::Intercellular channels formed of members of the gene family of connexins (Cxs) vary from being substantially cation selective to being anion selective. We took advantage of the ability of Cx46 to function as an unopposed hemichannel to examine the basis of Cx charge selectivity. Previously we showed Cx46 hemichannels ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76539-8
更新日期:2000-12-01 00:00:00
abstract::Force spectroscopy is commonly used to measure the kinetics of processes occurring in single biological molecules. These measurements involve attaching the molecule of interest to micron-sized or larger force probes via compliant linkers. Recent theoretical work has described how the properties of the probes and linke...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.06.011
更新日期:2016-07-26 00:00:00
abstract::We study DNA supercoiling in a quantitative fashion by micromanipulating single linear DNA molecules with a magnetic field gradient. By anchoring one end of the DNA to multiple sites on a magnetic bead and the other end to multiple sites on a glass surface, we were able to exert torsional control on the DNA. A rotatin...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77908-1
更新日期:1998-04-01 00:00:00
abstract::Homooligomerization of proline utilization A (PutA) bifunctional flavoenzymes is intimately tied to catalytic function and substrate channeling. PutA from Bradyrhizobium japonicum (BjPutA) is unique among PutAs in that it forms a tetramer in solution. Curiously, a dimeric BjPutA hot spot mutant was previously shown to...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2018.04.046
更新日期:2018-06-19 00:00:00
abstract::Molecular dynamics simulations have been applied to the DNA octamer d(GCGCA-GAAC). d(GTTCGCGC), which has an adenine bulge at the center to determine the pathway for interconversion between the stacked and extended forms. These forms are known to be important in the molecular recognition of bulges. From a total of ~35...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75705-0
更新日期:2001-07-01 00:00:00
abstract::Using polarography and suitable mathematical analysis, the oxygen permeability of an individual layer of a bilayered tissue may be determined if the oxygen consumption and permeability of the other layer are known. Results obtained on rabbit cornea indicate that the permeability of the epithelium is about four times t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(72)86083-1
更新日期:1972-03-01 00:00:00
abstract::Ca2+ regulates ryanodine receptor's (RyR) activity through an activating and an inhibiting Ca2+-binding site located on the cytoplasmic side of the RyR channel. Their altered sensitivity plays an important role in the pathology of malignant hyperthermia and heart failure. We used lanthanide ions (Ln3+) as probes to in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.03.023
更新日期:2017-05-23 00:00:00
abstract::The one-dimensional information of genomic DNA is hierarchically packed inside the eukaryotic cell nucleus and organized in a three-dimensional (3D) space. Genome-wide chromosome conformation capture (Hi-C) methods have uncovered the 3D genome organization and revealed multiscale chromatin domains of compartments and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.02.020
更新日期:2020-05-05 00:00:00
abstract::Dimerization of the transmembrane (TM) adaptor protein DAP12 plays a key role in mediating activation signals through TM-TM association with cell-surface receptors. Herein, we apply the TOXCAT assay and molecular dynamics simulation to analyze dynamics and dimerization of the TM helix of DAP12 in the membrane bilayer....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.01.054
更新日期:2013-04-02 00:00:00
abstract::A detailed picture of water and ion properties in small pores is important for understanding the behavior of biological ion channels. Several recent modeling studies have shown that small, hydrophobic pores exclude water and ions even if they are physically large enough to accommodate them, a mechanism called hydropho...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.080432
更新日期:2006-05-15 00:00:00
abstract::For immobilized nitroxide spin-labels with a well-defined interprobe geometry, resolved dipolar splittings can be observed in continuous wave electron paramagnetic resonance (CW-EPR) spectra for interelectron distances as large as 30 A using perdeuterated probes. In this work, algorithms are developed for calculating ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78832-5
更新日期:1997-04-01 00:00:00
abstract::Beat-to-beat alternation of the action potential duration (APD) in paced cardiac cells has been linked to the onset of lethal arrhythmias. Both experimental and theoretical studies have shown that alternans at the single cell level can be caused by unstable membrane voltage (V(m)) dynamics linked to steep APD-restitut...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.100982
更新日期:2007-02-15 00:00:00
abstract::Cofilin/ADF, beryllium fluoride complex (BeFx), and phalloidin have opposing effects on actin filament structure and dynamics. Cofilin/ADF decreases the stability of F-actin by enhancing disorder in subdomain 2, and by severing and accelerating the depolymerization of the filament. BeFx and phalloidin stabilize the su...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.087767
更新日期:2006-12-15 00:00:00
abstract::Low frequency audible vibrations are produced by human skeletal muscles undergoing sustained contraction. The effect is easily demonstrable with an electronic stethoscope which amplifies sound below 50 Hz. Autocorrelation analysis of the signal shows that it is periodic with a frequency 25 +/- 2.5 Hz. The quality of t...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85080-6
更新日期:1980-04-01 00:00:00
abstract::The fundamental backbone dynamics of unfolded proteins arising due to intrinsic ϕ-ψ dihedral angle fluctuations dictate the course of protein folding, binding, assembly, and function. These internal fluctuations are also critical for protein misfolding associated with a range of human diseases. However, direct observa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2016.07.023
更新日期:2016-08-23 00:00:00
abstract::Deuterium NMR spectroscopy was used to study how the positioning of a dimerization motif within a transbilayer polypeptide influences its orientation and dynamics in bilayers. Three polypeptide variants comprising glycophorin A transmembrane (GpATM) dimerization motifs incorporated into lysine-terminated poly-leucine-...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.12.3725
更新日期:2011-02-02 00:00:00
abstract::Potassium accumulation associated with outward membrane potassium current was investigated experimentally in myelinated fibers and analyzed in terms of two models-three-compartment and diffusion in an unstirred layer. In the myelinated fibers, as in squid giant axons, the three-compartment model satisfactorily describ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85028-4
更新日期:1980-12-01 00:00:00
abstract::We report applications of two-photon excitation fluorescence (2PEF) microscopy with subdiffraction-limit resolution for green-fluorescent-protein-tagged cell imaging. The microscope integrates 2PEF microscopy and stimulated emission depletion microscopy in one microscope that has the benefits of both techniques: intri...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.09.038
更新日期:2009-12-16 00:00:00
abstract::Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived fr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.109868
更新日期:2008-02-01 00:00:00
abstract::The pores of ion channel proteins are often modeled as static structures. In this view, selectivity reflects rigidly constrained backbone orientations. Such a picture is at variance with the generalization that biological proteins are flexible, capable of major internal motions on biologically relevant time scales. We...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78096-2
更新日期:1997-08-01 00:00:00
abstract::Electrical bursting oscillations of mammalian pancreatic beta-cells are synchronous among cells within an islet. While electrical coupling among cells via gap junctions has been demonstrated, its extent and topology are unclear. The beta-cells also share an extracellular compartment in which oscillations of K+ concent...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81092-0
更新日期:1993-08-01 00:00:00
abstract::The mitochondrial channel, VDAC, forms large (3 nm in diameter) aqueous pores through membranes. We measured ATP flow (using the luciferin/luciferase method) through these channels after reconstitution into planar phospholipid membranes. In the open state of VDAC, as many as 2 x 10(6) ATP molecules can flow through on...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78841-6
更新日期:1997-05-01 00:00:00
abstract::The effects of lipid chain packing and permeant size and shape on permeability across lipid bilayers have been investigated in gel and liquid crystalline dipalmitoylphosphatidylcholine (DPPC) bilayers by a combined NMR line-broadening/dynamic light scattering method using seven short-chain monocarboxylic acids (formic...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77711-2
更新日期:1998-12-01 00:00:00