Abstract:
:We present a qualitative computer graphics approach to the characterization of forces important to the assembly of beta domains that should have general utility for examining protein interactions and assembly. In our approach, the nature of the molecular surface buried by the domain contacts, the specificity of the residue-to-residue interactions, and the identity of electrostatic, hydrophobic, and hydrophilic interactions are elucidated. These techniques are applied to the beta barrel domains of Cu, Zn superoxide dismutase (SOD), immunoglobulin Fab, and tomato bushy stunt virus coat protein (TBSV), a plant viral capsid protein. By looking at a set of proteins having different numbers of interacting beta domains, we have been able to see some of the variety and also some of the patterns common to these assembled domains. Strong beta domain interactions (identified by their biochemical integrity) are apparently due to chemical, electrostatic, and shape complementarity of the molecular surfaces buried from interaction with solvent molecules. Although the amount of hydrophobic buried surface area appears to correlate with the strength of the interaction, electrostatic forces appear to be important in both stabilizing and destabilizing specific contacts. In TBSV, analysis of electrostatic interactions may help explain mechanisms of subunit accommodation to different environments, particle expansion, and pathways of assembly. The possible molecular basis for observed differences in the stability and flexibility of the domain complexes is discussed.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Getzoff ED,Tainer JA,Olson AJdoi
10.1016/S0006-3495(86)83634-7subject
Has Abstractpub_date
1986-01-01 00:00:00pages
191-206issue
1eissn
0006-3495issn
1542-0086pii
S0006-3495(86)83634-7journal_volume
49pub_type
杂志文章abstract::Polarized photolysis experiments have been performed on the carbon monoxide complex of myoglobin to assess the effects of photoselection on the kinetics of ligand rebinding and to investigate the reorientational dynamics of the heme plane. The results are analyzed in terms of the optical theory developed in the preced...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81446-2
更新日期:1993-03-01 00:00:00
abstract::We present a detailed motion analysis of retrograde nerve growth factor (NGF) endosomes in axons to show that mechanical tugs-of-war and intracellular motor regulation are complimentary features of the near-unidirectional endosome directionality. We used quantum dots to fluorescently label NGF and acquired trajectorie...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2015.04.036
更新日期:2015-06-02 00:00:00
abstract::The extracellular space of the brain is the heterogeneous porous medium formed by the spaces between the brain cells. Diffusion in this interstitial space is the mechanism by which glucose and oxygen are delivered to the brain cells from the vascular system. It is also a medium for the transport of certain information...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.095547
更新日期:2007-05-15 00:00:00
abstract::The main goal of this study is to investigate the role of mitochondrial [Ca(2+)], [Ca(2+)](m), in the possible up-regulation of the NADH production rate during increased workload. Such up-regulation is necessary to support increased flux through the electron transport chain and increased ATP synthesis rates. Intact ca...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75194-1
更新日期:2002-08-01 00:00:00
abstract::A challenge in the understanding of creatine kinase (CK) fluxes reflected by NMR magnetization transfer in the perfused rat heart is the choice of a kinetic model of analysis. The complexity of the energetic pathways, due to the presence of adenosine triphosphate (ATP)-inorganic phosphate (Pi) exchange, of metabolite ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75940-1
更新日期:2001-12-01 00:00:00
abstract::Experimental approaches such as fiber diffraction and cryo-electron microscopy reconstruction have defined regulatory positions of tropomyosin on actin but have not, as yet, succeeded at determining key atomic-level contacts between these proteins or fully substantiated the dynamics of their interactions at a structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.05.017
更新日期:2020-07-07 00:00:00
abstract::The origin of Ibetanull, the Ca2+ current of myotubes from mice lacking the skeletal dihydropyridine receptor (DHPR) beta1a subunit, was investigated. The density of Ibetanull was similar to that of Idys, the Ca2+ current of myotubes from dysgenic mice lacking the skeletal DHPR alpha1S subunit (-0.6 +/- 0.1 and -0.7 +...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77507-1
更新日期:1998-07-01 00:00:00
abstract::Actin filaments are semiflexible polymers that display large-scale conformational twisting and bending motions. Modulation of filament bending and twisting dynamics has been linked to regulatory actin-binding protein function, filament assembly and fragmentation, and overall cell motility. The relationship between act...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.07.009
更新日期:2010-09-22 00:00:00
abstract::The group-additive decomposition of the unfolding free energy of a protein in an osmolyte solution relative to that in water poses a fundamental paradox: whereas the decomposition describes the experimental results rather well, theory suggests that a group-additive decomposition of free energies is, in general, not va...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.08.011
更新日期:2013-09-17 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::Collagen fibrils play an important role in the human body, providing tensile strength to connective tissues. These fibrils are characterized by a banding pattern with a D-period of 67 nm. The proposed origin of the D-period is the internal staggering of tropocollagen molecules within the fibril, leading to gap and ove...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.09.003
更新日期:2014-10-21 00:00:00
abstract::It has been repeatedly noted that the change of conformation of the molecules that serve as the ion-selective channels for sodium and potassium conductance in the nerve membrane will be accompanied by a change in the dipole moment of the molecule. This time-dependent change of dipole moment will produce transient curr...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(77)85587-2
更新日期:1977-09-01 00:00:00
abstract::The interaction of an amphiphilic, 40-amino acid beta-amyloid (Abeta) peptide with liposomal membranes as a function of sterol mole fraction (X(sterol)) was studied based on the fluorescence anisotropy of a site-specific membrane sterol probe, dehydroergosterol (DHE), and fluorescence resonance energy transfer (FRET) ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.02.036
更新日期:2009-05-20 00:00:00
abstract::Phospholipids with covalently attached poly(ethylene glycol) (PEG lipids) are commonly used for the preparation of long circulating liposomes. Although it is well known that lipid/PEG-lipid mixed micelles may form above a certain critical concentration of PEG-lipid, little is known about the effects of PEG-lipids on l...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78066-4
更新日期:1997-07-01 00:00:00
abstract::The proline-, glutamate-, valine-, and lysine-rich (PEVK) domain of the giant muscle protein titin is thought to be an intrinsically unstructured random-coil segment. Various observations suggest, however, that the domain may not be completely devoid of internal interactions and structural features. To test the validi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.08.042
更新日期:2012-10-03 00:00:00
abstract::In a contracting muscle, myosin cross-bridges extending from thick filaments pull the interdigitating thin (actin-containing) filaments during cyclical ATP-driven interactions toward the center of the sarcomere, the structural unit of striated muscle. Cross-bridge attachments in the sarcomere have been reported to exh...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2020.01.002
更新日期:2020-03-10 00:00:00
abstract::In diseases of the brain, the distribution and properties of ion channels display deviations from healthy control subjects. We studied three cases of ion channel alteration related to epileptogenesis. The first case of ion channel alteration represents an enhanced sodium current, the second case addresses the downregu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.08.055
更新日期:2011-10-19 00:00:00
abstract::The interaction of α-helical peptides with lipid bilayers is central to our understanding of the physicochemical principles of biological membrane organization and stability. Mutations that alter the position or orientation of an α-helix within a membrane, or that change the probability that the α-helix will insert in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.02.041
更新日期:2011-04-20 00:00:00
abstract::Both the solution and the oriented film absorption and circular dichroic spectra of the bacteriorhodopsin (bR(568)) and M(412) intermediate of the purple membrane photocycle were compared over the wavelength region 800-183 nm to assess structural changes during this photocycle. The main findings are (a) loss of the ex...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(85)83943-6
更新日期:1985-04-01 00:00:00
abstract::Relations describing threshold fluctuation phenomena in nerves are derived by calculating the approximate response of the Hodgkin-Huxley (HH) axon to electrical noise. We use FitzHugh's reduced phase space approximation and describe the dynamics of a noisy nerve by a two-dimensional brownian motion. The theory predict...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(71)86277-X
更新日期:1971-12-01 00:00:00
abstract::To elucidate effects of electrostatic interactions resulting from surface charges on structures and phase stability of cubic phases of lipid membranes, membranes of 1-monoolein (MO) and dioleoylphosphatidic acid (DOPA) (DOPA/MO membrane) mixtures have been investigated by small-angle x-ray scattering method. As increa...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)75756-6
更新日期:2001-08-01 00:00:00
abstract::Fluorescence correlation spectroscopy (FCS) is a sensitive and widely used technique for measuring diffusion. FCS data are conventionally modeled with a finite number of diffusing components and fit with a least-square fitting algorithm. This approach is inadequate for analyzing data obtained from highly heterogeneous...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)75006-1
更新日期:2003-03-01 00:00:00
abstract::Calmodulin (CaM) is a highly flexible calcium-binding protein that mediates signal transduction through an ability to differentially bind to highly variable binding sequences in target proteins. To identify how binding affects CaM motions, and its relationship to conformational entropy and target peptide sequence, we ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.08.037
更新日期:2012-10-03 00:00:00
abstract::Despite the recognition that actin filaments are important for numerous cellular processes, and decades of investigation, the dynamics of in vitro actin filaments are still not completely understood. Here, we follow the time evolution of the length distribution of labeled actin reporter filaments in an unlabeled F-act...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.07.009
更新日期:2011-08-17 00:00:00
abstract::During inflammation, flowing leukocytes tether to and roll on vascular surfaces through the association and dissociation of selectin/ligand bonds. The interactions of P- and L- selectins with their respective ligands exhibit catch-slip bonds, such that increasing force initially prolongs and then shortens bond lifetim...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.05.040
更新日期:2010-08-09 00:00:00
abstract::We have refined the structure of the DNA Three-Way Junction complex, TWJ-TC, described in the companion paper by quantitative analysis of two 2D NOESY spectra (mixing times 60 and 200 ms) obtained in D2O solution. NOESY crosspeak intensities extracted from these spectra were used in two kinds of refinement procedure: ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)80183-9
更新日期:1995-01-01 00:00:00
abstract::Fiber orientation and ventricular geometry are incorporated in a mathematical model for ejection fraction of the human left ventricle. The inadequacy of circularly oriented or "constrictor" fibers to explain high ejection fractions of cylindrical, spherical, or ellipsoidal reference ventricles is demonstrated. A class...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(69)86429-5
更新日期:1969-07-01 00:00:00
abstract::Hair cells of the inner ear can power spontaneous oscillations of their mechanosensory hair bundle, resulting in amplification of weak inputs near the characteristic frequency of oscillation. Recently, dynamic force measurements have revealed that delayed gating of the mechanosensitive ion channels responsible for mec...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.11.019
更新日期:2018-01-23 00:00:00
abstract::Multiple molecular dynamics simulations of bacterioopsin pulling from its C-terminus show that its alpha-helices unfold individually. In the first metastable state observed in the simulations, helix G is unfolded at its C-terminal segment while the rest of helix G (residues 200-216) is folded and opposes resistance be...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.088591
更新日期:2006-11-01 00:00:00
abstract::Heterogeneity of ADP diffusion and regulation of respiration were studied in permeabilized cardiomyocytes and cardiac fibers in situ and in silico. Regular arrangement of mitochondria in cells was altered by short-time treatment with trypsin and visualized by confocal microscopy. Manipulation of matrix volumes by chan...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)70065-4
更新日期:2003-05-01 00:00:00