General Physiology and Biophysics 

About: General Physiology and Biophysics is an academic journal published by AEPress. The journal publishes majorly in the area(s): Oxidative stress & Membrane. It has an ISSN identifier of 0231-5882. It is also open access. Over the lifetime, 1977 publications have been published receiving 21352 citations.

Structure and flexibility within proteins as identified through small angle X-ray scattering.

Abstract: Flexibility between domains of proteins is often critical for function. These motions and proteins with large scale flexibility in general are often not readily amenable to conventional structural analysis such as X-ray crystallography, nuclear magnetic resonance spectroscopy (NMR) or electron microscopy. A common evolution of a crystallography project, once a high resolution structure has been determined, is to postulate possible sights of flexibility. Here we describe an analysis tool using relatively inexpensive small angle X-ray scattering (SAXS) measurements to identify flexibility and validate a constructed minimal ensemble of models, which represent highly populated conformations in solution. The resolution of these results is sufficient to address the questions being asked: what kinds of conformations do the domains sample in solution? In our rigid body modeling strategy BILBOMD, molecular dynamics (MD) simulations are used to explore conformational space. A common strategy is to perform the MD simulation on the domains connections at very high temperature, where the additional kinetic energy prevents the molecule from becoming trapped in a local minimum. The MD simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. A genetic algorithm is used to identify the minimal ensemble (minimal ensemble search, MES) required to best fit the experimental data. We demonstrate the use of MES in several model and in four experimental examples.

Malate dehydrogenases--structure and function.

Abstract: Malate dehydrogenases (MDH, L-malate:NAD oxidoreductase, EC 1.1.1.37), catalyze the NAD/NADH-dependent interconversion of the substrates malate and oxaloacetate. This reaction plays a key part in the malate/aspartate shuttle across the mitochondrial membrane, and in the tricarboxylic acid cycle within the mitochondrial matrix. They are homodimeric molecules in most organisms, including all eukaryots and the most bacterial species. The enzymes share a common catalytic mechanism and their kinetic properties are similar, which demonstrates a high degree of structural similarity. The three-dimensional structures and elements essential for catalysis are conserved between mitochondrial and cytoplasmic forms of MDH in eukaryotic cells even though these isoenzymes are only marginally related at the level of primary structure.

Voltage-dependent calcium channels.

Abstract: Voltage-activated calcium channels can be divided into two subgroups based on their activation threshold, low-voltage-activated (LVA) and high-voltage-activated (HVA) Auxiliary subunits of the HVA calcium channels contribute significantly to biophysical properties of the channels We have cloned and characterized members of two families of auxiliary subunits: alpha2delta and gamma Two new alpha2delta subunits, alpha2delta-2 and alpha2delta-3, regulate all classes of HVA calcium channels While the ubiquitous alpha2delta-2 modulates both neuronal and non-neuronal channels with similar efficiency, the alpha2delta-3 subunit regulates Ca(v)23 channels more effectively Furthermore, alpha2delta-2 may modulate the LVA Ca(v)31 channel Four new gamma subunits, gamma-2, gamma-3, gamma-4 and gamma-5, were characterized The gamma-2 subunit modulated both the non-neuronal Ca(v)12 channel and the neuronal Ca(v)21 channel The gamma-4 subunit affected only the Ca(v)21 channel The gamma-5 subunit may be a regulatory subunit of the LVA Ca(v)31 channel The Ca(v)12 channel is a major target for treatment of cardiovascular diseases We have mapped the interaction site for clinically important channel blockers - dihydropyridines (DHPs) - and analysed the underlying inhibition mechanism High-affinity inhibition is characterized by interaction with inactivated state of the channel Its structural determinants are amino acids of the IVS6 segment, with smaller contribution of the IS6 segment, which contributes to voltage-dependence of DHP inhibition Removal of amino acids responsible for the high-affinity inhibition revealed a low-affinity open channel block, in which amino acids of the IIIS5 and IIIS6 segments take part Experiments with a permanently charged DHP suggested that there is another low-affinity interaction site on the alpha(1) subunit We have cloned and characterized murine neuronal LVA Ca(v)31 channel The channel has high sensitivity to the organic blocker mibefradil, moderate sensitivity to phenytoin, and low sensitivity to ethosuximide, amiloride and valproat The channel is insensitive to tetrodotoxin and DHPs The inorganic blockers Ni2+ and Cd2+ are moderately effective compared to La3+ The current through the Ca(v)31 channel inactivates faster with Ba2+ compared to Ca2+ Molecular determinants of fast inactivation are located in amino side of the intracellular carboxy terminus The voltage dependence of charge movement is very shallow compared to the voltage dependence of current activation Transfer of 30 % of charge correlates with activation of 70 % of measurable macroscopic current Prolonged depolarization does not immobilize charge movement of the Ca(v)31 channel

Controversy of free radical hypothesis: reactive oxygen species--cause or consequence of tissue injury?

Abstract: For a decade or two, the hypothesis of causality of various disorders by reactive oxygen species (ROS), due to their potentially harmful effect towards cellular constituents, is one of the most frequently cited in biomedical sciences In fact, the ROS-mediated alterations of biomacromolecules are considered to be essential events in the etiopathogenesis of those diseases where involvement of ROS has been indicated ROS easily react in vitro with most biological molecules, causing their degradation and destruction This may implicitly suggest that, when excessively produced in vivo, ROS are deleterious to integral components of the cell and cause their dysfunctions Some experimental data indicate that ROS-mediated lipid peroxidation, protein oxidation and oxidative alterations to nucleic acids are crucial events of unfavorable actions of ROS Yet the most convincing evidence, ie unambiguous inhibition of tissue injury by pretreatment with antioxidants, has not been provided On the contrary, there are quite a few papers reporting failure in applying antioxidants to heal those pathologies where the causal role of ROS was supposed Other papers reported serious complications arising from antioxidant therapy, which is quite in contradiction to its expected effect On the other hand, an increasing number of recent findings have provided evidence of a key role of ROS in both intracellular signaling and intercellular communication, processes involved in maintaining homeostasis Hence, some investigators consider excessive production of ROS to be rather a "smoke after the fire" than "a deleterious fire" itself, suggesting the occurrence of overproduced ROS as being the consequence of some primary damage The present paper aims at summarizing some pros and cons of various opinions with an attempt to help better understand the involvement of ROS in tissue injury

Calcium binding chaperones of the endoplasmic reticulum

Abstract: The endoplasmic reticulum is a major Ca(2+) store of the cell that impacts many cellular processes within the cell. The endoplasmic reticulum has roles in lipid and sterol synthesis, protein folding, post-translational modification and secretion and these functions are affected by intraluminal endoplasmic reticulum Ca(2+). In the endoplasmic reticulum there are several Ca(2+) buffering chaperones including calreticulin, Grp94, BiP and protein disulfide isomerase. Calreticulin is one of the major Ca(2+) binding/buffering chaperones in the endoplasmic reticulum. It has a critical role in Ca(2+) signalling in the endoplasmic reticulum lumen and this has significant impacts on many Ca(2+)-dependent pathways including control of transcription during embryonic development. In addition to Ca(2+) buffering, calreticulin plays important role in the correct folding and quality control of newly synthesized glycoproteins.