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At least 577 records · Page 32Linked to original sources
PubMed2003

Golgi dynamics during meiosis are distinct from mitosis and are coupled to endoplasmic reticulum dynamics until fertilization.

One current theory of the Golgi apparatus views its organization as containing both a matrix fraction of structural proteins and a reservoir of cycling enzymes. During mitosis, the putative matrix protein GM130 is phosphorylated and relocalized to spindle poles. When the secretory pathway is inhibited during interphase, GM130 redistributes to regions adjacent to vesicle export sites on the endoplasmic reticulum (ER). Strikingly, meiotic maturation and fertilization in nonrodent mammalian eggs presents a unique experimental environment for the Golgi apparatus, because secretion is inhibited until after fertilization, and because the centrosome is absent until introduced by the sperm. Here, we test the hypothesis that phosphorylated GM130 associates not with meiotic spindle poles, but with ER clusters in the mature bovine oocyte. At the germinal vesicle stage, phosphorylated GM130 is observed as fragments dispersed throughout the cytoplasm. During meiotic maturation, GM130 reorganizes into punctate foci that associate near the ER-resident protein calreticulin and is notably absent from the meiotic spindle. GM130 colocalizes with Sec23, a marker for ER vesicle export sites, but not with Lens culinaris agglutinin, a marker for cortical granules. Because disruption of vesicle transport has been shown to block meiotic maturation and embryonic cleavage in some species, we also test the hypothesis that fertilization and cytokinesis are inhibited with membrane trafficking disruptor brefeldin A (BFA). Despite Golgi fragmentation after BFA treatment, pronuclei form and unite, and embryos cleave and develop through the eight-cell stage. We conclude that, while the meiotic phosphorylation cycle of GM130 mirrors that of mitosis, absence of a maternal centrosome precludes Golgi association with the meiotic spindle. Fertilization introduces the sperm centrosome that can reorganize Golgi proteins, but neither fertilization nor cytokinesis prior to compaction requires a functional Golgi apparatus.

Animals↗
PubMed2003

Dynamics of RNase-A and S-protein: a molecular dynamics simulation of the transition toward a folding intermediate.

The description at atomic level of protein folding is an ambitious goal in biophysics, particularly because of the difficulty in obtaining structural information on unfolded states. Computer simulations can contribute in achieving this goal. Here we report the results of a 10-ns comparative simulation on bovine ribonuclease A and its S-protein, obtained by removal from the native molecule of the first 20 residues, the so-called S-peptide. The atomic trajectories have been analyzed by standard procedures and by applying concepts previously developed for disordered systems. Furthermore, we used a novel approach, described in the preceding paper, to represent graphically the energy landscape of the simulated systems. Relative to RNase-A, the S-protein, while largely maintaining its structural organization, displays an increased structural flexibility, it gains ergodicity and its core loses order, thus indicating that the removal of the S-peptide from ribonuclease A triggers the transition to a folding intermediate with reduced compactness. This finding also has biochemical relevance since the S-protein is recognized as not properly folded by the machinery responsible for the control of the folding quality in the endoplasmic reticulum.

Computer Simulation↗
PubMed1998

Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA.

Models for the disease-associated expansion of (CTG)n.(CAG)n, (CGG)n.(CCG)n, and (GAA)n.(TTC)n trinucleotide repeats involve alternative DNA structures formed during DNA replication, repair and recombination. These repeat sequences are inherently flexible and can form a variety of hairpins, intramolecular triplexes, quadruplexes, and slipped-strand structures that may be important intermediates and result in their genetic instability.

Base Composition↗
PubMed2001

Dynamic Nef and Nef dynamics: how structure could explain the complex activities of this small HIV protein.

The Nef protein of the human immunodeficiency virus is as important for disease progression as it is perplexing in its plethora of target molecules and functions. In this article, it is proposed that the complex biology of Nef is regulated through conformational changes of the protein that are triggered by cellular location and specific interactions as Nef traffics through the infected cell.

Amino Acid Sequence↗
PubMed1995

Correlations between function and dynamics: time scale coincidence for ion translocation and molecular dynamics in the gramicidin channel backbone.

The polypeptide backbone of gramicidin lines the channel lumen, which maintains a single file string of water molecules and the occasional cation. Whether or not local motions of the backbone are important for facilitating cation transport has been the subject of debate. Here it is demonstrated that motions of the backbone occur on the same time scale as cation translation through this transmembrane channel. To characterize the frequency of the local motions, field-dependent 15N T1 relaxation times were interpreted in light of an independently determined motional model that defines the motions as occurring about the C alpha-C alpha axis. To overdamp these local motions, several models that involve extensive correlations of the molecular motions were considered. One of these schemes for correlated motions suggests a unidirectional reaction path that would minimize the time necessary for the cation to pass through the low-dielectric center of the bilayer.

Amino Acid Sequence↗
PubMed2004

The dynamics of conformational isomerization in flexible biomolecules. II. Simulating isomerizations in a supersonic free jet with master equation dynamics.

Infrared-induced conformational isomerization of N-acetyl-tryptophan methyl amide is studied theoretically using a microcanonical Rice-Ramsperger-Kassel-Marcus description of the rates on potential energy surfaces calculated using the AMBER and OPLS-AA force fields. The results are compared with the experimental data from Dian et al. in the preceding paper [J. Chem. Phys. 120, 133 (2004)]. An exhaustive search of the potential energy surfaces locates all minima and transition states on these surfaces. A simple model is proposed for the vibrational cooling, and an appropriate cooling rate is chosen as the standard conditions for the master equation simulations by comparison with experiment. The two potential energy surfaces differ in the relative energies of minima and the heights of key transition states, leading to differences in the dominant pathways and rates of conformational isomerization. The predicted quantum yields depend sensitively on the cooling rate, varying from the slow cooling limit in which equilibrium populations are achieved to the fast quenching limit in which conformational isomerization is shut off. The excitation energy is varied from 5 to 20 kcal mol(-1). At the lowest energies, isomerization is completely quenched, while at the highest energies, equilibrium conditions are achieved. In between these extremes, the quantum yields are sensitive to the excitation energy, and can be used to locate the rate-limiting barriers to isomerization.

Computer Simulation↗
PubMed2005

Dynamics of order formation by colloidal adsorption onto a substrate studied with Brownian dynamics.

Colloidal adsorption and spontaneous ordering of adsorbed particles on a substrate was simulated using a three-dimensional simulation model for colloidal dispersion system with an adsorptive surface under a specified bulk concentration, where the particle-particle and particle-substrate interactions were modeled on the DLVO theory. The key process for order formation is considered to be the adsorption of a particle that induces the transition from incomplete order to perfect order, and is found to involve a stochastic nature due to an energy barrier which must be overcome for the system to reach ordered state. Also, a model was developed to predict the energy barrier for order formation based on direct observation of the key process. Further, a model to describe the stochastic nature of the process was developed and its quantitative validity was demonstrated. Through the examination of the key process, it is concluded that the mechanism of the order formation is composed of two successive processes and the rate-determining step varies depending on the ionic strength.

Journal Article↗