LAP2alpha maintains a mobile and low assembly state of A-type lamins in the nuclear interior.

Lamins form stable filaments at the nuclear periphery in metazoans. Unlike B-type lamins, lamins A and C localize also in the nuclear interior, where they interact with lamin-associated polypeptide 2 alpha (LAP2α). Using antibody labeling, we previously observed a depletion of nucleoplasmic A-type lamins in mouse cells lacking LAP2α. Here, we show that loss of LAP2α actually causes formation of larger, biochemically stable lamin A/C structures in the nuclear interior that are inaccessible to lamin A/C antibodies. While nucleoplasmic lamin A forms from newly expressed pre-lamin A during processing and from soluble mitotic lamins in a LAP2α-independent manner, binding of LAP2α to lamin A/C during interphase inhibits formation of higher order structures, keeping nucleoplasmic lamin A/C in a mobile state independent of lamin A/C S22 phosphorylation. We propose that LAP2α is essential to maintain a mobile lamin A/C pool in the nuclear interior, which is required for proper nuclear functions.

Chromatin Viscoelasticity Measured by Local Dynamic Analysis.

The nucleus in eukaryotic cells is a crowded environment that consists of genetic code along the DNA, together with a condensed solution of proteins, RNA, and other molecules. It is subjected to highly dynamic processes, including cell division, transcription, and DNA repair. In addition, the genome in the nucleus is subjected to external forces applied by the cytoplasmic skeleton and neighboring cells, as well as to internal nuclear forces. These forces oppose the need to maintain the genome order, which may be compensated by the internal nuclear viscoelastic properties that can restrain these forces. The structural and mechanical properties of chromatin inside the nucleus are still not fully clear; however, their importance for the proper functioning of the cells is unquestionable. Different approaches have been developed for this aim, ranging from directly measuring the dynamic and elastic properties of chromatin to studying the interactions of chromatin with the surrounding envelope and nuclear bodies. Although the elasticity of naked DNA in vitro is well characterized, the elasticity of chromatin in live cells is more complex and is still not fully understood. Here, we studied the elastic properties of chromatin by dynamic measurements in live cells, followed by viscoelastic modeling. We measured the trajectories of single chromatin loci, centromeres, and telomeres in live cells and analyzed their dynamics using the Langevin formalism. We assumed that the overall effect of the chromatin network forces can be modeled for each locus by a local harmonic potential and calculated the effective force constant. In addition, we assumed that this harmonic force results from the chromatin network formed by the internal polymer structure together with cross-links formed by the protein complex. We show that lamin A has the greatest effect on chromatin viscoelasticity and that its removal leads to a significant reduction in the local harmonic force.

Chromatin dynamics governed by a set of nuclear structural proteins.

During the past three decades, the study of nuclear and chromatin organization has become of great interest. The organization and dynamics of chromatin are directly responsible for many functions including gene regulation, genome replication, and maintenance. In order to better understand the details of these mechanisms, we need to understand the role of specific proteins that take part in these processes. The genome in the nucleus is organized in different length scales, ranging from the bead-like nucleosomes through topological associated domains up to chromosome territories. The mechanisms that maintain these structures, however, remain to be fully elucidated. Previous works highlighted the significance of lamin A, an important nucleoplasmic protein; however, there are other nuclear structural proteins that are also important for chromatin organization. Studying the organizational aspects of the nucleus is a complex task, and different methods have been developed and adopted for this purpose, including molecular and imaging methods. Here we describe the use of the live-cell imaging method and demonstrate that the dynamics of the nucleus is strongly related to its organizational mechanisms. We labeled different genomic sites in the nucleus and measured the effect of nuclear structural proteins on their dynamics. We studied lamin A, BAF, Emerin, lamin B, CTCF, and Cohesin and discuss how each of them affect chromatin dynamics. Our findings indicate that lamin A and BAF have a significant effect on chromosomes dynamics, while other proteins mildly affect the type of the diffusion while the volume of motion is not affected.

Genome organization in the nucleus: From dynamic measurements to a functional model.

A biological system is by definition a dynamic environment encompassing kinetic processes that occur at different length scales and time ranges. To explore this type of system, spatial information needs to be acquired at different time scales. This means overcoming significant hurdles, including the need for stable and precise labeling of the required probes and the use of state of the art optical methods. However, to interpret the acquired data, biophysical models that can account for these biological mechanisms need to be developed. The structure and function of a biological system are closely related to its dynamic properties, thus further emphasizing the importance of identifying the rules governing the dynamics that cannot be directly deduced from information on the structure itself. In eukaryotic cells, tens of thousands of genes are packed in the small volume of the nucleus. The genome itself is organized in chromosomes that occupy specific volumes referred to as chromosome territories. This organization is preserved throughout the cell cycle, even though there are no sub-compartments in the nucleus itself. This organization, which is still not fully understood, is crucial for a large number of cellular functions such as gene regulation, DNA breakage repair and error-free cell division. Various techniques are in use today, including imaging, live cell imaging and molecular methods such as chromosome conformation capture (3C) methods to better understand these mechanisms. Live cell imaging methods are becoming well established. These include methods such as Single Particle Tracking (SPT), Continuous Photobleaching (CP), Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS) that are currently used for studying proteins, RNA, DNA, gene loci and nuclear bodies. They provide crucial information on its mobility, reorganization, interactions and binding properties. Here we describe how these dynamic methods can be used to gather information on genome organization, its stabilization mechanisms and the proteins that take part in it.

Exploring chromatin organization mechanisms through its dynamic properties.

The organization of the genome in the nucleus is believed to be crucial for different cellular functions. It is known that chromosomes fold into distinct territories, but little is known about the mechanisms that maintain these territories. To explore these mechanisms, we used various live-cell imaging methods, including single particle tracking to characterize the diffusion properties of different genomic regions in live cells. Chromatin diffusion is found to be slow and anomalous; in vast contrast, depletion of lamin A protein significantly increases chromatin motion, and the diffusion pattern of chromatin transforms from slow anomalous to fast normal. More than this, depletion of lamin A protein also affects the dynamics of nuclear bodies. Our findings indicate that chromatin motion is mediated by lamin A and we suggest that constrained chromatin mobility allows to maintain chromosome territories. Thus, the discovery of this function of nucleoplasmic lamin A proteins sheds light on the maintenance mechanism of chromosome territories in the interphase nucleus, which ensures the proper function of the genome.

Improved estimation of anomalous diffusion exponents in single-particle tracking experiments.

The mean square displacement is a central tool in the analysis of single-particle tracking experiments, shedding light on various biophysical phenomena. Frequently, parameters are extracted by performing time averages on single-particle trajectories followed by ensemble averaging. This procedure, however, suffers from two systematic errors when applied to particles that perform anomalous diffusion. The first is significant at short-time lags and is induced by measurement errors. The second arises from the natural heterogeneity in biophysical systems. We show how to estimate and correct these two errors and improve the estimation of the anomalous parameters for the whole particle distribution. As a consequence, we manage to characterize ensembles of heterogeneous particles even for rather short and noisy measurements where regular time-averaged mean square displacement analysis fails. We apply this method to both simulations and in vivo measurements of telomere diffusion in 3T3 mouse embryonic fibroblast cells. The motion of telomeres is found to be subdiffusive with an average exponent constant in time. Individual telomere exponents are normally distributed around the average exponent. The proposed methodology has the potential to improve experimental accuracy while maintaining lower experimental costs and complexity.

Universal algorithm for identification of fractional Brownian motion. A case of telomere subdiffusion.

We present a systematic statistical analysis of the recently measured individual trajectories of fluorescently labeled telomeres in the nucleus of living human cells. The experiments were performed in the U2OS cancer cell line. We propose an algorithm for identification of the telomere motion. By expanding the previously published data set, we are able to explore the dynamics in six time orders, a task not possible earlier. As a result, we establish a rigorous mathematical characterization of the stochastic process and identify the basic mathematical mechanisms behind the telomere motion. We find that the increments of the motion are stationary, Gaussian, ergodic, and even more chaotic--mixing. Moreover, the obtained memory parameter estimates, as well as the ensemble average mean square displacement reveal subdiffusive behavior at all time spans. All these findings statistically prove a fractional Brownian motion for the telomere trajectories, which is confirmed by a generalized p-variation test. Taking into account the biophysical nature of telomeres as monomers in the chromatin chain, we suggest polymer dynamics as a sufficient framework for their motion with no influence of other models. In addition, these results shed light on other studies of telomere motion and the alternative telomere lengthening mechanism. We hope that identification of these mechanisms will allow the development of a proper physical and biological model for telomere subdynamics. This array of tests can be easily implemented to other data sets to enable quick and accurate analysis of their statistical characteristics.

The localization and photosensitization of modified chlorin photosensitizers in artificial membranes.

In this work we investigate the localization and photophysical properties of twelve synthetically derived chlorins in artificial membranes, with the goal of designing more effective photosensitizers for photodynamic therapy (PDT). The studied chlorins incorporate substituents of varying lipophilicity at the C(5)-meso-position (H to C(5)H(11)), while the C(13)- and C(17)-positions have carboxylate "anchoring" groups tethered to the tetrapyrrole by alkyl chains (CH(2))(n) (n = 1-3). It was found that as n increases, the chromophoric part of the molecule, and thus the point of generation of singlet oxygen, is located at a deeper position in the bilayer. The vertical insertion of the sensitizers was assessed by two fluorescence-quenching techniques: by iodide ions that come from the aqueous phase and by spin-probe-labeled phospholipids that are incorporated into the bilayer, using the parallax method. These results demonstrate that elongation of the side chains endows the modified molecules with a larger affinity for artificial membranes and also causes the tetrapyrrole ring to be localized deeper in the lipid membrane. This location leads to a higher effective quantum yield for the chemical reaction of singlet oxygen with its chemical target 9,10-dimethylanthracene (DMA).

The binding of analogs of porphyrins and chlorins with elongated side chains to albumin.

In previous studies, we demonstrated that elongation of side chains of several sensitizers endowed them with higher affinity for artificial and natural membranes and caused their deeper localization in membranes. In the present study, we employed eight hematoporphyrin and protoporphyrin analogs and four groups containing three chlorin analogs each, all synthesized with variable numbers of methylenes in their alkyl carboxylic chains. We show that these tetrapyrroles' affinity for bovine serum albumin (BSA) and their localization in the binding site are also modulated by chain lengths. The binding constants of the hematoporphyrins and protoporphyrins to BSA increased as the number of methylenes was increased. The binding of the chlorins depended on the substitution at the meso position opposite to the chains. The quenching of the sensitizers' florescence by external iodide ions decreased as the side chains became longer, indicating to deeper insertion of the molecules into the BSA binding pocket. To corroborate this conclusion, we studied the efficiency of photodamage caused to tryptophan in BSA upon illumination of the bound sensitizers. The efficiency was found to depend on the side-chain lengths of the photosensitizer. We conclude that the protein site that hosts these sensitizers accommodates different analogs at positions that differ slightly from each other. These differences are manifested in the ease of access of iodide from the external aqueous phase, and in the proximity of the photosensitizers to the tryptophan. In the course of this study, we developed the kinetic equations that have to be employed when the sensitizer itself is being destroyed.

The influence of temperature on photodynamic cell killing in vitro with 5-aminolevulinic acid.

Cell survival was investigated after exposing cells in vitro to different temperatures before or after photodynamic therapy with 5-aminolevulinic acid. The photodynamic process was found to be temperature dependent. Cells exposed for 1h to 41 degrees C before light exposure or to 7 degrees C after light exposure showed decreased survival. Furthermore, the photobleaching rate of protoporphyrin IX in the cells was found to increase with increasing temperature during the light exposure. Thus, the photodynamic effect with 5-aminolevulinic acid may be enhanced by heating the tumour area before, and by cooling it immediately after the treatment.

On the correlation between hydrophobicity, liposome binding and cellular uptake of porphyrin sensitizers.

A crucial factor in choosing a porphyrin or analogous photosensitizer for photodynamic therapy (PDT) is its ability to incorporate into the cells. For hydrophobic compounds that partition passively into the cytoplasmic membrane, a partition coefficient between an organic solvent and water, P, is one factor that could be used to predict the molecule's ability to diffuse into biomembranes. We synthesized several porphyrins, modified with two, three or four meso-substituents and studied their spectroscopic and photophysical properties. The octanol-water partitioning coefficients, log P, were calculated as a parameter for hydrophobicity. We found these porphyrins to be very hydrophobic, with log P values in the range of 8.9-11.8. These were correlated with the binding constants of these porphyrins into liposomes, K(b), as well as to their uptake by cells. The correlation between the estimated log P and K(b) is nearly linear but negative, indicating, apparently, that there is lesser binding to liposomes with increased hydrophobicity. On the other hand, all of the studied porphyrins are taken up by cells, but there is no clear correlation between cellular uptake and the log P or K(b). Lipinski's pharmacological "rule of 5" predicts poor permeation of drugs into cells when log P is greater than five. This may be relevant for diffusional binding to liposomes, where aqueous aggregation can interfere strongly with cellular uptake. In such extreme conditions, neither liposome binding nor other rules seem to predict porphyrin behavior in vitro.

The effect of pH on the topography of porphyrins in lipid membranes.

The effect of the acidity of the environment on the topography and photophysics of sensitizer molecules in homogeneous solutions, and when embedded in a lipid microenvironment, was studied. Four hematoporphyrin (HP) analogs were studied, which have chemical "spacers" of varying lengths between the chromophoric tetrapyrrole and the carboxylate moiety. These derivatives have essentially the same chemical attributes and reactivity as the parent compound, HP IX, which is used in clinical procedures of photodynamic therapy. The binding constants of these HP derivatives to membrane model systems increase with the length of carboxylate chain in the pH range 3.0-6.6. This effect of chain length is attributed to an increase in the hydrophobicity of the molecule on elongation of the alkyl chains. A strong pH dependence of the quenching efficiency of the porphyrins' fluorescence by iodide ions was observed in aqueous solution and is attributed to a unique electrostatic interaction between the fluorophore and the quencher. The quenching efficiency in liposomes, relative to the quenching in buffer, as a function of pH, shows that porphyrins in the neutral form penetrate deeper inside the lipid bilayer and are less exposed to external quenching than when negatively charged at the carboxylic moiety. This vertical displacement in the membrane is also evidenced in the effect of pH on the photosensitized oxidation efficiency of a membrane-bound chemical target. Increasing the pH causes a significant decrease in the sensitization efficiency in liposomes. This trend is attributed to the vertical localization, and protonation of the carboxylic groups on lowering the pH leads to sinking of the sensitizer into the lipid bilayer and to a consequent generation of singlet oxygen at a deeper point. This increases the dwell time of singlet oxygen within the bilayer, which results in greater photodamage to a membrane-residing singlet oxygen target.

Porphyrin depth in lipid bilayers as determined by iodide and parallax fluorescence quenching methods and its effect on photosensitizing efficiency.

Photosensitization by porphyrins and other tetrapyrrole chromophores is used in biology and medicine to kill cells. This light-triggered generation of singlet oxygen is used to eradicate cancer cells in a process dubbed "photodynamic therapy," or PDT. Most photosensitizers are of amphiphilic character and they partition into cellular lipid membranes. The photodamage that they inflict to the host cell is mainly localized in membrane proteins. This photosensitized damage must occur in competition with the rapid diffusion of singlet oxygen through the lipid phase and its escape into the aqueous phase. In this article we show that the extent of damage can be modulated by employing modified hemato- and protoporphyrins, which have alkyl spacers of varying lengths between the tetrapyrrole ring and the carboxylate groups that are anchored at the lipid/water interface. The chromophore part of the molecule, and the point of generation of singlet oxygen, is thus located at a deeper position in the bilayer. The photosensitization efficiency was measured with 9,10-dimethylanthracene, a fluorescent chemical target for singlet oxygen. The vertical insertion of the sensitizers was assessed by two fluorescence-quenching techniques: by iodide ions that come from the aqueous phase; and by spin-probe-labeled phospholipids, that are incorporated into the bilayer, using the parallax method. These methods also show that temperature has a small effect on the depth when the membrane is in the liquid phase. However, when the bilayer undergoes a phase transition to the solid gel phase, the porphyrins are extruded toward the water interface as the temperature is lowered. These results, together with a previous publication in this journal, represent a unique and precedental case where the vertical location of a small molecule in a membrane has an effect on its membranal activity.