The intraglobular electrostatic field of an enzyme. II. Effect of environment polarization

The influence of polarization of surrounding medium on the intraglobular electric field of the alpha-chymotrypsin molecule is considered. The polarization is taken into account by the image charges method, the proper approximations for calculation of the fields due to intraglobular and surface charges are suggested. The polarization of surroundings does not change the qualitative picture of the electric field in the active center of the alpha-chymotrypsin molecule set up by protein dipoles, but reduces almost to zero the intraglobular field set up by surface ions.     

The intraglobular electrostatic field of an enzyme. 1. The primary field created by the polypeptide core, functional groups and ions of the alpha-chymotrypsin molecule

The electric field set up by the dipoles of peptide groups ad other dipoles at the atoms of substrate and catalytic groups of alpha-chymotrypsin is considered. It is shown that substantial electric potentials reaching some tenths of volts exist in the active center of the enzyme, the fact which must influence significantly the reactivity of corresponding groups. In contrast to low molecular weight liquids, the contribution to the total potential of dipoles located at different distances from the point under consideration often changes nonmonotonically with the distance, sometimes the predominant influence being exerted not by the nearest polar groups but by the more distant ones. The existence of electric fields having a complex spatial configuration determined by the protein structure can be defined as the effect of the polar medium preorganization. Emphasis is placed on the necessity of taking into account the polarization of the external medium by charges of protein atoms and ions (the difference of primary and secondary electric fields).     

Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxin

Ab initio quantum mechanical calculation of protein in solution is carried out to generate polarized protein-specific charge(s) (PPC) for molecular dynamics (MD) stimulation of protein. The quantum calculation of protein is made possible by developing a fragment-based quantum chemistry approach in combination with the implicit continuum solvent model. The computed electron density of protein is utilized to derive PPCs that represent the polarized electrostatic state of protein near the native structure. These PPCs are atom-centered like those in the standard force fields and are thus computationally attractive for molecular dynamics simulation of protein. Extensive MD simulations have been carried out to investigate the effect of electronic polarization on the structure and dynamics of thioredoxin. Our study shows that the dynamics of thioredoxin is stabilized by electronic polarization through explicit comparison between MD results using PPC and AMBER charges. In particular, MD free-energy calculation using PPCs accurately reproduced the experimental value of pK_a shift for ionizable residue Asp²⁶ buried inside thioredoxin, whereas previous calculations using standard force fields overestimated pK_a shift by twice as much. Accurate prediction of pK_a shifts by rigorous MD free energy simulation for ionizable residues buried inside protein has been a significant challenge in computational biology for decades. This study presented strong evidence that electronic polarization of protein plays an important role in protein dynamics.     

The effect of alpha-lactalbumin on the thermotropic phase behaviour of phosphatidylcholine bilayers, studied by fluorescence polarization, differential scanning calorimetry and Raman spectroscopy

The effects of bovine alpha-lactalbumin on the thermotropic properties of dimyristoylphosphatidylcholine liposomes are studied by Raman spectroscopy, fluorescence polarization and differential scanning calorimetry. The Raman spectrum reveals the drastic effects of the protein on the phospholipid structure. The transition temperature shifts downwards and the inter- and intrachain order in the lipid matrix progressively diminish with increasing protein concentration. Up to a lipid to protein molar ratio R = 25, the bilayer structure however is maintained. From fluorescence polarization data we conclude that the protein restricts the mobility of the DPH probe. In view of the Raman results, the lower probe mobility obviously cannot be associated with a more rigid lipid matrix. Nevertheless the transition temperatures of the alpha-lactalbumin-phospholipid complex increases. DSC measurements give no decisive way out for this discrepancy. These results confirm that different types of lipid order are involved in lipid-protein interactions. Compared to the free protein, the alpha-helicity of the protein has increased in the complex.     

The role of the ionic environment in the orientation of nucleic acids in electric fields

The relationship between polyelectrolyte theories based on linear charge density models and the electric-field induced orientation of the polyelectrolytes, poly(A), poly(C) and DNA is examined by varying their ionic environment with respect to ionic strength and acidity. The degree of counterion condensation on the polyelectrolytes predicted by the theories of Manning and Record is shown to be related linearly to the orientation as measured by their dichroism in the field. Micro-structural differences between poly(A) and poly(C) account for the differences in their dependence on the pH of the medium which affects the counterion condensation and thus the polarization in the orienting electric fields. The results consequently support recent treatments of linear polyelectrolytes having a high charge density which model them as smoothly charged linear polyions, but indicate that these models are insufficient to account for some of the effects of microstructural variations.     

Phenomenon of bifurcation of the circular polarization of the bremsstrahlung-generated pump field harmonics

The nonlinear dependence is considered of the circular polarization of the pump field harmonics generated in a plasma in collisions of the oscillating electrons with ions on the strength of the pump field and on the degree of its circular polarization. For the third, fifth, and seventh harmonics, the threshold pump electric field strengths are determined above which the harmonics with complete circular polarization are generated when the pump field is only of partial circular polarization. It is shown that there exists a broad range of degrees of circular polarization of the above-threshold pump field in which the harmonics have almost complete circular polarization. On the other hand, it is only in a narrow range of strengths of relatively intense pump fields having almost linear polarization that the degree of circular polarization of the harmonics changes from nearly positive to nearly negative.     

The field-dependence of the solid-state photo-CIDNP effect in two states of heliobacterial reaction centers

The solid-state photo-CIDNP (photochemically induced dynamic nuclear polarization) effect is studied in photosynthetic reaction centers of Heliobacillus mobilis at different magnetic fields by ¹³C MAS (magic-angle spinning) NMR spectroscopy. Two active states of heliobacterial reaction centers are probed: an anaerobic preparation of heliochromatophores (“Braunstoff”, German for “brown substance”) as well as a preparation of cells after exposure to oxygen (“Grünstoff”, “green substance”). Braunstoff shows significant increase of enhanced absorptive (positive) signals toward lower magnetic fields, which is interpreted in terms of an enhanced differential relaxation (DR) mechanism. In Grünstoff, the signals remain emissive (negative) at two fields, confirming that the influence of the DR mechanism is comparably low.     

On the calculation of electrostatic interactions in proteins

In this paper we present a classical treatment of electrostatic interactions in proteins. The protein is treated as a region of low dielectric constant with spherical charges embedded within it, surrounded by an aqueous solvent of high dielectric constant, which may contain a simple electrolyte. The complete analysis includes the effects of solvent screening, polarization forces, and self energies, which are related to solvation energies. Formulae, and sample calculations of forces and energies, are given for the special case of a spherical protein. Our analysis and model calculations point out that any consistent treatment of electrostatic interactions in proteins should account for the following. Solvent polarization is an important factor in the calculation of pairwise electrostatic interactions. Solvent polarization substantially affects both electrostatic energies and forces acting upon charges. No simple expression for the effective dielectric constant, Deff, can generally be valid, since Deff is a sensitive function of position. Solvent screening of pairwise interactions involving dipolar groups is less effective than the screening of charges. In fact for many interactions involving dipoles, solvent screening can be essentially ignored. The self energy of charges makes a large contribution to the total electrostatic energy of a protein. This must be compensated by specific interactions with other groups in the protein. Strategies for applying our analysis to proteins whose structures are known are discussed.     

The photoexcited triplet state as a probe of chromophore-protein interaction in myoglobin.

The photoexcited metastable triplet state of Mg(2+)-mesoporphyrin IX (MgMPIX) or Mg(2+)-protoporphyrin IX (MgPPIX) located in the heme pocket of horse myoglobin (Mb) was investigated by optical and electron paramagnetic resonance (EPR) spectroscopy, and its properties were compared with the model complexes, MgMPIX, MgPPIX, and Mg2+ etioporphyrin I (MgETIOI), in noncoordinating and coordinating organic glasses. Zero-field splitting parameters, line shape, and Jahn-Teller distortion in the temperature range of 3.8-110 K are discussed in terms of porphyrin-protein interactions. The triplet line shapes for MgMPIXMb and MGPPIXMb show no temperature-dependent spectral line shape changes suggestive of Jahn-Teller dynamics, and it is concluded that the energy splitting is >> 150 cm-1, suggesting symmetry breaking from the anisotropy of intermal electric fields of the protein, and consistent with previous predictions (Geissinger et al. 1995. J. Phys. Chem. 99:16527-16529). Both MgMPIXMb and MgPPIXMb demonstrate electron spin polarization at low temperature, and from the polarization pattern it can be concluded that intersystem crossing occurs predominantly into in-plane spin sublevels of the triplet state. The splitting in the Q0.0 absorption band and the temperature dependence and splitting of the photoexcited triplet state of myoglobin in which the iron was replaced by Mg2+ are interpreted in terms of effects produced by electric field asymmetry in the heme pocket.     

Electric field-induced polarization of charged cell surface proteins does not determine the direction of galvanotaxis

Galvanotaxis, that is, migration induced by DC electric fields, is thought to play a significant role in development and wound healing, however, the mechanisms by which extrinsic electric fields orchestrate intrinsic motility responses are unknown. Using mammalian cell lines (3T3, HeLa, and CHO cells), we tested one prevailing hypothesis, namely, that electric fields polarize charged cell surface molecules, and that these polarized molecules drive directional motility. Negatively charged sialic acids, which contribute the bulk of cell surface charge, redistribute preferentially to the surface facing the direction of motility, as measured by labeling with fluorescent wheat germ agglutinin. We treated cells with neuraminidase to remove sialic acids; as expected, this decreased total cell surface charge. We also changed cell surface charge independent of sialic acid moieties, by conjugating cationic avidin to the surface of live cells. Neuraminidase inhibited the electric field-induced directional polarization of membrane ruffling and alpha4 integrin, while avidin treatment actually reversed the directional polarization of sialic acids. Neuraminidase treatment inhibited directionality but did not alter speed of motility. Surprisingly, avidin treatment did not significantly alter either directionality or speed of motility. Thus, our results demonstrate that electric field-induced polarization of charged species indeed occurs. However, polarization of the bulk of charged cell surface proteins is neither necessary nor sufficient to cause motility, thus contradicting the second part of our hypothesis. Because neuraminidase inhibited directional motility, we also conclude that sialic acids are required constituents of some cell surface molecule(s) through which electric fields mount a polarized transmembrane response.     

PATJ regulates tight junction formation and polarity in mammalian epithelial cells

Recent studies have revealed an important role for tight junction protein complexes in epithelial cell polarity. One of these complexes contains the apical transmembrane protein, Crumbs, and two PSD95/discs large/zonula occludens domain proteins, protein associated with Lin seven 1 (PALS1)/Stardust and PALS1-associated tight junction protein (PATJ). Although Crumbs and PALS1/Stardust are known to be important for cell polarization, recent studies have suggested that Drosophila PATJ is not essential and its function is unclear. Here, we find that PATJ is targeted to the apical region and tight junctions once cell polarization is initiated. We show using RNAi techniques that reduction in PATJ expression leads to delayed tight junction formation as well as defects in cell polarization. These effects are reversed by reintroduction of PATJ into these RNAi cells. This study provides new functional information on PATJ as a polarity protein and increases our understanding of the Crumbs-PALS1-PATJ complex function in epithelial polarity.     

Spontaneous and electric field–controlled front–rear polarization of human keratinocytes

It has long been known that electrical fields (EFs) are able to influence the direction of migrating cells, a process commonly referred to as electrotaxis or galvanotaxis. Most studies have focused on migrating cells equipped with an existing polarity before EF application, making it difficult to delineate EF-specific pathways. Here we study the initial events in front–rear organization of spreading keratinocytes to dissect the molecular requirements for random and EF-controlled polarization. We find that Arp2/3-dependent protrusive forces and Rac1/Cdc42 activity were generally required for both forms of polarization but were dispensable for controlling the direction of EF-controlled polarization. By contrast, we found a crucial role for extracellular pH as well as G protein coupled–receptor (GPCR) or purinergic signaling in the control of directionality. The normal direction of polarization toward the cathode was reverted by lowering extracellular pH. Polarization toward the anode was also seen at neutral pH when GPCR or purinergic signaling was inhibited. However, the stepwise increase of extracellular pH in this scenario led to restoration of cathodal polarization. Overall our work puts forward a model in which the EF uses distinct polarization pathways. The cathodal pathway involves GPCR/purinergic signaling and is dominant over the anodal pathway at neutral pH.     

The light-harvesting chlorophyll a/b protein acts as a torque aligning chloroplasts in a magnetic field

Displacement of particles from the purified light-harvesting chlorophyll a/b protein aggregate (LHC) was studied in magnetic fields of various strengths (0 to 1.6 T) by polarized fluorescence measurements. Macromolecular aggregates of LHC have a considerable magnetic susceptibility which enables the particles to rotate and align with their nematic axes parallel with H. As LHC is embedded in a transmembrane direction thylakoids should align perpendicular to H, the mode of alignment experimentally observed in thylakoids. The value of the magnetic susceptibility could be estimated by relating it to the integral susceptibility of the chlorophyll molecules in LHC. The fitting of this value with the field strength dependency of the fluorescence polarization ratio (FP) revealed a relationship between the LHC content of various photosynthetic membranes and their capacity for alignment, which suggested that LHC might be the torque ordering chloroplasts in a magnetic field.Abbreviations LHC light-harvesting chlorophyll a/b protein - FP fluorescence polarization ratio, Iz/Iy     

Molecular Dynamics Simulations with Interaction Potentials Including Polarization Development of a Noniterative Method and Application to Water

A general method is suggested for the implementation of polarization in molecular dynamics simulations of small molecules. Induced dipole moments are evaluated on selected polarizability centers and represented by separation of charges. The positive polarization charges reside on the selected atoms. The negative polarization charges are treated as additional particles. The positions of these polarization charges are determined from the electrical fields due to the permanent charges of the system. Thus the induction is treated explicitly, while the higher order contributions, the polarization due to induced dipoles, are taken into account in an average way by modification of potential parameters. The forces can be evaluated for the new charge distribution in the conventional way. As an illustration of this approach initial results are reported for the development of a polarizable water model. The higher order polarization is treated in an average way by slight increase of the permanent charges as compared to the values that would give the gas phase dipole moment. The increase in CPU time is comparable to the addition of one atom per polarizable center.     

The concentration polarization effect in a multicomponent electrolyte solution—The human erythrocyte

A thermodynamic model describing the concentration polarization of solutes within cells during osmotic experiments is presented. The intracellular RBC solution is modeled as an ideal, hydrated and non-dilute salt-protein-water electrolyte solution in which the various solute species are allowed to diffuse independently. Application of this model to the case of human erythrocytes being cooled at subzero temperatures indicates that at the optimum cooling rate for the cryopreservation of RBCs a significant amount of solute polarization occurs within the intracellular solution, resulting in the temporary spatial separation of the salt and protein components. The concentration polarization process also significantly affects the transport of water out of RBCs during the cooling process. On the basis of these results, we believe that the concentration polarization phenomenon plays a significant role in determining the survival probability of cells at both high and low cooling rates.     

Inhibition of the establishment of zygotic polarity by protein tyrosine kinase inhibitors leads to an alteration of embryo pattern in Fucus

Fucoid algae, including the genus Fucus and Pelvetia, are recognized as model systems to study early embryogenesis in plants. In particular the zygotes of these fucoid algae are highly suitable experimental systems for investigating the establishment of polarity and its requirement for later embryogenesis. However, the transduction pathways involved in the initiation of polarization are still poorly understood, and the link between the early polarization processes and embryo long-term patterning has never been experimentally demonstrated. We, therefore, have investigated the putative role of protein phosphorylation in the regulation of early embryogenesis, using a combined pharmacological and biochemical approach. Among the various protein kinase inhibitors tested, a subset of well-known PTK inhibitors, including genistein, prevented germination but had no effect on growth of germinated zygotes and embryos. Inhibition of germination appeared to be a direct consequence of prevention of polarization since genistein and other PTK inhibitors specifically inhibited axis formation in a light-independent manner. Genistein inhibited cellular events associated with polarization such as polarized secretion of cell wall sulfated compounds. Anchorage of F-actin at the rhizoid pole was also inhibited and F-actin redistributed in response to a new light vector. Zygotes inhibited in the polarization process over the period of axis formation recovered from the treatment and displayed differentiated cellular structures after a few days. However, they exhibited a deeply disorganized pattern, suggesting that the early polarization process is essential for normal patterning of the embryo. Western blot analysis of protein phosphorylation showed that the patterns of protein phosphorylation changed during development and were disturbed by treatments with genistein. This drug also inhibited in vitro autophosphorylation. The nature of the genistein-sensitive kinases required for polarization and long-term patterning is discussed in light of these data.     

The Polarization of Light in a Tropical Rain Forest1

The light environment within forests presents complex patterns of brightness and spectral distribution of light. The polarized light field is no less complex. Using an imaging polarized light analyzer, we examined the natural fields of linearly polarized light in the tropical rain forest of Guatopo National Park, Venezuela. We found that the celestial polarization pattern remains visible underneath the forest canopy, although cloud and fog coverage may diffuse the light and reduce the polarization signal. We characterized several distinct light environments, each having a characteristic polarized light field. Furthermore, objects throughout the forest reflect light that is polarized in a predictable fashion depending upon the material, structure, and orientation of the reflecting surface. As a consequence of these patterns in the distribution of polarized light, some functions of polarization vision, such as navigation, must be limited to the spaces exposed to several extended portions of the sky, while others, such as remote sensing of surface orientation, object detection, and breaking of camouflage would be useful throughout the forest. The polarization of light adds another dimension to the complexity of the rain forest photic environment.     

An assessment of protein-ligand binding site polarizability

Electronic polarizability, an important physical property of biomolecules, is currently ignored in most biomolecular calculations. Yet, it is widely believed that polarization could account for a substantial fraction of the total nonbonded energy of a system. This belief is supported by studies of small complexes in vacuum. This perception is driving the development of a new class of polarizable force fields for biomolecular calculations. However, the quantification of this term for protein-ligand complexes has never been attempted. Here we explore the polarizable nature of protein-ligand complexes in order to evaluate the importance of this effect. We introduce two indexes describing the polarizability of protein binding sites. These we apply to a large range of pharmaceutically relevant complexes. We offer a recommendation of particular complexes as test systems with which to determine the effects of polarizability and as test cases with which to test the new generation of force fields. Additionally, we provide a tabulation of the amino acid composition of these binding sites and show that composition can be specific for certain classes of proteins. We also show that the relative abundance of some amino acids is different in binding sites than elsewhere in a protein's structure.