Factors controlling the drop evaporation constant

In this paper, we discuss the factors affecting drop evaporation. We found that the droplet morphology at a specific temperature was controlled by the physical properties of the liquid itself, such as the molecular weight, density, diffusion coefficient in air, and heat of vaporization. Two processes are included in drop evaporation: diffusion of liquid molecules into the air (diffusion part) and flow of the liquid molecules from inside the drop to the free outer shell liquid layer within the liquid-vapor interface (evaporation part). The diffusion part remained steady during drying and was not sensitive to the variation of temperature. The evaporation part, however, was an active factor and determined the differences in drop evaporation behaviors.     

Factors controlling the reactivity of zinc finger cores

Although the Zn(2+) cation in Zn·Cys(4), Zn·Cys(3)His, Zn·Cys(2)His(2), and Zn(2)Cys(6) cores of zinc finger (Zf) proteins typically plays a structural role, the Zn-bound thiolates in some Zf cores are reactive. Such labile Zf cores can serve as drug targets for retroviral or cancer therapies. Previous studies showed that the reactivity of a Zn-bound thiolate toward electrophiles is significantly reduced if it forms S---NH hydrogen bonds with the backbone amide. However, we found several well-known inactive Zf cores containing Cys ligands with no H-bonding interactions. Here, we show that H bonds from the peptide backbone or bonds from a second Zn cation to Zn-bound S atoms suppress the reactivity not only of these S atoms, but also of Zn-bound S* atoms with no interactions. Indeed, two or more indirect NH---S hydrogen bonds raise the free energy barrier for methylation of a Zn-bound S* in a Cys(4) core more than a direct NH---S* hydrogen bond. These findings help to elucidate why several well-known Zf cores have Cys ligands with no H bonds, but are unreactive. They also help to provide guidelines for distinguishing labile Cys-rich Zn sites from structural ones, which in turn help to identify novel potential Zf drug targets.     

Factors controlling the electrofusion of murine embryonic cells

A wide variety of physical and biological factors are involved in determining the success of electrofusion procedures. The optimal conditions for the fusion and survival of mouse two-cell embryos have been determined by manipulating the electric field parameters, medium composition, degree of cell-cell contact and the relationship between current flow and membrane orientation. The experiments demonstrate that the events which initiate embryonic cell fusion are dependent upon a closely defined electric field strength and associated pulse duration. We show further that high cell fusion rates are the product of an inverse relationship between dc field strength and pulse duration and the initiation of pore formation by electric field application is insufficient to induce successful fusion unless accompanied by appropriate post-pulse medium and adequate membrane contact. Manipulation of the direction of current flow, membrane orientation and degree of cell-cell contact have shown that the initiation of pore formation occurs across the entire surface of the cell membrane.     

Factors controlling the efficiencies of photoinduced electron-transfer reactions

The overall efficiencies of photoinduced electron transfer reactions in polar solvents are usually determined by the efficiency with which separated radical ions are formed from the initially formed geminate radical-ion pairs. These separation efficiencies are determined by the competition between retum electron transfer and separation within the geminate pairs. A method is described for determining whether variations in the quantum yields for formation of separated radical ions are due to changes in the reorganization parameters for the return electron transfer reactions, or to other factors. The use of the method is illustrated in studies of the effects of varying steric bulk and molecular size of the donors, and also in studies of the effect of using a charged sensitizer.     

Factors controlling the addition of carbon-centered radicals to alkenes

The addition rate constants of radicals to alkenes are strongly substituent dependent because of enthalpic, polar and steric effects. Recent absolute experimental and high level ab initio data for many prototype additions of small radicals are analyzed with the aid of the state correlation diagram. This leads to a unifying rationalization of the various effects and allows the prediction of rate constants to one order of magnitude or better. Propagation rate coefficients of homo- and copolymerizations and penultimate effects are also discussed.     

Factors controlling the mechanism of NAD(+) non-redox reactions

β-Nicotinamide adenine dinucleotide (NAD(+)) is an indispensable coenzyme or substrate for enzymes involved in catalyzing redox and non-redox reactions. ADP-ribosylating enzymes catalyze cleavage of the nicotinamide-glycosyl bond of NAD(+) and addition of a nucleophilic group from their substrate proteins to the N-ribose anomeric carbon of NAD(+). Although the role of the nicotinamide-ribose fragment in the mechanism of NAD(+) hydrolysis has been examined, the role of the doubly negatively charged, flexible, and chemically reactive NAD(+) diphosphate moiety in the reaction process has largely been neglected. Thus, the participation of the pyrophosphate group in stabilizing intra- and intermolecular interactions in the ground state and transition state has not been explored. Furthermore, the roles of other factors such as the type/nucleophilicity of the attacking nucleophile and the medium in influencing the reaction pathway have not been systematically evaluated. In this study, we endeavor to fill in these gaps and elucidate the role of these factors in controlling the NAD(+) nicotinamide-glycosyl bond cleavage. Using density functional theory combined with continuum dielectric methods, we modeled both S(N)1 and S(N)2 reaction pathways and assessed the role of the diphosphate group in stabilizing the (i) NAD(+) ground state, (ii) oxocarbocation intermediate, (iii) reaction product, and (iv) nucleophile. We also assessed the chemical nature of the attacking nucleophile and the role of the protein matrix in affecting the reaction mechanism. Our results reveal an intricate interplay among various factors in controlling the reaction pathway, which in turn suggests ways in which the enzyme can accelerate the reaction.     

Factors controlling the barriers to degenerate hydrogen atom transfers

High-level electronic structure calculations have been used to study the factors contributing to the barriers to degenerate hydrogen-atom transfer (HAT) reactions. Understanding of these reactions is a prerequisite to the development of any more general theory of HAT reactions, and yet, the existing models for such reactions perform quite poorly when applied to even simple self-exchanges. The reasons behind these failures are elucidated in the present work. They include a near cancellation of bond-strength effects between reactant and transition state, as well as a strong dependence of the geometry of the transition state on the nature of the heavy atoms.     

Polymer ultrathin films with immobilized photosynthetic reaction center proteins

Properties of mixed monolayers of lipid-photosynthetic reaction center proteins (RC) were studied and the optimum conditions for stable films fabrication were determined. The following synthetic: N-acryloylphosphatidylethanolamine (ACPE), tetracosa-11, 13-diinoic acid (TDA), pentacosa-10, 12-diinoic acid (PDA), dioctadecyldienoylphosphatidylcholine (DODL) and natural lipids: L-α-phosphatidylethanolamine (PE), L-α-phosphatidylcholine (PC) were used. The rate of polymerization of the mixed ACPE-RC and TDA-RC monolayers is lower in comparison with corresponding values for pure lipid-like monomers on air/water interface. The optical and photoelectrical measurements provide evidence for an orientation of RCs on interface. Hydrophilic H-subunit in monomeric and polymeric ACPE-RCs, and monomeric DODL-RCs monolayers is preferentially oriented towards water as in the pure RC monolayers. Opposite orientation was found with TDA-RCs and PDA-RCs films. No preferential orientation for lipid-RCs from C. aurantiacus monolayers was found because of the RCs having low assymmetry of hydrophobic subunits (M and L).     

Factors controlling the alkyne prins cyclization: the stability of dihydropyranyl cations

The relative stability of the intermediates involved in the alkyne Prins cyclization and the competitive 2-oxonia-[3,3]-sigmatropic rearrangement was studied. This rearrangement was shown to occur slowly under typical alkyne Prins cyclization conditions when the allenyl oxocarbenium ion that results from the rearrangement is similar to or higher in energy than the starting alkynyl oxocarbenium ion. The formal 2-oxonia-[3,3]-sigmatropic rearrangement may be disfavored by destabilizing the resultant allenyl oxocarbenium ion or by stabilizing an intermediate dihydropyranyl cation. The trimethylsilyl group as a substituent at the alkyne and electron-withdrawing groups (CH2Cl and CH2CN) located at the alpha-position to the carbinol center are shown to be effective. DFT calculations suggest that these substituents stabilize the dihydropyranyl cations, thus leading to a more uniform reorganization of the electronic density in the ring, and do not have a direct effect on the formally positively charged carbon atom.     

Factors affecting the ultraviolet laser desorption of proteins

The production of high-mass quasimolecular ions from proteins by matrix-assisted ultraviolet laser desorption is described. A simple time-of-flight system using a Q-switched frequency-quadrupled Nd-YAG laser to desorb protein molecules is shown to have a mass range of up to 116,000 u by the observation of intact, singly charged quasimolecular ions from 700 fmol of beta-galactosidase subunit (mol.wt = 116,336 Da). Both positive- and negative-ion spectra of proteins are shown. Four new matrix materials, with properties as good as or better than nicotinic acid, are described. A mass resolution of approximately 500 (full width at half maximum definition) is demonstrated for proteins with mol.wt less than 20,000 Da. Product species, formed by fast photochemical reactions in the matrix, are observed to form adduct ions with protein molecules. These adduct ions are a significant cause of the observed broadness of protein quasimolecular ion peaks. The practical physical considerations in detection of large-mass quasimolecular ions from laser desorption, such as detector overloading, are discussed.     

Characterizing the adsorption of proteins on glass capillary surfaces using electrospray-differential mobility analysis

We quantify the adsorption and desorption of a monoclonal immunoglobulin-G antibody, rituxamab (RmAb), on silica capillary surfaces using electrospray-differential mobility analysis (ES-DMA). We first develop a theory to calculate coverages and desorption rate constants from the ES-DMA data for proteins adsorbing on glass capillaries used to electrospray protein solutions. This model is then used to study the adsorption of RmAb on a bare silica capillary surface. A concentration-independent coverage of ≈4.0 mg/m(2) is found for RmAb concentrations ranging from 0.01 to 0.1 mg/mL. A study of RmAb adsorption to bare silica as a function of pH shows maximum adsorption at its isoelectric point (pI of pH 8.5) consistent with literature. The desorption rate constants are determined to be ≈10(-5) s(-1), consistent with previously reported values, thus suggesting that shear forces in the capillary may not have a considerable effect on desorption. We anticipate that this study will allow ES-DMA to be used as a "label-free" tool to study adsorption of oligomeric and multicomponent protein systems onto fused silica as well as other surface modifications.     

Factors controlling sulfur dioxide solubilities in organic solvents

Sulfur dioxide solubility in a liquid phase was studied as affected by the donor-acceptor interactions of the system’s components, these interactions being dependent on the basicity of organic solvents. Other factors of influence were also studied in order for fitting solubility data by means of linear multiparameter equations, primarily, the nonspecific solvation ability of solvents and their cohesion energy, which counteracts the incorporation of gas molecules into the liquid phase.     

Factors controlling extremely strong AAA-DDD triply hydrogen-bonded complexes

Triply hydrogen-bonded complexes of the form AAA-DDD are shown to have the strongest interaction when the complex is substituted with electron withdrawing groups on the donor molecule (DDD) and electron donating groups on the acceptor molecule (AAA). In particular, the largest effects are observed when the withdrawing groups act through resonance. This serves to flatten the entire system resulting in more linear, and consequently stronger, hydrogen bonds. Furthermore, the present calculations show that the binding energy correlates with the electron density at the bond critical points and inversely with the hydrogen bond lengths.     

Factors controlling metal-ion selectivity in the binding sites of calcium-binding proteins. The metal-binding properties of amide donors. A crystallographic and thermodynamic study

The metal-ion complexing properties of the ligand EDTAM (ethylenediamine-N,N,N',N'-tetraacetamide) are investigated as a model for the role of amide oxygen donors in the binding sites of Ca-binding proteins. The structures of the complexes [Ca(EDTAM)NO3]NO3 (1), [La(EDTAM)(H2O)4](NO3)3.H2O (2), and [Cd(EDTAM)(NO3)]NO3 (3) are reported: 1 monoclinic, P2(1)/c, a = 10.853(2) angstroms, b = 12.893(3) angstroms, c = 13.407(3) angstroms, beta = 103.28(3) degrees, Z = 4, R = 0.0281; 2 triclinic, P, a = 8.695(2) angstroms, b = 9.960(2) angstroms, c = 16.136(3) angstroms, alpha = 95.57(3) degrees, beta = 94.84(3) degrees, gamma = 98.72(3) degrees, Z = 2, R = 0.0394; 3 monoclinic, P2(1)/c, a = 10.767(2) angstroms, b = 12.952(2) angstroms, c = 13.273(2) angstroms, beta = 103.572(3) degrees, Z = 4, R = 0.0167. Compounds 1 and 3 are isostructural, and the EDTAM binds to the metal ion through its two N-donors and four O-donors from the amide groups. Ca(II) in 1 is 8-coordinate with a chelating NO3- group, while Cd(II) in 3 may possibly be 7-coordinate, with an asymmetrically coordinated NO3- that is best regarded as unidentate. The La(III) in 2 is coordinated to the EDTAM in a manner similar to that of 1 and 3, but it is 10-coordinate with four water molecules coordinated to the La(III). The formation constants (log K1) for complexes of a variety of metal ions with EDTAM are reported in 0.1 M NaNO3 at 25.0 +/- 0.1 degrees C. These are compared to the log K1 values for en (ethylenediamine) and THPED (N,N,N',N'-tetrakis(2-hydroxypropyl)-ethylenediamine). For large metal ions, such as Ca2+ or La3+, log K1 increases strongly when the four acetamide groups are added to en to give EDTAM, whereas for a small metal ion, such as Mg2+, this increase is small. The log K1 values for EDTAM compared to THPED suggest that the amide oxygen is a much stronger base than the alcoholic oxygen. Structures of binding sites in 40 Ca-binding proteins are examined. It is shown that the Ca-O=C bond angles involving coordinated amides in these sites are large, commonly being in the 150-180 degrees range. This is discussed in terms of the idea that for purely ionic bonding the M-O=C bond angle will approach 180 degrees, while for covalent bonding the angle should be closer to 120 degrees. How this fact might be used by the proteins to control selectivity for different metal ions is discussed.     

Global conformations of proteins as predicted from the modeling of their CZE mobility data

Estimations of protein global conformations in well-specified physicochemical microenvironments are obtained through global structural parameters defined from polypeptide-scale analyses. For this purpose protein electrophoretic mobility data must be interpreted through a physicochemical CZE model to obtain estimates of protein equivalent hydrodynamic radius, effective and total charge numbers, hydration, actual ionizing pK and pH-near molecule. The electrical permittivity of protein domain is also required. In this framework, the solvent drag on proteins is obtained via the characteristic friction power coefficient associated with the number of amino acid residues defining the global chain conformation in solution. Also, the packing dimension related to the spatial distribution of amino acid residues within the protein domain is evaluated and discussed. These scaling coefficients together with the effective and total charge number fractions of proteins provide relevant interpretations of protein global conformations mainly from collapsed globule to hybrid chain regimes. Also, protein transport properties may be estimated within this framework. In this regard, the central role played by the friction power coefficient in the evaluation of these properties is highlighted.     

Understanding and controlling the interaction of nanomaterials with proteins in a physiological environment

Nanomaterials hold promise as multifunctional diagnostic and therapeutic agents. However, the effective application of nanomaterials is hampered by limited understanding and control over their interactions with complex biological systems. When a nanomaterial enters a physiological environment, it rapidly adsorbs proteins forming what is known as the protein 'corona'. The protein corona alters the size and interfacial composition of a nanomaterial, giving it a biological identity that is distinct from its synthetic identity. The biological identity determines the physiological response including signalling, kinetics, transport, accumulation, and toxicity. The structure and composition of the protein corona depends on the synthetic identity of the nanomaterial (size, shape, and composition), the nature of the physiological environment (blood, interstitial fluid, cell cytoplasm, etc.), and the duration of exposure. In this critical review, we discuss the formation of the protein corona, its structure and composition, and its influence on the physiological response. We also present an 'adsorbome' of 125 plasma proteins that are known to associate with nanomaterials. We further describe how the protein corona is related to the synthetic identity of a nanomaterial, and highlight efforts to control protein-nanomaterial interactions. We conclude by discussing gaps in the understanding of protein-nanomaterial interactions along with strategies to fill them (167 references).     

A genetic approach for controlling the binding and orientation of proteins on nanoparticles

Although silver nanoparticles are excellent surface enhancers for Raman spectroscopy, their use to probe the conformation of large proteins at interfaces has been complicated by the fact that many polypeptides adsorb weakly or with a random orientation to colloidal silver. To address these limitations, we sought to increase binding affinity and control protein orientation by fusing a silver-binding dodecapeptide termed Ag4 to the C-terminus of maltose-binding protein (MBP), a well-characterized model protein with little intrinsic silver binding affinity. Quartz crystal microbalance measurements conducted with the MBP-Ag4 fusion protein revealed that its affinity for silver (Kd approximately 180 nM) was at least 1 order of magnitude higher than a control protein, MBP2, containing a non-silver-specific C-terminal extension. Under our experimental conditions, MBP-Ag4 SERS spectra exhibited 2-4 fold higher signal-to-background relative to MPB2 and contained a number of amino acid-assigned vibrational modes that were either weak or absent in control experiments performed with MBP2. Changes in amino acid-assigned peaks before and after MBP-Ag4 bound maltose were used to assess protein orientation on the surface of silver nanoparticles. The genetic route described here may prove useful to study the orientation of other proteins on a variety of SERS-active surfaces, to improve biosensors performance, and to control functional nanobiomaterials assembly.