Structure-mechanics statistical learning uncovers mechanical relay in proteins

A protein''s adaptive response to its substrates is one of the key questions driving molecular physics and physical chemistry. This work employs the recently developed structure-mechanics statistical learning method to establish a mechanical perspective. Specifically, by mapping all-atom molecular dynamics simulations onto the spring parameters of a backbone-side-chain elastic network model, the chemical moiety specific force constants (or mechanical rigidity) are used to assemble the rigidity graph, which is the matrix of inter-residue coupling strength. Using the S1A protease and the PDZ3 signaling domain as examples, chains of spatially contiguous residues are found to exhibit prominent changes in their mechanical rigidity upon substrate binding or dissociation. Such a mechanical-relay picture thus provides a mechanistic underpinning for conformational changes, long-range communication, and inter-domain allostery in both proteins, where the responsive mechanical hotspots are mostly residues having important biological functions or significant mutation sensitivity.

Protein residues exhibit specific routes of mechanical relay as the adaptive responses to substrate binding or dissociation. On such physically contiguous connections, residues experience prominent changes in their coupling strengths.     

Computational characterization of low-lying states and intramolecular charge transfers in N-phenylpyrrole and the planar-rigidized fluorazene

Low-lying states and intramolecular charge transfers in N-phenylpyrrole (PP) and its planar-rigidized derivative fluorazene (FPP) have been investigated by ab initio methodologies. On the basis of calculations, properties of the excited states and plausible dual-fluorescence mechanisms have been elucidated. Present results show that S2 as a key state is involved in the consecutive photophysical processes. The S2 state is easily populated under excitation. In the polar MeCN solution, S2 can evolve to either a lower-energy locally excited state or a lower-energy solvated intramolecular charge-transfer state (S-ICT). The former emits a normal fluorescence back to the ground state, and the latter is exclusively responsible for the red-shifted fluorescence band. Calculations reveal that the emissive ICT states in both FPP and PP have similar geometric features, an elongated N-phenyl bond, a pyramidal carbon atom linking the pyrrole ring, and a quinonoid phenyl ring. The twisting of molecule around the N-phenyl bond is not necessary for the intramolecular charge transfer. Predicted absorption and emission spectra are in reasonable agreement with the experimental observations.     

Competitive adsorption of model charged proteins: the effect of total charge and charge distribution

The adsorption of mixtures of charged proteins on charged surfaces is studied using a molecular theory. The theory explicitly treats each of the molecular species in the system. The mixtures treated in this work are composed by two types of proteins, dissociated monovalent salt and solvent. The intermolecular and surface interactions include electrostatic, van der Waals and excluded volume. The theory is more general than the Poisson-Boltzmann approach since the size and shape of all the molecular components are explicitly treated. The studies presented in this work concentrate on the differences in competitive adsorption when the proteins in the mixtures differ in their total charge or in the spatial distribution of the charges within the proteins. In the cases of mixtures that differ in the number of charges it is found, as expected, that the particles with the larger charge adsorb in excess. The ratio of adsorbed proteins can vary by 3-5 orders of magnitude by varying the bulk salt concentration from 1 to 100 mM. This is the result of an increase on the adsorption of the proteins with larger charge and an even stronger decrease on the adsorption of the less charged particles. The simple model systems studied provide guidelines on how to separate charge ladder proteins and proteins with different charge distributions. In the case of proteins with the same total charge but different charge distribution, it is found that the partition of the proteins depends upon the bulk composition. However, in general the particles with the highest localized charge tend to adsorb more on the surfaces. The proteins are adsorbed in one or more layers. The structure of the second adsorbed layer is determined mostly by the bulk properties of the solution. In all cases it is found that in the range of salt concentrations studied the number of adsorbed ions from the salt is very large. This is due to competitive adsorption with the proteins and their very low bulk concentration compared to the salt. The limitations of the theory and directions for improvement of the approach as well as the model for the proteins are discussed.     

Electron photoejection and its application in studies of electron transfers

The principle of electron photoejection technique is explained. This approach leads to the formation of transient spectra of unstable intermediates, allowing their recording and providing their extinction coefficients. Moreover, it permits determination of their electron affinities and the rates of their reactions, whether spontaneous or with some added substrates. Application of this technique to studies of disproportionation of radical anions have been most profitable. It led to the determination of the forward and backward rate constants of disproportionation of a variety of radical anions, and to discovery and quantification of some subtle features of these reactions. Electron photoejection technique provided the data characterizing the electron transfer initiation of anionic polymerization and clarified some of its features. Other opportunities provided by the electron photoejection in studies on electron transfer processes are suggested.     

Electron photoejection and its application in studies of electron transfers

The principle of the electron photoejection technique is explained. This approach leads to the formation of transient spectra of unstable intermediates, allowing their recording and providing their extinction coefficients. Moreover, it permits determination of their electron affinities and the rates of their reactions, whether spontaneous or with some added substrates. Application of this technique to studies of disproportionation of radical anions has been most profitable. It led to the determination of the forward and backward rate constants of disproportionation of a variety of radical anions, and to discovery and quantification of some subtle features of these reactions. The electron photoejection technique provided the data characterizing the electron transfer initiation of anionic polymerization and clarified some of its features. Other opportunities provided by the electron photoejection in studies of electron transfer processes are suggested. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: v–xiii, 1998     

Ultrafast exciton transfers in DNA and its nonlinear optical spectroscopy

We have calculated the nonlinear response function of a DNA duplex helix including the contributions from the exciton population and coherence transfers by developing an appropriate exciton theory as well as by utilizing a projector operator technique. As a representative example of DNA double helices, the B-form (dA)10-(dT)10 is considered in detail. The Green functions of the exciton population and coherence transfer processes were obtained by developing the DNA exciton Hamiltonian. This enables us to study the dynamic properties of the solvent relaxation and exciton transfers. The spectral density describing the DNA base-solvent interactions was obtained by adjusting the solvent reorganization energy to reproduce the absorption and steady-state fluorescence spectra. The time-dependent fluorescence shift of the model DNA system is found to be ultrafast and it is largely determined by the exciton population transfer processes. It is further shown that the nonlinear optical spectroscopic techniques such as photon echo peak shift and two-dimensional photon echo can provide important information on the exciton dynamics of the DNA double helix. We have found that the exciton-exciton coherence transfer plays critical roles in the peculiar energy transfer and ultrafast memory loss of the initially created excitonic state in the DNA duplex helix.     

Pulse radiolysis studies of intermolecular charge transfers involving tryptophan and three-electron-bonded intermediates derived from methionine

The oxidation processes of the radiation-generated, three-electron-bonded intermediates AcMet₂ [S??S]⁺ and AcMet [S??Br] were investigated by pulse radiolysis via their reactions with tryptophan (TrpH). These intermediates were derived from N-acetyl-methionine amide (N-AcMetNH₂) and N-acetyl-methionine methyl ester (N-AcMetOMe). The bimolecular rate constant k of the reaction between each intermediate and l-tryptophan (TrpH) was measured. For N-AcMetNH₂, k for the reaction of AcMet₂ [S??S]⁺ with TrpH were 3.4?×?10⁸ and 2.2?×?10⁸?dm³?mol^?1?s^?1 at pH?=?1 and 4.5, respectively. For N-AcMetOMe, k for the reaction of AcMet₂ [S??S]⁺ with TrpH were 4.0?×?10⁸ and 2.8?×?10⁸?dm³?mol^?1?s^?1 at pH 1 and 4.5, respectively. The rate constants for the intermolecular transformation of Met [S??Br] into TrpH⁺ or Trp were also estimated. For N-AcMetNH₂, k for the reaction of AcMet₂ [S??Br] with TrpH were 2.6?×?10⁸ and 3.3?×?10⁸?dm³?mol^?1?s^?1 at pH 1 and 4.5, respectively. Related mechanisms were discussed.     

On the mechanism of charge transport in pentacene

Terahertz transient conductivity measurements are performed on pentacene single crystals, which directly demonstrate a strong coupling of charge carriers to low frequency molecular motions with energies centered around 1.1 THz. We present evidence that the strong coupling to low frequency motions is the factor limiting the conductivity in these organic semiconductors. Our observations explain the apparent paradox of the "bandlike" temperature dependence of the conductivity beyond the validity limit of the band model.     

CO oxidation catalyzed by silver nanoclusters: mechanism and effects of charge

The mechanism of the CO oxidation promoted by a neutral Ag(55) cluster was investigated extensively, using density functional theory calculations. The CO oxidation process catalyzed by anionic and cationic Ag(55) clusters was also studied, to clarify the effects of the charge state. The Eley-Rideal (ER) and Langmuir-Hinshelwood (LH) mechanisms were discussed in detail. Six reaction pathways were found for the Ag(55)-mediated CO oxidation. It was found that the ER mechanism competed with the LH mechanism. The rate-limiting step of the CO oxidation was the reaction of CO with the Ag(55)O species. All of the anionic, neutral, and cationic Ag(55) clusters were able to promote CO oxidation at low temperatures. The present results enrich our understanding of the catalytic oxidation of CO by nano-sized Ag-based catalysts.     

Surface charge spectroscopy and its applications

Surface Charge Spectroscopy (SCS) is a surface sensitive technique for measuring potential distributions across an ultrathin (<100Å) insulator/semiconductor structure. Although the applicability of the technique is rather narrowly confined to such a specific sample structure, SCS bears considerable industrial significance because insulator/semiconductor structures are the most commonly used functional elements in microelectronics, and because gate insulators used in the industry are indeed getting to a nanometer thickness scale. The basic SCS concept relies on the measurements of the potential energies of electronic states using the conventional photoemission spectroscopic method, energy data which bear the information of the electrical potential gradient across the probed surface region. Surface sensitivity of SCS is thus contained in the framework of photoemission spectroscopy. Unlike conventional photoemission studies, SCS always measures the potential gradients corresponding to a specific surface potential. In fact, its analytical power is only shown when the surface potential of a sample can be controlled, and coincidentally an insulator/semiconductor device structure in microelectronics is only functional when the potential gradient extending into the semiconductor region can be changed effectively by the surface potential of the insulator. When SCS data are examined beyond the simple space-charge model commonly employed by electrical characterisation techniques like capacitance-voltage measurements, they can give information other than the relationship between the insulator surface potential and semiconductor surface potential (and thus interface state distributions across the bandgap of the semiconductor). Rather, they also provide unique information on the depth distributions of various types of fixed charges in the sample structure at an atomic level, and on the insulator breakdown mechanisms.     

Dynamics and mechanism of bridge-dependent charge separation in pyrenylurea-nitrobenzene pi-stacked protophanes

Herein are reported the synthesis, structure, and electronic properties of a series of tertiary di- and polyarylureas possessing pyrene and nitrobenzene end groups separated by a variable number of internal phenylenediamine bridging groups. These molecules adopt folded "protophane" structures in which the adjacent arenes are loosely pi-stacked. The behavior of both the pyrene and nitrobenzene singlet states has been investigated by means of femtosecond broadband pump-probe spectroscopy, and the transients have been assigned on the basis of comparison to reference molecules. Femtosecond time resolution permits direct observation of the fast internal conversion process for both the pyrene and nitrobenzene upper singlet states, as well as the intersystem crossing of nitrobenzene. The ultrafast (ca. 100 fs) charge separation of the donor-acceptor urea having no bridging group is attributed to an internal conversion process. The slower charge separation and charge recombination of the donor-acceptor urea having a single bridging group occur via a bridge-mediated superexchange process. Addition of a second bridging unit results in a role reversal for the pyrene singlet state, which now serves as an excited-state acceptor with the bridging units serving as the electron donors. The change in the directionality of electron transfer upon addition of a second bridging phenylenediamine is a consequence of a decrease in the bridge oxidation potential as well as a decrease in the rate constant for single-step superexchange electron transfer.     

Fragmentation and deformation mechanism of glycine isomers in gas phase: Investigations of charge effect

The structural parameters, relative stability, proton transfer energy barriers of four typical and life related isomers and conformers of different charged (n=0,+/-1,+/-2) glycine species have been investigated using B3LYP, BHLYP, and CCSD(T) methods. Results indicate that those neutral and (+/-1)-charged species are stable. For the (+2)-charged cases, all four triplet-state glycine species and only the singlet-state zwitterionic one are stable. On the other hand, only the singlet-state zwtterionic glycine ((1)GlyZW(-2)) and the corresponding neutral form counterpart ((1)Gly(-2)) are stable for the (-2)-charged cases. Either of the two stable structures holds a proton lying in the position (2-3 A) of being separated from its corresponding parental species. Those unstable divalent glycine species are dissociated into different smaller species spontaneously according to the characters of their different structures and electron spins. The presented fragmentation and deformation mechanisms can effectively predict and satisfactorily explain some experimental phenomena, which had been puzzling the mass spectrometry chemists. Also, the mechanisms should be suitable for any other similar molecule systems. Comparisons of the relative energies of the four (+1)-charged glycine species show that doublet-state glycine III ((2)GlyIII1) is more stable in energy by 12.1 kcal/mol than the (+1)-charged glycine Gly ((2)Gly1). This is consistent with the energy ordering of their corresponding mono-valence metal ion-bound derivatives. In addition, calculations show that an intramolecular proton transfer of (2)Gly(-1) to become its zwitterionic counterpart is preferred due to its least activation energy barrier (5.8 kcal/mol) among four discussed processes.     

Oxidative-stability enhancement and charge transport mechanism in glyme-lithium salt equimolar complexes

The oxidative stability of glyme molecules is enhanced by the complex formation with alkali metal cations. Clear liquid can be obtained by simply mixing glyme (triglyme or tetraglyme) with lithium bis(trifluoromethylsulfonyl)amide (Li[TFSA]) in a molar ratio of 1:1. The equimolar complex [Li(triglyme or tetraglyme)(1)][TFSA] maintains a stable liquid state over a wide temperature range and can be regarded as a room-temperature ionic liquid consisting of a [Li(glyme)(1)](+) complex cation and a [TFSA](-) anion, exhibiting high self-dissociativity (ionicity) at room temperature. The electrochemical oxidation of [Li(glyme)(1)][TFSA] takes place at the electrode potential of ~5 V vs Li/Li(+), while the oxidation of solutions containing excess glyme molecules ([Li(glyme)(x)][TFSA], x > 1) occurs at around 4 V vs Li/Li(+). This enhancement of oxidative stability is due to the donation of lone pairs of ether oxygen atoms to the Li(+) cation, resulting in the highest occupied molecular orbital (HOMO) energy level lowering of a glyme molecule, which is confirmed by ab initio molecular orbital calculations. The solvation state of a Li(+) cation and ion conduction mechanism in the [Li(glyme)(x)][TFSA] solutions is elucidated by means of nuclear magnetic resonance (NMR) and electrochemical methods. The experimental results strongly suggest that Li(+) cation conduction in the equimolar complex takes place by the migration of [Li(glyme)(1)](+) cations, whereas the ligand exchange mechanism is overlapped when interfacial electrochemical reactions of [Li(glyme)(1)](+) cations occur. The ligand exchange conduction mode is typically seen in a lithium battery with a configuration of [Li anode|[Li(glyme)(1)][TFSA]|LiCoO(2) cathode] when the discharge reaction of a LiCoO(2) cathode, that is, desolvation of [Li(glyme)(1)](+) and insertion of the resultant Li(+) into the cathode, occurs at the electrode-electrolyte interface. The battery can be operated for more than 200 charge-discharge cycles in the cell voltage range of 3.0-4.2 V, regardless of the use of ether-based electrolyte, because the ligand exchange rate is much faster than the electrode reaction rate.     

Separation of cationic proteins via charge reversal in capillary electrophoresis

Analysis of proteins by capillary electrophoresis requires strategies which minimize coulombic interactions with the capillary surface. Thus buffers with pH's above the isoelectric points (pI) of proteins, or near the pI of silanol are required for efficient separation. Covalent modification of the capillary surface is also effective; however, this strategy is technically difficult, abolishes endosmotic flow and suffers from the inherent lability of the siloxane bond. Finally, "dynamic coating" agents, which interact weakly with the capillary surface and therefore, must be included in the separation buffer, suffer from the potential interaction of coating agent with analytes, altering the selectivity of the system. In the following paper, we describe another approach which overcomes all of these difficulties, and demonstrate the ease of use, nondenaturing property, stability and selectivity of the coating strategy with several model protein systems.     

Prediction of the charge states of folded proteins in electrospray ionization

Earlier work from this laboratory dealt with the observation that the charge states of non-denatured proteins can be decreased by use of buffer salts in which the gas-phase basicity of conjugate base B, GB(B), of the buffer cations is high. A theoretical model was developed and applied to several small proteins. The predictions of the charge states were found to be in good agreement with those observed experimentally. Because the computational model is based on the charge residue model (CRM), the observed agreement lends support for the CRM. In the present work, the same model is applied to recent data by Catalina et al. who showed that very large charge reductions are achieved with very high GB(B) proton sponges. Their data included lysozyme but also the very much larger proteins, p-hydroxybenzoate hydroxylase (PHBH), 90 kDa and glutamate synthase (GLTS), 166 kDA. The present work examines the performance of the model for the much stronger bases and the very much larger proteins. It is found that the predictions of the charge states agree well for the small protein lysozyme but somewhat less well with the experimental results for PHBH and GLTS. The causes for the lack of good agreement with the large proteins are examined.     

Photoemission from sodium on ice: a mechanism for positive and negative charge coexistence in the mesosphere

Photoemission from sodium deposited on ice films is described. Deposition of 0.02 ML of sodium is found to dramatically reduce the threshold for photoemission from the ice film to (2.3+/-0.2) eV. Thus, the cross-section for photoemission reaches >10(-18) cm2 in the visible region of the spectrum. It is proposed that the initial state is a solvated electron on the ice surface, which is supported by optical transmission spectroscopy. The potential significance of these results in understanding unexplained charging phenomena in the mesosphere is discussed.     

Nonuniform charge scaling (NUCS): a practical approximation of solvent electrostatic screening in proteins

In molecular mechanics calculations, electrostatic interactions between chemical groups are usually represented by a Coulomb potential between the partial atomic charges of the groups. In aqueous solution these interactions are modified by the polarizable solvent. Although the electrostatic effects of the polarized solvent on the protein are well described by the Poisson--Boltzmann equation, its numerical solution is computationally expensive for large molecules such as proteins. The procedure of nonuniform charge scaling (NUCS) is a pragmatic approach to implicit solvation that approximates the solvent screening effect by individually scaling the partial charges on the explicit atoms of the macromolecule so as to reproduce electrostatic interaction energies obtained from an initial Poisson--Boltzmann analysis. Once the screening factors have been determined for a protein the scaled charges can be easily used in any molecular mechanics program that implements a Coulomb term. The approach is particularly suitable for minimization-based simulations, such as normal mode analysis, certain conformational reaction path or ligand binding techniques for which bulk solvent cannot be included explicitly, and for combined quantum mechanical/molecular mechanical calculations when the interface to more elaborate continuum solvent models is lacking. The method is illustrated using reaction path calculations of the Tyr 35 ring flip in the bovine pancreatic trypsin inhibitor.