Davydov Soliton Dynamics in Proteins: III. Applications and Calculation of Vibrational Spectra

The mechanism for energy and signal transport in proteins as suggested by Davydov is discussed. The idea is based on a coupling of amide-I oscillators to acoustic phonons in a hydrogen bonded chain. Results as obtained with the usually used ansätze are discussed. The quality of these states for an approximate solution of the time-dependent Schrödinger equation is investigated. It is found that the semiclassical ansatz is a poor approximation, while the more sophisticated |D₁> state seems to represent the exact dynamics quite well. This was shown by extensive calculations, both analytically and numerically in the two preceding papers. Calculations at a temperature of 300K for one chain, as well as for three coupled ones (as they are present in an α-helix) are presented and discussed. From the calculations it is evident, that Davydov solitons are stable for reasonable parameter values at 300K for special initial excitations close to the terminal sites of the chain. Further vibrational spectra are presented and discussed. Our results suggest, that due to their strong dependence on the initial state, the Davydov |D₁> model system might be a (quantum) chaotic one.     

Davydov Soliton Dynamics in Proteins: II. The General Case

We performed long time simulations using the |D₁> approximation for the solution of the Davydov Hamiltonian. In addition we computed expectation values of the relevant operators with the state (_D/J)|D₁> and the deviation |> from the exact solution over long times, namely 10 ns. We found that in the very long time scale the |D₁> ansatz is very close to an exact solution, showing expectation values of the relevant physical observables in the state (_D/J)|D₁> being about 5-6 orders of magnitudes larger than in the deviation state |>. In the intermediate time scale of the ps range such errors, as known from our previous work, are somewhat larger, but still more or less negligibly. Thus we also report results from an investigation of the very short time (in the range 0-0.4 ps) behaviour of the |D₁> state compared with that of an expansion of the exact solution in powers of time t. This expansion is reliable for about 0.12 ps for special cases as shown in the previous paper. However, the accuracy of the exactly known value of the norm and the expectation value of the Hamiltonian finally indicates up to what time a given expansion is valid, as also shown in the preceding paper. The comparison of the expectation values of the operators representing the relevant physical observables, formed with the third order wave function and with the corresponding results of |D₁> simulations has shown, that our expansion is valid up to a time of roughly 0.10-0.15 ps. Within this time the second and third order corrections turned out to be not very important. This is due to the fact that our first order state contains already some terms of the expansion, summed up to inifinite order. Further we found good agreement of the results obtained with our expansion and those from the corresponding |D₁> simulations within the time of about 0.10 ps. At later times, the factors with explicit powers of t in second and third order become dominant, making the expansion meaningless. Possibilities for the use of such expansions for larger times are described. Alltogether we have shown (together with previous work on medium times), that the |D₁> state, although of approximative nature, is very close to an exact solution of the Davydov model on time scales from some femtoseconds up to nanoseconds. Especially the very small time region is of importance, because in this time a possible soliton formation from the initial excitation would start.     

Davydov Soliton Dynamics in Proteins: I. Initial States and Exactly Solvable Special Cases

For the Davydov Hamiltonian several special cases are known which can be solved analytically. Starting from these cases we show that the initial state for a simulation using Davydovs |D₁> approximation has to be constructed from a given set of initial lattice displacements and momenta in form of a coherent state with its amplitudes independent of the lattices site, corresponding to Davydovs |D₂> approximation. In the |D₁> ansatz the coherent state amplitudes are site dependent. The site dependences evolve from this initial state exclusively via the equations of motion. Starting the |D₁> simulation from an ansatz with site dependent coherent state amplitudes leads to an evolution which is different from the analytical solutions for the special cases. Further we show that simple construction of such initial states from the expressions for displacements and momenta as functions of the amplitudes leads to results which are inconsistent with the expressions for the lattice energy. The site-dependence of coherent state amplitudes can only evolve through the exciton-phonon interactions and cannot be introduced already in the initial state. Thus also in applications of the |D₁> ansatz to polyacetylene always |D₂> type initial states have to be used in contrast to our previous suggestion [W. Förner, J. Phys.: Condens. Matter 1994, 6, 9089-9151, on p. 9105]. Further we expand the known exact solutions in Taylor serieses in time and compare expectation values in different orders with the exact results. We find that for an approximation up to third order in time (for the wave function) norm and total energy, as well as displacements and momenta are reasonably correct for a time up to 0.12-0.14 ps, depending somewhat on the coupling strengh for the transportless case. For the oscillator system in the decoupled case the norm is correct up to 0.6-0.8 ps, while the expectation values of the number operators for different sites are reasonably correct up to roughly 0.6 ps, when calculated from the third order wave function. The most important result for the purpose to use such expansions for controlling the validity of ansatz states is, however, that the accuracy of S(t) and H(t) (constant in time, exact values known in all cases) is obviously a general indicator for the time region in which a given expansion yields reliable values also for the other, physically more interesting expectation values.     

Tilting after Dutch windmills: probably no long-lived Davydov solitons in proteins

We present a summary of picosecond pump-probe and photon echo experiments in the mid-IR at 6 μm on the protein myoglobin. The intriguing temperature dependence of the amide I band in Mb is rather similar to the temperature dependence of the amide I band of acetanilide, the molecule that launched Al Scott down the road of looking for Davydov solitons in biology. Alas, after much effort, we believe the data show that there is no long-lived Davydov soliton, at least in myoglobin. This work was supported by the Office of Naval Research and the Stichting voor Fundamenteel Onderzoek der Materie (FOM).     

The Davydov/Scott Model for Energy Storage and Transport in Proteins

The current status of the Davydov/Scott model for energy transfer in proteins is reviewed. After a brief introduction to the theoretical framework and to the basic results, the problems of finite temperature dynamics and of the full quantum and mixed quantum-classical approximations are described, as well as recent results obtained within each of these approximations. A short survey of experimental evidence in support of the Davydov/Scott model is made and absorption spectra are calculated that show the same temperature dependence as that measured in crystalline acetanilide. Future applications of the Davydov/Scott model to protein folding and function and to misfolding diseases are outlined.     

Significance of Troponin Dynamics for Ca2+-mediated Regulation of Contraction and Inherited Cardiomyopathy

Ca²⁺ dissociation from troponin causes cessation of muscle contraction by incompletely understood structural mechanisms. To investigate this process, regulatory site Ca²⁺ binding in the NH₂-lobe of subunit troponin C (TnC) was abolished by mutagenesis, and effects on cardiac troponin dynamics were mapped by hydrogen-deuterium exchange (HDX)-MS. The findings demonstrate the interrelationships among troponin''s detailed dynamics, troponin''s regulatory actions, and the pathogenesis of cardiomyopathy linked to troponin mutations. Ca²⁺ slowed HDX up to 2 orders of magnitude within the NH₂-lobe and the NH₂-lobe-associated TnI switch helix, implying that Ca²⁺ greatly stabilizes this troponin regulatory region. HDX of the TnI COOH terminus indicated that its known role in regulation involves a partially folded rather than unfolded structure in the absence of Ca²⁺ and actin. Ca²⁺-triggered stabilization extended beyond the known direct regulatory regions: to the start of the nearby TnI helix 1 and to the COOH terminus of the TnT-TnI coiled-coil. Ca²⁺ destabilized rather than stabilized specific TnI segments within the coiled-coil and destabilized a region not previously implicated in Ca²⁺-mediated regulation: the coiled-coil''s NH₂-terminal base plus the preceding TnI loop with which the base interacts. Cardiomyopathy-linked mutations clustered almost entirely within influentially dynamic regions of troponin, and many sites were Ca²⁺-sensitive. Overall, the findings demonstrate highly selective effects of regulatory site Ca²⁺, including opposite changes in protein dynamics at opposite ends of the troponin core domain. Ca²⁺ release triggers an intramolecular switching mechanism that propagates extensively within the extended troponin structure, suggests specific movements of the TnI inhibitory regions, and prominently involves troponin''s dynamic features.     

Estimation of Free Energy Systematic Errors in Molecular Simulations of Globular Proteins Surrounded by Finite Water Clusters. One Center Multipole Expansion of Reaction Field Differences

Free energy calculated in simulations on the atomic level (Monte Carlo or Molecular Dynamics) has a systematic error, if the water shell surrounding a globular protein is finite. The error (“cluster error”) is equal to a difference of free energies obtained in simulations with an infinite and finite water shell. In this work a continuum dielectric model was used to estimate the “cluster error”. A multipole expansion of the estimate was performed for a water shell with a spherical outer boundary. The expansion has very simple form. Each term is a product of two functions, one of them depending only on the charge's conformation, and the other one only on dielectric properties of the system. There are two practical uses of the expansion. First, it may be used to estimate the “cluster error” in a simulation already made; second, it may be used to plan a simulation in such a way that the “cluster error” is minimal. Numerical values of the largest terms in the multipole expansion corresponding to a typical system in simulations of globular proteins are given.     

Dynamics of the Antigen-binding Grooves in CD1 Proteins: REVERSIBLE HYDROPHOBIC COLLAPSE IN THE LIPID-FREE STATE*

CD1 proteins mediate the presentation of endogenous and foreign lipids on the cell surface for recognition by T cell receptors. To sample a diverse antigen pool, CD1 proteins are repeatedly internalized and recycled, assisted, in some cases, by lipid transfer proteins such as saposins. The specificity of each CD1 isoform is, therefore, conferred in part by its intracellular pathway but also by distinct structural features of the antigen-binding domain. Crystal structures of CD1-lipid complexes reveal hydrophobic grooves and pockets within these binding domains that appear to be specialized for different lipids. However, the mechanism of lipid loading and release remains to be characterized. Here we gain insights into this mechanism through a meta-analysis of the five human CD1 isoforms, in the lipid-bound and lipid-free states, using all-atom molecular dynamics simulations. Strikingly, for isoforms CD1b through CD1e, our simulations show the near-complete collapse of the hydrophobic cavities in the absence of the antigen. This event results from the spontaneous closure of the binding domain entrance, flanked by two α-helices. Accordingly, we show that the anatomy of the binding cavities is restored if these α-helices are repositioned extrinsically, suggesting that helper proteins encountered during recycling facilitate lipid exchange allosterically. By contrast, we show that the binding cavity of CD1a is largely preserved in the unliganded state because of persistent electrostatic interactions that keep the portal α-helices at a constant separation. The robustness of this binding groove is consistent with the observation that lipid exchange in CD1a is not dependent on cellular internalization.     

蛋白质的反胶团萃取机制及动力学模型研究进展

反胶团萃取是近年发展起来的分离和纯化生化物质的新方法,本文介绍了反胶团萃取蛋白质技术的原理和机制、影响反胶团中蛋白质稳定性的因素,改进的蛋白质反萃取工艺,反胶团的酶动力学研究以及反胶团萃取技术的研究展望。     

丹麦森林土壤反硝化作用的动力学分析

本项研究将乙炔和氯霉素抑制技术结合起来 ,对丹麦一森林土壤的反硝化作用进行了研究 ,并考察温度对其还原酶活性的影响 .反硝化还原酶活性和合成过程受O2 的抑制 ,厌氧培养时 ,需要一定时间消耗系统中残余的O2 来解除这种抑制作用 .在无抗生素抑制蛋白质合成时 ,硝酸还原酶只有少量合成 ,而N2 O还原酶却显著地诱导产生 .这一结果对土壤吸收N2 O能力的研究具有重要意义 .在各处理下 ,系统中未发生亚硝酸盐的明显积累 ,表明亚硝酸还原酶活性大于硝酸还原酶 .外加葡萄糖加速了反硝化作用 ,并能促进酶的合成和消除还原过程中的电子竞争 .供试土壤表现出很强的厌氧呼吸作用 ,并受外加C源的促进 .反硝化作用的活化能低于土壤厌氧呼吸的活化能 ,因此反硝化作用的Q1 0值较低 ,CO2 和N2 O的产生比例随温度升高而加大 .     

Phylogenetic Differences in Content and Intensity of Periodic Proteins

Many proteins exhibit sequence periodicity, often correlated with a visible structural periodicity. The statistical significance of such periodicity can be assessed by means of a chi-squared-based test, with significance thresholds being calculated from shuffled sequences. Comparison of the complete proteomes of 45 species reveals striking differences in the proportion of periodic proteins and the intensity of the most significant periodicities. Eukaryotes tend to have a higher proportion of periodic proteins than eubacteria, which in turn tend to have more than archaea. The intensity of periodicity in the most periodic proteins is also greatest in eukaryotes. By contrast, the relatively small group of periodic proteins in archaea also tend to be weakly periodic compared to those of eukaryotes and eubacteria. Exceptions to this general rule are found in those prokaryotes with multicellular life-cycle phases, e.g., Methanosarcina sp., or Anabaena sp., which have more periodicities than prokaryotes in general, and in unicellular eukaryotes, which have fewer than multicellular eukaryotes. The distribution of significantly periodic proteins in eukaryotes is over a wide range of period lengths, whereas prokaryotic proteins typically have a more limited set of period lengths. This is further investigated by repeating the analysis on the NRL-3D database of proteins of solved structure. Some short-range periodicities are explicable in terms of basic secondary structure, e.g., alpha helices, while middle-range periodicities are frequently found to consist of known short Pfam domains, e.g., leucine-rich repeats, tetratricopeptides or armadillo domains. However, not all can be explained in this way.Reviewing Editor: Dr. John Oakeshott     

Mixed salts containing croconate violet, lanthanide and potassium ions: Crystal structures and spectroscopic characterization of supramolecular compounds

The vibrational spectra and crystal structures of four lanthanide and potassium salts of 3,5-bis(dicyanomethylene)cyclopentane-1,2,4-trionate (), known as croconate violet (CV), are described in this work. All LnKC₂₂N₈O₆ (Ln = La⁺³, Nd⁺³, Gd⁺³ and Ho⁺³) compounds are isostructural, crystallizing in the triclinic space group. In each compound the lanthanide ion is acting as both monodentate and chelate metal sites, whereas the potassium presents only monodentate coordination. The crystal structure shows the formation of a periodic 2D structure extended by K-N bonds parallel to the crystallographic [0 0 1] direction; these 2D sheets form hydrogen bonds with water molecules giving rise to a 3D extended arrangement. It is not possible to observe any type of π-interaction and the main forces responsible to stabilize the structures are the hydrogen bonds. The vibrational spectra of all the compounds are very similar, and the most important vibrational markers for the croconate violet ion, namely the ν(CN) and ν(CO) modes, behave differently: the ν(CN) modes are not shifted by the presence of the lanthanide ion species, only showing small band intensity differences, whereas the ν(CO) bands are shifted to higher wavenumbers, due to their coordination to the metal sites.     

Femtosecond IR Pump-Probe Spectroscopy of Nonlinear Energy Localization in Protein Models and Model Proteins

This paper reviews our experimental and theoretical efforts toward understanding vibrational self-trapping of the amide I and N–H mode of crystalline acetanilide (ACN), other similar hydrogen-bonded crystals, as well as of model peptides. In contrast to previous works, we used nonlinear IR spectroscopy as the experimental tool, which is specifically sensitive to the anharmonic contributions of the intramolecular interactions (as the nonlinear IR response of set of harmonic oscillators vanishes exactly). Our work reconfirms the previous assignment of the two bands of the amide I mode of ACN as being a self-trapped and a free exciton state, but in addition also establishes the lifetimes of these states and identifies the relevant phonons. Furthermore, we provide evidence for vibrationally self-trapped states also in model α-helices. However, given the short lifetime, any biological relevance in the sense of Davydov’s initial proposal can probably be ruled out.     

Spectroscopic Characterization of a VO<Superscript>2+</Superscript> Complex of Oxodiacetic Acid and its Bioactivity on Osteoblast-like Cells in Culture

The oxovanadium(IV) complex of oxodiacetic acid (H₂oda) of stoichiometry [VO(oda)(H₂O)₂], which presents an unprecedented tridentate OOO coordination, was thoroughly characterized by infrared, Raman, electronic, and electron paramagnetic resonance spectroscopies. The biological activity of the complex on the cell proliferation and differentiation was tested on osteoblast-like cells (MC3T3E1 osteoblastic mouse calvaria-derived cells and UMR106 rat osteosarcoma-derived cells) in culture. The complex caused inhibition of cellular proliferation in both osteoblast-like cells in culture, but the cytotoxicity was stronger in the normal (MC3T3E1) than in the tumoral (UMR106) osteoblasts. The effect of the complex in cell differentiation was tested through the specific activity of alkaline phosphatase of the UMR106 cells because they expressed a high activity of this enzyme. What occurs with other vanadium compounds [VO(oda)(H₂O)₂] is an inhibitory agent of osteoblast differentiation.     

The Absorption and Fluorescence Spectra of the Cyanobacterial Phycobionts of Cryptoendolithic Lichens in the High-Polar Regions of Antarctica

The algologically pure cultures of the green–brown cyanobacterium Chroococcidiopsissp. and three cyanobacteria of the genus Gloeocapsa, the blue–green Gloeocapsa sp.₁, the brown Gloeocapsa sp.₂, and the red–orange Gloeocapsa sp.₃, were isolated from sandstones and rock fissures in the high-polar regions of Antarctica. These cyanobacteria are the most widespread phycobionts of cryptoendolithic lichens in these regions. The comparative analysis of the absorption and the second-derivative absorption spectra of the cyanobacteria revealed considerable differences in the content of chlorophyll a and in the content and composition of carotenoids and phycobiliproteins. In addition to phycocyanin, allophycocyanin, and allophycocyanin B, which were present in all of the cyanobacteria studied, Gloeocapsa sp.₂ also contained phycoerythrocyanin and Gloeocapsa sp.₃ phycoerythrocyanin and C-phycoerythrin (the latter pigment is typical of nitrogen-fixing cyanobacteria). The fluorescence spectra of Gloeocapsa sp.₂ and Gloeocapsa sp.₃ considerably differed from the fluorescence spectra of the other cyanobacteria as well. The data obtained suggest that various zones of the lichens may be dominated either by photoheterotrophic or photoautotrophic cyanobacterial phycobionts, which differ in the content and composition of photosynthetic pigments.     

Pinocytosis and locomotion of amoebae: XII. Dynamics and motive force generation during induced pinocytosis in A. proteus

Summary The mechanism of induced pinocytosis was investigated in Amoeba proteus by light and electron microscopy. The application of nine different inducing substances revealed that pinocytotic channel formation, elongation, vesiculation, shortening and disappearance are the result of the successive or simultaneous action of both traction and pressure forces, which are produced by the contractile activity of a plasma membrane-associated layer of filaments ranging from a few hundred nm to several in thickness. The initial phase of channel formation is caused by traction forces according to the membrane flow concept, whereas channel elongation and vesiculation mainly result from pressure forces in conjunction with the extrusion of small hyaline pseudopodia. Shortening and disappearance of the pinocytotic channels are brought about by local contractions of the cortical filament layer in the basal region of the hyaline pseudopodia. Experiments using latex beads as marker particles together with inducing substances show that a rapid membrane turnover during pinocytosis can be excluded, and that the plasma membrane slides as an entire structure over the underlying cytoplasm.The authors are most grateful to Mrs. J. Ruch for technical assistance     

Fragmentation of Ar 3 + : The Role of Rotational and Vibrational Predissociation Dynamics

The quantum study of the fragmentation dynamics of argon trimer ions has been carried out using two different ab-initio potential energy surfaces. Different computational methods have been employed and the effects of the total angular momentum of the system have been evaluated. It is found that the observed metastability can be explained with the lengthening of the lifetimes produced by the centrifugal barrier.