Intermolecular Communication Research Articles

Rem uncouples excitation-contraction coupling in adult skeletal muscle fibers.

In skeletal muscle, excitation-contraction (EC) coupling requires depolarization-induced conformational rearrangements in L-type Ca(2+) channel (Ca(V)1.1) to be communicated to the type 1 ryanodine-sensitive Ca(2+) release channel (RYR1) of the sarcoplasmic reticulum (SR) via transient protein-protein interactions. Although the molecular mechanism that underlies conformational coupling between Ca(V)1.1 and RYR1 has been investigated intensely for more than 25 years, the question of whether such signaling occurs via a direct interaction between the principal, voltage-sensing α(1S) subunit of Ca(V)1.1 and RYR1 or through an intermediary protein persists. A substantial body of evidence supports the idea that the auxiliary β(1a) subunit of Ca(V)1.1 is a conduit for this intermolecular communication. However, a direct role for β(1a) has been difficult to test because β(1a) serves two other functions that are prerequisite for conformational coupling between Ca(V)1.1 and RYR1. Specifically, β(1a) promotes efficient membrane expression of Ca(V)1.1 and facilitates the tetradic ultrastructural arrangement of Ca(V)1.1 channels within plasma membrane-SR junctions. In this paper, we demonstrate that overexpression of the RGK protein Rem, an established β subunit-interacting protein, in adult mouse flexor digitorum brevis fibers markedly reduces voltage-induced myoplasmic Ca(2+) transients without greatly affecting Ca(V)1.1 targeting, intramembrane gating charge movement, or releasable SR Ca(2+) store content. In contrast, a β(1a)-binding-deficient Rem triple mutant (R200A/L227A/H229A) has little effect on myoplasmic Ca(2+) release in response to membrane depolarization. Thus, Rem effectively uncouples the voltage sensors of Ca(V)1.1 from RYR1-mediated SR Ca(2+) release via its ability to interact with β(1a). Our findings reveal Rem-expressing adult muscle as an experimental system that may prove useful in the definition of the precise role of the β(1a) subunit in skeletal-type EC coupling.

Redox‐Controlled Exchange Bias in a Supramolecular Chain of Fe4 Single‐Molecule Magnets

AbstractTetrairon(III) single‐molecule magnets [Fe4(pPy)2(dpm)6] (1) (H3pPy=2‐(hydroxymethyl)‐2‐(pyridin‐4‐yl)propane‐1,3‐diol, Hdpm=dipivaloylmethane) have been deliberately organized into supramolecular chains by reaction with RuIIRuII or RuIIRuIII paddlewheel complexes. The products [Fe4(pPy)2(dpm)6][Ru2(OAc)4](BF4)x with x=0 (2 a) or x=1 (2 b) differ in the electron count on the paramagnetic diruthenium bridges and display hysteresis loops of substantially different shape. Owing to their large easy‐plane anisotropy, the s=1 diruthenium(II,II) units in 2 a act as effective seff=0 spins and lead to negligible intrachain communication. By contrast, the mixed‐valent bridges (s=3/2, seff=1/2) in 2 b introduce a significant exchange bias, with concomitant enhancement of the remnant magnetization. Our results suggest the possibility to use electron transfer to tune intermolecular communication in redox‐responsive arrays of SMMs.

Redox-Controlled Exchange Bias in a Supramolecular Chain of Fe4 Single-Molecule Magnets.

Tetrairon(III) single-molecule magnets [Fe4(pPy)2(dpm)6] (1) (H3pPy=2-(hydroxymethyl)-2-(pyridin-4-yl)propane-1,3-diol, Hdpm=dipivaloylmethane) have been deliberately organized into supramolecular chains by reaction with Ru(II)Ru(II) or Ru(II)Ru(III) paddlewheel complexes. The products [Fe4(pPy)2(dpm)6][Ru2(OAc)4](BF4)x with x=0 (2 a) or x=1 (2 b) differ in the electron count on the paramagnetic diruthenium bridges and display hysteresis loops of substantially different shape. Owing to their large easy-plane anisotropy, the s=1 diruthenium(II,II) units in 2 a act as effective s(eff)=0 spins and lead to negligible intrachain communication. By contrast, the mixed-valent bridges (s=3/2, s(eff)=1/2) in 2 b introduce a significant exchange bias, with concomitant enhancement of the remnant magnetization. Our results suggest the possibility to use electron transfer to tune intermolecular communication in redox-responsive arrays of SMMs.

Intermolecular Communication in a Supramolecular Assembly of Porphyrins and Phthalocyanines

Programmable construction of a multiple molecular system is the best measure for bringing out the integrated properties evolved from the intermolecular communications in the molecular assemblies. Especially, controlling sequential and spatial arrangements of building components in the molecular array is crucial for developing novel functions of the designer nanoarchitecture. Since organized assemblies of porphyrins and phthalocyanines are promising for generating higher functionalized systems, we have recently reported the supramolecular arrays in which a porphyrin and a phthalocyanine are connected by four-fold rotaxanes [1-4] and sequential and spatial organization of metalloporphyrins inside a peptide duplex [5]. In this paper, we will present construction of the suplamolecular arrays of a metallo-porphyrin and a metallo-phthalocyanine through four-fold rotaxane formation between a tetradactyl porphyrin with alkylammmonium moieties and a phthalocyanine bearing four crown ethers (Figure 1a) and significant electronic communications between the metal complexes (Figure 1b). Since synthetic strategy for the rotaxane is applicable to pre- and post-metallation of both porphyrin and phthalocyanine centers, the four-fold rotaxane framework is suitable for homo- and hetero-assemblage of metal ions. In a homo-dinuclear Cu2+ complex of the four-fold rotaxane, the Cu2+-porphyrin and the Cu2+-phthalocyanine showed a switching behavior in the spin–spin interaction through change of the spatial distance between the two metal centers induced by protonation and deprotonation. 1) Y. Yamada, M. Okamoto, K. Furukawa, T. Kato, and K. Tanaka, Angew. Chem. Int. Ed., 51, 709–713 (2012). 2) Y. Yamada, N. Mihara, and K. Tanaka, Dalton Trans., 42, 15873-15876 (2013). 3) Y. Yamada, N. Mihara, S. Shibano, K. Sugimoto, and K. Tanaka, J. Am. Chem. Soc., 135, 11505-11508 (2013). 4) Y. Yamada, M. Okada, and K. Tanaka, Chem. Commun., 49, 11053-11055 (2013). 5) Y. Yamada, T. Kubota, M. Nishio, and K. Tanaka, J. Am. Chem. Soc., 136, 6505-6509 (2014). Figure 1

A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex.

The dynamic cross correlation (DCC) analysis is a popular method for analyzing the trajectories of molecular dynamics (MD) simulations. However, it is difficult to detect correlative motions that appear transiently in only a part of the trajectory, such as atomic contacts between the side-chains of amino acids, which may rapidly flip. In order to capture these multi-modal behaviors of atoms, which often play essential roles, particularly at the interfaces of macromolecules, we have developed the “multi-modal DCC (mDCC)” analysis. The mDCC is an extension of the DCC and it takes advantage of a Bayesian-based pattern recognition technique. We performed MD simulations for molecular systems modeled from the (Ets1)2–DNA complex and analyzed their results with the mDCC method. Ets1 is an essential transcription factor for a variety of physiological processes, such as immunity and cancer development. Although many structural and biochemical studies have so far been performed, its DNA binding properties are still not well characterized. In particular, it is not straightforward to understand the molecular mechanisms how the cooperative binding of two Ets1 molecules facilitates their recognition of Stromelysin-1 gene regulatory elements. A correlation network was constructed among the essential atomic contacts, and the two major pathways by which the two Ets1 molecules communicate were identified. One is a pathway via direct protein-protein interactions and the other is that via the bound DNA intervening two recognition helices. These two pathways intersected at the particular cytosine bases (C110/C11), interacting with the H1, H2, and H3 helices. Furthermore, the mDCC analysis showed that both pathways included the transient interactions at their intermolecular interfaces of Tyr396–C11 and Ala327–Asn380 in multi-modal motions of the amino acid side chains and the nucleotide backbone. Thus, the current mDCC approach is a powerful tool to reveal these complicated behaviors and scrutinize intermolecular communications in a molecular system.

Conformational heterogeneity of the AAA ATPase p97 characterized by single particle cryo-EM

p97, a member of the AAA (ATPase Associated with various Activities) ATPase family, is essential and centrally involved in a wide variety of cellular processes. Single amino-acid substitutions in p97 have been associated with the severe degenerative disorder of Inclusion Body Myopathy associated with Paget disease of bone and Frontotemporal Dementia (IBMPFD) as well as amytropic leteral sclerosis (ALS). Current models propose that p97 acts as a motor transmitting the energy from the ATPase cycle to conformational changes of substrate protein complexes causing segregation, remodeling or translocation. Mutations at the interface between the N and the D1 domains impact the ATPase activity and the conformation of D2 on the opposite side of the protein complex, suggesting intermolecular communication. Because of limited structural information, the molecular mechanisms on how p97 drives its activities and the molecular basis for transmission of information within the molecule remain elusive. Structural heterogeneity is observed in vitro and is likely relevant for the in vivo biological function of p97. Single particle cryo-EM is the method of choice to study a flexible complex. The technique allows study in solution and also deals with sample heterogeneity by image classification. We have set-up the characterization of the conformational heterogeneity in WT and disease relevant p97 mutant using multi-likelihood classification and Hybrid Electron Microscopy Normal Mode Analysis HEMNMA. The multi-likelihood analysis shows a link between the conformations of the N and D2 domains. HEMNMA allows the analysis of the asymmetry of the conformational changes. Together these studies describe the structural flexibility of p97 and the coupling of the ATPase activity with conformational changes in health and in disease. Study of this model system also allows the development of new methods to understand the conformational heterogeneity of other protein complexes.

Insights into the AIEE of 1,8-naphthalimides (NPIs): inverse effects of intermolecular interactions in solution and aggregates.

Systematic structural perturbation has been used to fine-tune and understand the luminescence properties of three new 1,8-naphthalimides (NPIs) in solution and aggregates. The NPIs show blue emission in the solution state and their fluorescence quantum yields are dependent upon their molecular rigidity. In concentrated solutions of the NPIs, intermolecular interactions were found to quench the fluorescence due to the formation of excimers. In contrast, upon aggregation (in THF/H2O mixtures), the NPIs show aggregation-induced emission enhancement (AIEE). The NPIs also show moderately high solid-state emission quantum yields (ca. 10-12.7 %). The AIEE behaviour of the NPIs depends on their molecular rigidity and the nature of their intermolecular interactions. The NPIs 1-3 show different extents of intermolecular (π-π and C-H⋅⋅⋅O) interactions in their solid-state crystal structures depending on their substituents. Detailed photophysical, computational and structural investigations suggest that an optimal balance of structural flexibility and intermolecular communication is necessary for achieving AIEE characteristics in these NPIs.

Functional Adaptations to Cardiac Troponin I Phosphomimetic Substitutions

Protein kinase C phosphorylation of S43/45 on cardiac troponin I (cTnI) increases during periods of cardiac stress to modulate cardiac myocyte contractile performance, but the functional impact of this phosphorylation remains controversial. Adenoviral gene transfer of phosphomimetic cTnIS43D, cTnIS45D or cTnIS43/S45D into adult rat myocytes produced partial replacement and non-additive alterations in contractile function 2 days after gene transfer. More extensive replacement of endogenous cTnI is observed by 4 days along with an adaptive functional response in the form of accelerated shortening and re-lengthening. The present study focused on identifying the adaptive responses observed in myocytes expressing these phospho-mimetic cTnI substitutions. Adaptations due to intramolecular communication within cTnI were investigated by measuring cTnIS23/24 phosphorylation in myocytes expressing cTnI with S43D, S45D, and S43/45D. Increased expression of these phosphomimetics elevated cTnIS23/24 phosphorylation compared to controls. Western blot analysis also indicated intermolecular interactions contributed to this adaptive response, as phosphorylation of S282 on cardiac myosin binding protein C (cMyBP-C) and S16 on phospholamban (PLB) increased significantly in myocytes. The increased PLB phosphorylation correlated with changes in Ca2+ cycling observed in these myocytes compared to controls. Additional studies performed under acidotic stress produced similar changes in the phosphorylation of cTnIS23/24. Ongoing studies are testing whether similar changes in cMyBP-CS282 develop with acidosis. The underlying signaling mechanism responsible for this change in phosphorylation turnover is currently under investigation. Overall, these results suggest cTnI substitutions and cellular stress initiate intramolecular and intermolecular communication to generate an adaptive myofilament response. The shared response produced by cTnI substitutions and cellular acidosis suggests this communication may be important for understanding the myofilament response under conditions of contractile dysfunction.

Dynamics fingerprint and inherent asymmetric flexibility of a cold-adapted homodimeric enzyme. A case study of the Vibrio alkaline phosphatase

BackgroundProtein dynamics influence protein function and stability and modulate conformational changes. Such motions depend on the underlying networks of intramolecular interactions and communicating residues within the protein structure. Here, we provide the first characterization of the dynamic fingerprint of the dimeric alkaline phosphatase (AP) from the cold-adapted Vibrio strain G15-21 (VAP), which is among the APs with the highest known kcat at low temperatures. MethodsMultiple all-atom explicit solvent molecular dynamics simulations were employed in conjunction with different metrics to analyze the dynamical patterns and the paths of intra- and intermolecular communication. ResultsInteractions and coupled motions at the interface between the two VAP subunits have been characterized, along with the networks of intramolecular interactions. It turns out a low number of intermolecular interactions and coupled motions, which result differently distributed in the two monomers. The paths of long-range communication mediated from the catalytic residues to distal sites were also characterized, pointing out a different information flow in the two subunits. ConclusionsA pattern of asymmetric flexibility is evident in the two identical subunits of the VAP dimer that is intimately linked to a different distribution of intra- and intermolecular interactions. The asymmetry was also evident in pairs of cross-correlated residues during the dynamics. General significanceThe results here discussed provide a structural rationale to the half-of-site mechanism previously proposed for VAP and other APs, as well as a general framework to characterize asymmetric dynamics in homomeric enzymes.

Coconfinement of Fluorescent Proteins: Spatially Enforced Communication of GFP and mCherry Encapsulated within the P22 Capsid

The precise architectures of viruses and virus-like particles are proving to be highly advantageous in synthetic materials applications. Not only can these nanocontainers be harnessed as active materials, but they can be exploited for examining the effects of in vivo "cell-like" crowding and confinement on the properties of the encapsulated cargo. Here we report the first example of intermolecular communication between two proteins coencapsulated within the capsid architecture of the bacteriophage P22. Using a genetically engineered three-protein fusion between the P22 scaffold protein, and the FRET pair, GFP, and a red fluorescent protein (mCherry), we were able to direct the encapsulation of the genetic fusion when coexpressed with P22 coat protein. These self-assembled P22 capsids are densely packaged, occupying more than 24% of the available volume, and the molecular design assures a 1:1 ratio of the interacting proteins. To probe the effect of crowding and confinement on the FRET communication in this nanoenvironment, we spaced the donor-acceptor pair with variable length flexible linkers and examined the effect on FRET inside the capsid compared to the same tethered FRET pairs free in solution. The P22 system is unique in that the capsid morphology can be altered, without losing the encapsulated cargo, resulting in a doubling of the capsid volume. Thus, we have additionally examined the encapsulated fusions at two different internal concentrations. Our results indicate that FRET is sensitive to the expansion of the capsid and encapsulation enforces significant intermolecular communication, increasing FRET by 5-fold. This P22 coencapsulation system is a promising platform for studying crowding, enforced proximity, and confinement effects on communication between active proteins.

ChemInform Abstract: Ion Translocation in Artificial Molecule‐Based Systems Induced by Light, Electrons, or Chemicals

AbstractReview: 84 ref.

Intermolecular Communication on a Liposomal Membrane: Enzymatic Amplification of a Photonic Signal with a Gemini Peptide Lipid as a Membrane-Bound Artificial Receptor

A supramolecular system that can activate an enzyme through photo-isomerization was constructed by using a liposomal membrane scaffold. The design of the system was inspired by natural signal transduction systems, in which enzymes amplify external signals to control signal transduction pathways. The liposomal membrane, which provided a scaffold for the system, was prepared by self-assembly of a photoresponsive receptor and a cationic synthetic lipid. NADH-dependent L-lactate dehydrogenase, the signal amplifier, was immobilized on the liposomal surface by electrostatic interactions. Recognition of photonic signals by the membrane-bound receptor induced photo-isomerization, which significantly altered the receptor's metal-binding affinity. The response to the photonic signal was transmitted to the enzyme by Cu(2+) ions. The enzyme amplified the chemical information through a catalytic reaction to generate the intended output signal.

Functionalized Tetrathienoanthracene: Enhancing π–π Interactions Through Expansion of the π-Conjugated Framework

The functionalization of tetrathienoanthracene (TTA) with bromine and 2-hexylthiophene moieties is described, and their influence at both the molecular and solid-state level has been investigated. Comparative optical and electrochemical studies indicate an increase in conjugation for the thiophene derivative compared to the parent TTA. In the solid state, these materials form slipped π-stack structures with a number of close intermolecular contacts. Comparison of the two structures reveals a more steeply inclined slipped π-stack for the thiophene derivative resulting in a closer interplanar separation. This, coupled with the extended molecular framework, leads to an enhanced number of π–π interactions within the stack. The combination of increased conjugation at the molecular level, and π-stacked structures with strong intermolecular communication at the solid-state level, augurs well for the use of TTA materials in optoelectronic applications.

METHODS OF FUEL PRODUCTION FROM ORGANIC RAW MATERIALS BY PLASMA CONVERTERS

The conducted analysis of methods of reception of fuels and energy from organic raw materials allows to make a conclusion that application of plasma converters provides rupture of intermolecular communications of hydrocarbonic raw materials by fast pyrolysis of initial components with the subsequent synthesis of the new substances differing by physical and chemical properties from the initial.

Coherent Infra-Red as logically necessary to explain Piagetian psychology and neuro-microanatomy — Two independent corroborations for Gurwitsch's findings, and the importance of self-consistent theory

We can infer mechanisms underlying advanced human intelligence via •physics, chemistry and information-technology; but also •epistemology: analysing all knowledge-building processes (based on selection amongst micro-ideas). Hence Piaget offered "schèmes" as such items of thought/action, to account for actual human behaviour. In microphysiological terms, basic "schèmes" should have digital properties and a one-dimensional organization. That implied RNA-like molecules (and their "chorus" groups). — However for the necessary fast intermolecular communication, traditional action-potential "spikes" would be much too coarse. The alternative is Infra-Red. It then appears that myelinated nerve fibres seem suitable for an unexpected second role as coaxial cables for IR! Such opticalinterpretations also explain several enigmas: •What keeps (myelin-thickness / axon-diameter) ≈ constant? — (a mystery since 1905). •Why PNS myelination is delayed until the axon diameter reaches 1μm. •Why myelin often stops growing at a predictable angle in its wrapping. •Callahan's anomalous failure to detect sensory action-potentials even though his insects were responding to invisible IR signals. (Meanwhile RNA-like coding explains inherited behavioural traits, and memory-"recording" as Darwinian!) The important point: Here IR is independently identified as a necessary solution to logistical problems. In contrast the Gurwitsch tradition first discovered emissions, and then sought explanations. Thus the two approaches corroborate.

Hot Spots for Allosteric Regulation on Protein Surfaces

Recent work indicates a general architecture for proteins in which sparse networks of physically contiguous and coevolving amino acids underlie basic aspects of structure and function. These networks, termed sectors, are spatially organized such that active sites are linked to many surface sites distributed throughout the structure. Using the metabolic enzyme dihydrofolate reductase as a model system, we show that: (1) the sector is strongly correlated to a network of residues undergoing millisecond conformational fluctuations associated with enzyme catalysis, and (2) sector-connected surface sites are statistically preferred locations for the emergence of allosteric control in vivo. Thus, sectors represent an evolutionarily conserved "wiring" mechanism that can enable perturbations at specific surface positions to rapidly initiate conformational control over protein function. These findings suggest that sectors enable the evolution of intermolecular communication and regulation.

A shortcut to a skeletal muscle DHPR knock‐in?

A shortcut to a skeletal muscle DHPR knock‐in?

Intermolecular communication between DnaK and GrpE in the DnaK chaperone system

Intermolecular communication between DnaK and GrpE in the DnaK chaperone system

Ion Translocation in Artificial Molecule-based Systems Induced by Light, Electrons, or Chemicals

Synthetic molecules and nanodevices, like their more elaborate biological counterparts, have been shown to perform several sophisticated functions, using even fairly simple molecular architectures. One limitation to developing artificial molecular arrays and networks from these miniscule building blocks is the lack of a unifying strategy whereby they can communicate or interact together, which has been successfully developed in natural systems. Understanding and harnessing these efficient biological processes could prove key in the development of future integrated molecule-based nanodevices and networks. Herein, we give a short overview of some manifestations of intra- and intermolecular communication based on chemical messengers in artificial systems, in some ways analogous to natural systems, which are in turn controlled by light, a redox process or a chemical reaction or interaction. Some advantages, limitations, and challenges are highlighted.

Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces.

Wordom is a versatile, user-friendly, and efficient program for manipulation and analysis of molecular structures and dynamics. The following new analysis modules have been added since the publication of the original Wordom paper in 2007: assignment of secondary structure, calculation of solvent accessible surfaces, elastic network model, motion cross correlations, protein structure network, shortest intra-molecular and inter-molecular communication paths, kinetic grouping analysis, and calculation of mincut-based free energy profiles. In addition, an interface with the Python scripting language has been built and the overall performance and user accessibility enhanced. The source code of Wordom (in the C programming language) as well as documentation for usage and further development are available as an open source package under the GNU General Purpose License from http://wordom.sf.net. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011