Conformational Memory Research Articles

Cellular forgetting, desensitisation, stress and ageing in signalling networks. When do cells refuse to learn more?

Recent findings show that single, non-neuronal cells are also able to learn signalling responses developing cellular memory. In cellular learning nodes of signalling networks strengthen their interactions e.g. by the conformational memory of intrinsically disordered proteins, protein translocation, miRNAs, lncRNAs, chromatin memory and signalling cascades. This can be described by a generalized, unicellular Hebbian learning process, where those signalling connections, which participate in learning, become stronger. Here we review those scenarios, where cellular signalling is not only repeated in a few times (when learning occurs), but becomes too frequent, too large, or too complex and overloads the cell. This leads to desensitisation of signalling networks by decoupling signalling components, receptor internalization, and consequent downregulation. These molecular processes are examples of anti-Hebbian learning and 'forgetting' of signalling networks. Stress can be perceived as signalling overload inducing the desensitisation of signalling pathways. Ageing occurs by the summative effects of cumulative stress downregulating signalling. We propose that cellular learning desensitisation, stress and ageing may be placed along the same axis of more and more intensive (prolonged or repeated) signalling. We discuss how cells might discriminate between repeated and unexpected signals, and highlight the Hebbian and anti-Hebbian mechanisms behind the fold-change detection in the NF-κB signalling pathway. We list drug design methods using Hebbian learning (such as chemically-induced proximity) and clinical treatment modalities inducing (cancer, drug allergies) desensitisation or avoiding drug-induced desensitisation. A better discrimination between cellular learning, desensitisation and stress may open novel directions in drug design, e.g. helping to overcome drug resistance.

“Nature or nurture” – How environmental factors influence the conformational memory of amyloid fibrils

Amyloid fibrils are complex protein structures with multilayered chiral architecture, that are known to self-propagate. The replication of the mother seed structure by daughter fibrils is known as conformational or templated memory. Using vibrational circular dichroism (VCD), electronic circular dichroism (ECD), transmission electron microscopy (TEM), and cryo-electron microscopy (cryo-EM) we have shown that environmental factors (here agitation) can be a competing force against the templated growth of human lysozyme fibrils. In the cross-seeding experiment non-agitated daughters preserved the structure of agitated mothers, whereas agitated daughters did not always exhibit the same characteristics as their non-agitated mothers. This pattern was reflected on various levels of fibril architecture (secondary structure, protofilament handedness, morphology), demonstrating that the structural indeterminism originates from deeper levels of the fibril structure. This observation may contribute to a better understanding of the processes behind fibril formation.

Stability and Conformational Memory of Electrosprayed and Rehydrated Bacteriophage Ms2 Virus Coat Proteins

Stability and Conformational Memory of Electrosprayed and Rehydrated Bacteriophage Ms2 Virus Coat Proteins

Stability and conformational memory of electrosprayed and rehydrated bacteriophage MS2 virus coat proteins.

Proteins are innately dynamic, which is important for their functions, but which also poses significant challenges when studying their structures. Gas-phase techniques can utilise separation and a range of sample manipulations to transcend some of the limitations of conventional techniques for structural biology in crystalline or solution phase, and isolate different states for separate interrogation. However, the transfer from solution to the gas phase risks affecting the structures, and it is unclear to what extent different conformations remain distinct in the gas phase, and if resolution in silico can recover the native conformations and their differences. Here, we use extensive molecular dynamics simulations to study the two distinct conformations of dimeric capsid protein of the MS2 bacteriophage. The protein undergoes notable restructuring of its peripheral parts in the gas phase, but subsequent simulation in solvent largely recovers the native structure. Our results suggest that despite some structural loss due to the experimental conditions, gas-phase structural biology techniques provide meaningful data that inform not only about the structures but also conformational dynamics of proteins.

Imparting conformational memory for material adhesion.

Adhesion between similar and dissimilar materials is essential to many biological systems and synthetic materials, devices, and machines. Since the inception of adhesion science more than five decades ago, adhesion to a surface has long been recognized as beyond two-dimensional. Similarly, molecular conformation - the three-dimensional arrangement of atoms in a molecule - is ubiquitous in biology and fundamental to the binding of biomolecules. However, the connection between these concepts, which could link molecular conformation in biology to micro- and macroscopic adhesion in materials science, remains elusive. Herein, we examine this connection by manipulating the molecular conformation of a mussel-inspired universal coating, which imparts a memory for recognizing different hydrogels. This approach leads to significantly (several fold) increased interfacial adhesion between the coating and hydrogels across a broad range of length scales, from molecular to macroscopic. Furthermore, we demonstrate that imparting memory is a general and facile noncovalent approach for enhancing interfacial adhesion that, with suitable energy dissipation, can be used for the bonding of materials.

Roaming Dynamics and Conformational Memory in Photolysis of Formic Acid at 193\u2009nm Using Time-resolved Fourier-transform Infrared Emission Spectroscopy

In photodissociation of trans-formic acid (HCOOH) at 193 nm, we have observed two molecular channels of CO + H2O and CO2 + H2 by using 1 μs-resolved Fourier-transform infrared emission spectroscopy. With the aid of spectral simulation, the CO spectra are rotationally resolved for each vibrational state (v = 1–8). Each of the resulting vibrational and rotational population distributions is characteristic of two Boltzmann profiles with different temperatures, originating from either transition state pathway or OH-roaming to form the same CO + H2O products. The H2O roaming co-product is also spectrally simulated to understand the interplay with the CO product in the internal energy partitioning. Accordingly, this work has evaluated the internal energy disposal for the CO and H2O roaming products; especially the vibrational-state dependence of the roaming signature is reported for the first time. Further, given a 1 μs resolution, the temporal dependence of the CO/CO2 product ratio at v ≥ 1 rises from 3 to 10 of study, thereby characterizing the effect of conformational memory and well reconciling with the disputed results reported previously between absorption and emission methods.

Encapsulation-Controlled Photoisomerization of a Styryl Derivative: Stereoselective Formation of the Anti Z-Isomer in the Cucurbit[7]uril Cavity.

The photochemical isomerization of a styrylpyridinium dye (SP) bearing an unsymmetrically attached benzo-15-crown-5 ether has been studied in aqueous solution in the absence and presence of cucurbit[7]uril (CB[7]). The detailed analysis of the UV/Vis and NMR spectra showes that the isomeric composition of the photostationary mixtures of SP can be modulated by the host-guest complexation with CB[7]. It was found that steric hindrance caused by encapsulation of SP in the host cavity induces the exclusive formation of the anti conformer of Z-SP in contrast with the mixture of both anti and syn conformers obtained during photoisomerization of the dye without CB[7]. Remarkably, the displacement of anti Z-SP from CB[7] does not lead to the transformation of the anti Z-isomer into the syn Z-isomer pointing out the conformational memory of the system. The results provide an interesting example of the supramolecular stereorecognition by the achiral CB[7] host.

What is strain in neurodegenerative diseases?

Neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease, are characterized by the aggregation of misfolded proteins, including Aβ, tau and α-synuclein. It is well recognized that these misfolded proteins are able to self-propagate and spread throughout the nervous system and cause neuronal injury in a way that resembles prion disease. These disease-specific misfolded proteins demonstrate unique features, including the seeding barrier, the conformational memory effect, strain selection and strain evolution, based on the presence of various strains. However, the accurate definition of the term strain remains to be clarified. Here, a clear interpretation is proposed by a retrospective of its history in prion research and the recent progress in neurodegeneration research. Furthermore, the causes contributing to the genesis of various strains are also summarized. Deeper insight into strains helps us to understand the phenomena we observe in this field and it also enlightens us on the elusive mechanisms and management of neurodegeneration.

Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding.

Conformational memory in single-molecule dynamics has attracted recent attention and, in particular, has been invoked as a possible explanation of some of the intriguing properties of transition paths observed in single-molecule force spectroscopy (SMFS) studies. Here we study one candidate for a non-Markovian model that can account for conformational memory, the generalized Langevin equation with a friction force that depends not only on the instantaneous velocity but also on the velocities in the past. The memory in this model is determined by a time-dependent friction memory kernel. We propose a method for extracting this kernel directly from an experimental signal and illustrate its feasibility by applying it to a generalized Rouse model of a SMFS experiment, where the memory kernel is known exactly. Using the same model, we further study how memory affects various statistical properties of transition paths observed in SMFS experiments and evaluate the performance of recent approximate analytical theories of non-Markovian dynamics of barrier crossing. We argue that the same type of analysis can be applied to recent single-molecule observations of transition paths in protein and DNA folding.

Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding.

Conformational memory in single-molecule dynamics has attracted recent attention and, in particular, has been invoked as a possible explanation of some of the intriguing properties of transition paths observed in single-molecule force spectroscopy (SMFS) studies. Here we study one candidate for a non-Markovian model that can account for conformational memory, the generalized Langevin equation with a friction force that depends not only on the instantaneous velocity but also on the velocities in the past. The memory in this model is determined by a time-dependent friction memory kernel. We propose a method for extracting this kernel directly from an experimental signal and illustrate its feasibility by applying it to a generalized Rouse model of a SMFS experiment, where the memory kernel is known exactly. Using the same model, we further study how memory affects various statistical properties of transition paths observed in SMFS experiments and evaluate the performance of recent approximate analytical theories of non-Markovian dynamics of barrier crossing. We argue that the same type of analysis can be applied to recent single-molecule observations of transition paths in protein and DNA folding.

Amyloidogenic cross-seeding of Tau protein: Transient emergence of structural variants of fibrils.

Amyloid aggregates of Tau protein have been implicated in etiology of many neurodegenerative disorders including Alzheimer's disease (AD). When amyloid growth is induced by seeding with preformed fibrils assembled from the same protein, structural characteristics of the seed are usually imprinted in daughter generations of fibrils. This so-called conformational memory effect may be compromised when the seeding involves proteins with non-identical sequences leading to the emergence of distinct structural variants of fibrils (amyloid ‘strains’). Here, we investigate cross-seeding of full-length human Tau (FL Tau) with fibrils assembled from K18 and K18ΔK280 fragments of Tau in the presence of poly-L-glutamate (poly-Glu) as an enhancer of Tau aggregation. To study cross-seeding between Tau polypeptides and the role of the conformational memory effect in induction of Tau amyloid polymorphism, kinetic assays, transmission electron microscopy, infrared spectroscopy and limited proteolysis have been employed. The fastest fibrillization was observed for FL Tau monomers seeded with preformed K18 amyloid yielding daughter fibrils with unique trypsin digestion patterns. Morphological features of daughter FL Tau fibrils induced by K18 and K18ΔK280 seeds were reminiscent of the mother fibrils (i.e. straight paired fibrils and paired helical filaments (PHFs), respectively) but disappeared in the following generations which became similar to unpaired FL Tau amyloid fibrils formed de novo. The structural evolution observed in our study was accompanied by disappearance of the unique proteolysis profile originated from K18. Our findings may have implications for understanding molecular mechanisms of the emergence and stability of Tau amyloid strains.

Conformational memory in the association of the transmembrane protein phospholamban with the sarcoplasmic reticulum calcium pump SERCA

The sarcoplasmic reticulum Ca2+-ATPase SERCA promotes muscle relaxation by pumping calcium ions from the cytoplasm into the sarcoplasmic reticulum. SERCA activity is regulated by a variety of small transmembrane peptides, most notably by phospholamban in cardiac muscle and sarcolipin in skeletal muscle. However, how phospholamban and sarcolipin regulate SERCA is not fully understood. In the present study, we evaluated the effects of phospholamban and sarcolipin on calcium translocation and ATP hydrolysis by SERCA under conditions that mimic environments in sarcoplasmic reticulum membranes. For pre-steady-state current measurements, proteoliposomes containing SERCA and phospholamban or sarcolipin were adsorbed to a solid-supported membrane and activated by substrate concentration jumps. We observed that phospholamban altered ATP-dependent calcium translocation by SERCA within the first transport cycle, whereas sarcolipin did not. Using pre-steady-state charge (calcium) translocation and steady-state ATPase activity under substrate conditions (various calcium and/or ATP concentrations) promoting particular conformational states of SERCA, we found that the effect of phospholamban on SERCA depends on substrate preincubation conditions. Our results also indicated that phospholamban can establish an inhibitory interaction with multiple SERCA conformational states with distinct effects on SERCA's kinetic properties. Moreover, we noted multiple modes of interaction between SERCA and phospholamban and observed that once a particular mode of association is engaged it persists throughout the SERCA transport cycle and multiple turnover events. These observations are consistent with conformational memory in the interaction between SERCA and phospholamban, thus providing insights into the physiological role of phospholamban and its regulatory effect on SERCA transport activity.

FAK, talin and PIPKIγ regulate endocytosed integrin activation to polarize focal adhesion assembly.

Integrin endocytic recycling is critical for cell migration, yet how recycled integrins assemble into new adhesions is unclear. By synchronizing endocytic disassembly of focal adhesions (FAs), we find that recycled integrins reassemble FAs coincident with their return to the cell surface and dependent on Rab5 and Rab11. Unexpectedly, endocytosed integrins remained in an active but unliganded state in endosomes. FAK and Src kinases co-localized with endocytosed integrin and were critical for FA reassembly by regulating integrin activation and recycling, respectively. FAK sustained the active integrin conformation by maintaining talin association with Rab11 endosomes in a type I phosphatidylinositol phosphate kinase (PIPKIγ)-dependent manner. In migrating cells, endocytosed integrins reassembled FAs polarized towards the leading edge, and this polarization required FAK. These studies identify unanticipated roles for FA proteins in maintaining endocytosed integrin in an active conformation. We propose that the conformational memory of endocytosed integrin enhances polarized reassembly of FAs to enable directional cell migration.

The uncoupled ATPase activity of the ABC transporter BtuC2D2 leads to a hysteretic conformational change, conformational memory, and improved activity.

ABC transporters comprise a large and ubiquitous family of proteins. From bacteria to man they translocate solutes at the expense of ATP hydrolysis. Unlike other enzymes that use ATP as an energy source, ABC transporters are notorious for having high levels of basal ATPase activity: they hydrolyze ATP also in the absence of their substrate. It is unknown what are the effects of such prolonged and constant activity on the stability and function of ABC transporters or any other enzyme. Here we report that prolonged ATP hydrolysis is beneficial to the ABC transporter BtuC2D2. Using ATPase assays, surface plasmon resonance interaction experiments, and transport assays we observe that the constantly active transporter remains stable and functional for much longer than the idle one. Remarkably, during extended activity the transporter undergoes a slow conformational change (hysteresis) and gradually attains a hyperactive state in which it is more active than it was to begin with. This phenomenon is different from stabilization of enzymes by ligand binding: the hyperactive state is only reached through ATP hydrolysis, and not ATP binding. BtuC2D2 displays a strong conformational memory for this excited state, and takes hours to return to its basal state after catalysis terminates.

Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy.

Proteins are supramolecular machines that carry out a wide range of different functions, many of which require flexibility. Up until now spontaneous conformational fluctuations of proteins have always been assumed to reflect a stochastic random process. However, if changing between different conformational states was random, then it would be difficult to understand how conformational control of protein function could have evolved. Here we demonstrate that a single protein can show conformational memory. This is exactly the process that can facilitate the evolution of control of switching between two conformational states that can then be used to regulate protein function.

From roaming atoms to hopping surfaces: mapping out global reaction routes in photochemistry.

The photodissociation of small molecules occurs upon irradiation by ultraviolet or visible light, and it is a very important chemical process in Earth's atmosphere, in the atmospheres of other planets, and in interstellar media. Photodissociation is an important method used to thoroughly investigate the fundamental issues of chemical reactivity. Photodissociation involves molecules and reaction fragments moving over ground- and excited-state potential surfaces (PESs). Molecules can move on a single PES (adiabatic pathway) or can cross over from one PES to another (nonadiabatic pathways). For a full theoretical understanding of a photodissociation mechanism, all of the important nonadiabatic and adiabatic pathways must be determined. This is not an easy task. We have developed an efficient computational method, called the global reaction route mapping (GRRM) strategy, that allows a theoretical exploration of ground- and excited-state PESs and their crossing seams in an automatic manner. In this Perspective, we summarize our approaches and present examples of their application together with newly determined chemical insights. These include the complex photodissociation mechanism of the formaldehyde molecule, the exclusive excited-state roaming dynamics of the nitrate radical, and all product channels and conformational memory in the photodissociation of the formic acid molecule. Finally, perspectives for the theoretical design of photofunctional molecules are discussed.

Changing enzymatic conformation in organic media with pH buffer lyophilized powder

The conformational memory of enzyme has a significant application in biocatalysis. In this work, pH modification of tannase and the relevant factors were studied. This results indicate that direct addition of pH buffer lyophilized powder in organic media can remarkably change the conformation as did pH tunning, and the conformation variation closely correlates with the balance between hydrophilic solvents and hydrophobic solvents in reaction system. pH tunning of inner tannase and free tannase was performed. The results show that the variation may be affected by its spatial redundancy. It will be potentially applied in biocatalysis in organic media.

Extracting conformational memory from single-molecule kinetic data.

Single-molecule data often come in the form of stochastic time trajectories. A key question is how to extract an underlying kinetic model from the data. A traditional approach is to assume some discrete state model, that is, a model topology, and to assume that transitions between states are Markovian. The transition rates are then selected according to which ones best fit the data. However, in experiments, each apparent state can be a broad ensemble of states or can be hiding multiple interconverting states. Here, we describe a more general approach called the non-Markov memory kernel (NMMK) method. The idea is to begin with a very broad class of non-Markov models and to let the data directly select for the best possible model. To do so, we adapt an image reconstruction approach that is grounded in maximum entropy. The NMMK method is not limited to discrete state models for the data; it yields a unique model given the data, it gives error bars for the model, and it does not assume Markov dynamics. Furthermore, NMMK is less wasteful of data by letting the entire data set determine the model. When the data warrants, the NMMK gives a memory kernel that is Markovian. We highlight, by numerical example, how conformational memory extracted using this method can be translated into useful mechanistic insight.

Tensile Deformation of Polybutene-1 with Stable Form I at Elevated Temperature

Stretching-induced structural changes in polybutene-1 with stable crystalline modification of form I at elevated temperature was investigated by means of the in-situ synchrotron wide-angle X-ray diffraction technique. It was found that oriented metastable form II crystallites with the polymer chain aligned along the stretching direction gradually appear during tensile deformation. Based on the fact that a solid state I to II phase transition cannot take place due to the restriction in chain conformations and lattice dimensions in both phases, the observed occurrence of transition from form I to form II must proceed via a two-step process. First, those form I crystallites with their polymer chain direction tilted with respect to the stretching direction undergo a stress-induced melting process because they experience larger shear stress than the rest. Second, the freed polymer chain segments which have lost their conformational memory in stable form I recrystallize into metastable form II crystallites with their chain direction preferentially aligned along the stretching direction. This result is considered to provide a direct evidence for the stress-induced melting–recrystallization mechanism during tensile deformation of semicrystalline polymers.

Conformational Memory Effect Reverses Chirality of Vortex-Induced Insulin Amyloid Superstructures

Formation of amyloid fibrils is often associated with intriguing far-from-equilibrium phenomena such as conformational memory effects or flow-driven self-assembly. Insulin is a model amyloidogenic polypeptide forming distinct structural variants of fibrils, which self-propagate through seeding. According to infrared absorption, fibrils from bovine insulin ([BI]) and Lys(B31)-Arg(B32) human insulin analogue ([KR]) cross-seed each other and imprint distinct structural features in daughter fibrils. In the absence of preformed [KR] amyloid seeds, bovine insulin agitated at 60 °C converts into chiral amyloid superstructures exhibiting negative extrinsic Cotton effect in bound thioflavin T. However, when agitated bovine insulin is simultaneously cross-seeded with [KR] amyloid, daughter fibrils reveal a positive extrinsic Cotton effect. Our study indicates that dramatic changes in global properties of amyloid superstructures may emerge from subtle conformational-level variations in single fibrils (e.g., alignment and twist of β-strands) that are encoded by memory effects.