Conformational Memory Research Articles

Practice and exploration of conformational memory method in teaching of laboratory animal science

Laboratory animal science has become a main support for the development of life science and has occupied an importance place in higher medical education.The paper analyzed the characteristics and problems of laboratory animal science and proposed the ideas of applying conformational memory teaching in laboratory animal science teaching from there aspects:teaching method,teaching frame and teaching effect.These measures established the foundation for the cultivation of applied talents with comprehensive competence. Key words: Laboratory animal science; Teaching reform; Conformational memory teaching

Automated Exploration of Photolytic Channels of HCOOH: Conformational Memory via Excited-State Roaming.

To elucidate the photodissociation mechanism of HCOOH, we systematically explored reaction pathways starting from the first excited singlet state (S1) by using automated reaction path search methods. All critical points, that is, minima, transition states, minimum energy conical intersections, and minima on seam of crossing, for the S0, T1, and S1 potential energy surfaces (PESs) obtained in the present search were optimized at the CASPT2 level. The structure list obtained by the search explained all experimentally reported photolytic channels. A new mechanism for the previously suggested but unexplained conformational memory in the 193 nm photolysis is proposed, which involves two steps: partial dissociation and succeeding roaming of one of H atoms on the S1 PES, followed by intramolecular recombination on the S0 PES after radiationless transition through a conical intersection at a partially dissociated geometry. This is partially similar to the excited-state roaming recently discovered for the NO3 radical.

Synthesis of enantiomerically enriched (R)-13C-labelled 2-aminoisobutyric acid (Aib) by conformational memory in the alkylation of a derivative of L-alanine

The method of Kouklovsky and coworkers for the enantioselective alkylation of cyclic N-naphthoyl derivatives of amino acids was used to introduce a 13C label into one of the two enantiotopic methyl groups of 2-aminoisobutyric acid (Aib) by retentive alkylation of L-alanine with 13CH3I. Conditions were identified for optimization of yield and enantiomeric purity, and the absolute configuration of the labelled product was established.

An auto-catalytic surface for conformational replication of amyloid fibrils--genesis of an amyloid world?

Amyloid fibrils are composed of self assembled stacked peptide or protein molecules folded and trapped in a stable cross-beta-sheet conformation. The amyloid fibrillation mechanism represents an intriguing self-catalyzed process rendering replication of a molecular conformational memory of interest for prebiotic chemistry. Herein we describe how a solid surface can be rendered auto-catalytic for fibrillation of a protein solution. We have discovered that a hydrophobic silicon or glass surface can be made to continuously fibrillate solutions of insulin monomers under stressed conditions (pH 1.6, 65°C). It was found that the surface acts as a platform for the formation of nascent seeds that induce fibril replication on and at the surface. This autocatalytic effect stems from a layer a few insulin molecules thick representing an oligomeric layer of misfolded, conformationally trapped, insulin molecules that rapidly through epitaxial growth catalyze the rate determining step (nucleation) during fibril replication. This autocatalytic layer is generated by the protein-solid surface interaction and conformational changes of the adsorbed protein during exposure at the air-water interface. The resulting autocatalytic surface thus both initiates local conformational molecular self-replication and acts as a reservoir for fibril seeds budding off into solution spreading fibril replication entities to the surrounding medium. The possibility of catalysis of the conformational replication process by minute amounts of nucleation sites located on a recruiting surface can evade the issue of dramatic concentration dependence of amyloidogenesis.

The Role of Conformations in the Interplay of Structure and Dynamics in Macromolecular and Supramolecular Systems

AbstractSummary: Following Paul J. Flory, the role of local chain conformation in determining the structure and dynamics of macromolecules is elucidated, employing advanced solid state NMR spectroscopy supported by X‐ray scattering and dielectric spectroscopy. Topics covered include the local conformation in amorphous polymers, conformational memory, chain organization and dynamics in semicrystalline polymers, polypeptides, and rod‐coil copolymers.

Conformational Changes of CaMKII: A Model of Activation

The ubiquitously expressed calcium/calmodulin dependent protein kinase II (CaMKII) functions as a transducer of calcium (Ca2+) signaling by responding to the amplitude, duration, and frequency of Ca2+ transients. Autophosphorylation at Thr286 following binding of calcium-calmodulin (Ca2+/CaM) leads to a Ca2+-independent activity referred to as a conformational memory of prior activation. While CaM binding, autophosphorylation, and catalytic-regulatory domain autoinhibition have been linked to CaMKII function, the underlying structural and dynamic framework of activation and conformational memory is poorly understood. Here we utilize site-directed spin labeling and electron paramagnetic resonance (SDSL-EPR) to explore the conformational changes associated with CaMKII activation and conformational memory. The structure of the regulatory domain was investigated via spin label mobility under several conditions representing various intermediates of activation. Inter-domain movements were also examined through distance measurements between regulatory and catalytic domains. We found that CaMKII activation is associated with regulatory-catalytic domain disengagement, causing a disruption of autoinhibition and producing significant conformational changes which are propagated throughout the regulatory domain. Here we detail a mechanistic description of activation and are currently using EPR data to computationally model conformational changes associated with CaMKII activation.

Structural dynamics of CaMKII activation

The ubiquitously expressed calcium/calmodulin dependent protein kinase II (CaMKII) functions as a transducer of calcium (Ca2+) signaling by responding to the amplitude, duration, and frequency of Ca2+ transients. During periods of elevated Ca2+, CaMKII is activated by calcium-calmodulin (Ca2+/CaM) binding. A subsequent autophosphorylation at Thr286 allows for Ca2+-independent activity and endows this enzyme with a conformational memory of prior activation. CaMKII activity is regulated by a myriad of factors including CaM binding, autophosphorylation, and catalytic-regulatory domain interactions referred to as autoinhibition. While these variables have been linked to CaMKII function, the underlying structural and dynamic framework of activation and conformational memory is poorly understood. Here we utilize site-directed spin labeling and electron paramagnetic resonance (SDSL-EPR) to explore the conformational changes associated with CaMKII activation and conformational memory. EPR parameters were collected for the regulatory domain where CaM binding and autophosphorylation sites are located. Our results indicate the regulatory domain undergoes significant structural changes between several discrete conformations dependent on autophosphorylation and CaM binding. The CaM binding region is flexible in the apo state but has an induced rigidity in the presence of Ca2+/CaM indicative of a binding event. Investigation of the regulatory domain outside the CaM binding region revealed an increase in protein backbone dynamics with a Thr286Glu autophosphorylation mimic and/or in the presence of Ca2+/CaM. This data provides a structural and dynamic perspective consistent with the current biochemical activation model where CaM binding disrupts autoinhibition by disengaging regulatory and catalytic domains. We predict the enhanced flexibility facilitates Ca2+/CaM binding and may play a role in Ca2+ independent activity. The adjacent regulatory loop showed similar flexibility suggesting this region functions as a hinge between regulatory and catalytic domains allowing for release and reinstatement of autoinhibition.

Preliminary experience of cerecyte coils in the treatment of intracranial aneurysms.

Coil embolization of intracranial aneurysms is the first choice treatment in many centres worldwide. The ISAT study reported in favour of endovascular treatment even though coil embolization carries a higher risk of revascularization than surgical clipping. Bioactive coils boosting fibrosis within the aneurysm and neointimal production could counteract the tendency of embolized aneurysms to re-open. We reviewed our cohort in a retrospective study based on the following inclusion criteria: 1) Cerecyte coils (Micrus Endovascular, San Jose, Calif) were the only bioactive coils deployed. 2) Cerecyte coils were used in the first embolization procedure. Between July 2005 and December 2007 39 patients matched these inclusion criteria, 15 men and 24 women (average age 63.5 years) with 44 aneurysms. Treatment outcomes were: 30 aneurysms completed excluded from the circulation, 13 aneurysms almost completed excluded from the circulation, one incomplete aneurysm occlusion. Two aneurysms out of 44 recurred during follow-up (4.54%) and were re-embolized. The radio-opacity and conformational memory of the Cerecyte coils were satisfactory and they were easy to manoeuvre and detach.

Thermosensitive and Salt-Sensitive Molecularly Imprinted Hydrogel for Bovine Serum Albumin

A novel stimuli-responsive protein imprinted polymer for selective recognition of bovine serum albumin is presented. N-[3-(Dimethylamino)propyl]-methacrylamide, which is positively charged in neutral solution and is able to self-assemble onto the template protein through electrostatic interaction, was chosen as the functional monomer. Polymerization was carried out in the presence of N-isopropylacrylamide as an assistant monomer, which resulted in a stimuli-responsive protein imprinted polymer. The template proteins were easily removed by treatment with 500 mmol L(-1) NaCl solution. The influences of the external stimuli, such as temperature and ionic strength, on the polymer affinity were investigated, and a clear conformational memory was observed. The association constant ( Ka) and binding capacity ( Qmax) for the specific interaction between the protein imprinted polymer and the template protein were determined by Scatchard plots and found to be 9.6 x 10(4) L mol(-1) and 4.7 micromol g(-1), respectively. Several proteins different in molecular weight and isoelectric point were employed as reference, and it was shown that the charge effect and the shape memory effect were the major factors affecting the imprint formation and template recognition. Finally, this imprinted polymer was used to purify the bovine serum albumin from the protein mixture and real sample, which demonstrated its high selectivity.

Conformation preserved in a weak-to-strong or strong-to-weak [ PSI +] conversion during transmission to Sup35 prion variants

The cytoplasmic [ PSI + ] element of budding yeast represents the prion conformation of translation release factor Sup35. Much interest lies in understanding how prions are able to generate variation in isogenic strains. Recent observations suggest that a single prion domain, PrD, is able to adopt several conformations that account for prion strains. We report novel PrD variants of Sup35 that convert weak [ PSI +] to strong [ PSI +], and vice versa, upon transmission from wild-type Sup35. During the transmission from wild-type Sup35 to variant Sup35s, no conformational changes were detected by proteolytic fingerprinting and the original [ PSI + ] strain was remembered upon return to wild-type Sup35. These findings suggest that during transmission to variant Sup35s, the [ PSI + ] phenotype is variable while the original conformation is remembered. A mechanism of “conformational memory” to remember specific [ PSI + ] conformations during transmission is proposed.

Seeding-dependent Propagation and Maturation of Amyloid Fibril Conformation

Recent studies of amyloid fibrils have focused on the presence of multiple amyloid forms even with one protein and their propagation by seeding, leading to conformational memory. To establish the structural basis of these critical features of amyloid fibrils, we used the amyloidogenic fragment Ser20-Lys41 (K3) of beta2-microglobulin, a protein responsible for dialysis-related amyloidosis. In 20% (v/v) 2,2,2-trifluoroethanol and 10 mM HCl (pH approximately 2), K3 peptide formed two types of amyloid-like fibrils, f218 and f210, differing in the amount of beta-sheet as measured by circular dichroism spectroscopy and Fourier transform infrared spectroscopy. Atomic force microscopy showed that the fibril with a larger amount of beta-sheet (f210) is thinner and longer. Both fibrils were reproduced by seeding, showing the template-dependent propagation of a fibril's conformation. However, upon repeated self-seeding, f218 fibrils were gradually transformed into f210 fibrils, revealing the conformational maturation. The observed maturation can be explained fully by a competitive propagation of two fibrils. The maturation of amyloid fibrils might play a role during the development of amyloidosis.

On the Conformational Memory in the Photodissociation of Formic Acid

The photodissociation of formic acid at 248 and 193 nm was investigated by classical trajectory and RRKM calculations using an interpolated potential energy surface, iteratively constructed using the B3LYP/aug-cc-pVDZ level of calculation. Several sampling schemes in the ground electronic state were employed to explore the possibility of conformational memory in formic acid. The CO/CO2 branching ratios obtained from trajectories initiated at the cis and at the trans conformers are almost identical to each other and in very good accordance with the RRKM results. In addition, when a specific initial excitation that simulates more rigorously the internal conversion process is used, the calculated branching ratio does not vary with respect to those obtained from cis and trans initializations. This result is at odds with the idea of conformational memory in the ground state proposed recently for the interpretation of the experimental results. It was also found that the calculated CO vibrational distributions after dissociation of the parent molecule at 248 nm are in agreement with the experimental available data.

13C solid state NMR investigation of structural relaxation of the polymer backbone in poly (ethylmethacrylate)

Geometry and time scale of structural relaxation of poly( n-alkylmethacrylates) above the glass transition is studied by temperature dependent one- and two-dimensional 13C-NMR spectroscopy. The geometry of the isotropization of the polymer backbone as deduced from detailed analysis of spectral line shapes is identified as random angular jumps. Analysis of echo decays confirms that at a given temperature this isotropization can adequately be described with a single correlation time. The results are discussed in terms of conformational memory and local structure recently identified in these polymeric glasses.

Memory of chirality in the transannular cyclization of cyclodecenyl radicals.

The transannular cyclization of an enantioenriched cyclodecenyl radical proceeds in a 5-exo fashion to produce scalemic bicyclo[5.3.0]decanes. This cyclization is notable because it demonstrates chirality transfer through conformational memory of an unstabilized secondary radical. [reaction: see text]

Hydrogels as adsorbents of organosulphur compounds currently found in diesel

Hydrogels of chitosan were synthesised using glutaric dialdehyde as the crosslinking agent in an acetonitrile/water solution (1:4, v/v). These hydrogels recognised and adsorbed the dibenzothiophene sulfone (DBTS) against other related compounds found in diesel, e.g. dibenzothiophene (DBT), fluorene (FLE) and 4,6-dimethyl DBT (DMDBT). In order to improve the recognition and adsorption of DBTS, the latter compound served as a template for the building of recognition sites inside the hydrogel matrix through the use of the molecular imprinting technique (MIT). Despite the adsorption capacity of the molecular imprinted hydrogel (MIH) was not increased, the imprinting process of chitosan allowed both an enhancement of two orders of magnitude in ligand affinity constant and material homogeneity as seen by SEM. The change in swelling degree ( Q) suggested the presence of a conformational memory of the hydrogel that might allow the design of stimuli-response but also tailored-made hydrogels responding at a required factor as temperature. The imprinting process improved ligand recognition and consequently hydrogel’s specificity as shown by a monolayer adsorption. In contrast, the adsorption isotherm of DBTS by the non-imprinted hydrogel showed a multilayer adsorption due to non-specific interactions.

A CASSCF/MR-CI study toward the understanding of wavelength-dependent and geometrically memorized photodissociation of formic acid.

The S(0), T(1), and S(1) potential energy surfaces for the HCOOH dissociation and isomerization processes have been mapped with different ab initio methods. The wavelength-dependent mechanism for the HCOOH dissociation was elucidated through the computed potential energy surfaces and the surface crossing points. The HCOOH molecules in S(1) by excitation at 248 nm mainly decay to the ground state via the S(0) and S(1) vibronic interaction, followed by molecular eliminations in the ground state. The S(1) direct dissociation to HCO((2)A') + OH((2)Pi) is the dominant pathway upon photoexcitation at 240-210 nm. Meanwhile, there is a slight probability that the system relaxes to the ground state via the S(0) and S(1) vibronic interaction at these wavelengths. After irradiation of HCOOH at 193 nm, the S(1) direct dissociation into HCO((2)A') + OH((2)Pi) is energetically the most favorable pathway. In view of high IC efficiency at the S(0)/S(1) conical crossing, the S(1) --> S(0) internal conversion via the S(0)/S(1) point can occur with considerable efficiency. In addition, the S(1) isomerization probably plays a dominant role in the partially conformational memory of the HCOOH photodissociation, which has been discussed in detail.

Structural relaxation of polymers at the glass transition: conformational memory in poly(n-alkylmethacrylates).

Conformational memory is introduced as a new aspect of structural relaxation of polymers. In poly(n-alkylmethacrylates) extended backbone chain conformations are identified by advanced NMR techniques as the molecular units involved in structural relaxation. They retain conformational memory over many steps of restricted axial chain motion. Randomization of conformation and isotropization of backbone orientation occur on the same time scale, yet much slower than the slowest relaxation process identified so far. Behavior typical of fragile glass formers is found for this new process of chain relaxation.

Direct Determination of Kinetic Rates from Single-Molecule Photon Arrival Trajectories Using Hidden Markov Models.

The measurement of fluorescence from single protein molecules has become an important new tool in the study of dynamic processes, allowing for the direct visualization of the motions experienced by individual proteins and macromolecular complexes. The data from such single-molecule experiments are in the form of photon trajectories, consisting of arrival times and wavelength information on individual photons. The analysis of photon trajectories can be difficult, particularly if the motions are occurring at rates comparable to the photon arrival rate or in the presence of noise. In this paper, we introduce the use of hidden Markov models (HMMs) for the analysis of photon trajectory data that operate using the photon data directly, without the need for ensemble averaging of the data as implied by correlation function analysis. Using a simple kinetic model, we examine the relationship between the uncertainty in the estimates of the motional rate and the photon detection rate. Remarkably, we obtain relative uncertainties in the rate constants of as little as 3% even when the interconversion rate is equal to the photon detection rate, and the uncertainty increases to only 10% when the interconversion rate is 10 times the photon detection rate. This suggests that useful information can be obtained for much faster kinetic regimes than have typically been studied. We also examine the impact of background photons on the determination of the rate and demonstrate that the HMM-based approach is robust, displaying small uncertainties for background photon arrival rates approaching that of the signal. These results not only are relevant in establishing the theoretical limits on precision, but are also useful in the context of experimental design. Finally, to demonstrate how the methodology can be extended to more complex kinetic models and how it can allow one to make use of the full power of statistics for purposes of model evaluation and selection, we consider a four-state kinetic model for protein conformational transitions previously studied by Schenter et al. (J. Phys. Chem. A1999, 103, 10477). We show how an HMM can be used as an alternative to higher-order correlation function analysis for the detection of "conformational memory" and apparent non-Markovian dynamics arising from such temporally inhomogeneous kinetic schemes.

Reversible Molecular Memory and pH-Switchable Swelling Transitions in Polyelectrolyte Multilayers

The systematic design of materials that alter their macroscopic properties in response to environmental stimuli continues to provide a basis for stimuli-responsive applications in biomaterials and microelectronics. We report discrete volume phase transitions in ultrathin polyelectrolyte multilayers (PEMs) driven by changes in environmental pH of the post-assembled film. These films exhibit a history-dependent swelling behavior and molecular conformational memory. We illustrate that the same two polymerspoly(allylamine hydrochloride)/poly(styrenesulfonic acid) (PAH/SPS)can be incorporated into a multilayer film with specifically designed molecular architectures (by virtue of assembly pH conditions) that enable them to be either virtually insensitive or highly responsive to small changes in post-assembly pH. We thus provide a general design strategy for PEMs that exhibit multiple conformational states and related phenomena. We further demonstrate the ability to spatially regulate the affinity of molecular s...

Conformational memory in photodissociation of formic acid.

The trans and cis forms of formic acid (HCOOH) in solid argon favor essentially different photodissociation (193 nm) products, H2O + CO and H2 + CO2, respectively. The branching ratio of these channels differs between the two conformers by a factor of >10. The observed selective photodissociation features conformational memory when the transition state of a molecule is reached before torsional randomization. These data demonstrate that the photodissociation products can be efficiently steered with selective narrow-band infrared radiation promoting rotational isomerism, which makes a strong case of optically controlled chemical reactions