Concerted Mode Research Articles

Exploring three-body fragmentation of acetylene trication.

The three-body breakup of [C2H2]3+ formed in collision with Xe9+ moving at 0.5 atomic units of velocity is studied by using recoil ion momentum spectroscopy. Three-body breakup channels leading to (H+, C+, CH+) and (H+, H+, C2 +) fragments are observed in the experiment and their kinetic energy release is measured. The breakup into (H+, C+, CH+) occurs via concerted and sequential modes, whereas the breakup into (H+, H+, C2 +) shows only the concerted mode. By collecting events coming exclusively from the sequential breakup leading to (H+, C+, CH+), we have determined the kinetic energy release for the unimolecular fragmentation of the molecular intermediate, [C2H]2+. By using ab initio calculations, the potential energy surface for the lowest electronic state of [C2H]2+ is generated, which shows the existence of a metastable state with two possible dissociation pathways. A discussion on the agreement between our experimental results and these ab initio calculations is presented.

Zn substituted hydroxide/oxyhydroxide heterostructure activates proton conduction

The recent explorations on high performance aqueous electrode materials have witnessed an intensive interest in proton conduction. Transitional metal layer double hydroxides (LDHs) are considered as one potential candidate due to their rich detachable hydrogen atoms, however, proton conduction in LDH has rarely been reported. Herein, we construct a NiCo-hydroxide/oxyhydroxide heterostructure by Zn substitution. Experimental and theoretical results verify that Zn dopant can accelerate the partial transition of hydroxides to oxyhydroxides with the fixed interlayer distance, which just like locks, effectively restrains the interlayer expansion of neighboring LDH in electrochemical process. As a result, the OH− shuttle between interlayers is prohibited and the proton conduction is activated by a unique concerted mode between O-H bonds and water molecules in interlayer space, achieving a capacity rise of 160% and a superior cyclability with capacity retention of 120% after 37000 cycles at 30 A g−1. This success on proton conduction in LDH affords new insights into rational design and preparation of advanced aqueous electrode materials by activating proton conduction.

Boosting the Energy Density of Aqueous Batteries via Facile Grotthuss Proton Transport.

The recent developments in rechargeable aqueous batteries have witnessed a burgeoning interest in the mechanism of proton transport in the cathode materials. Herein, for the first time, we report the Grotthuss proton transport mechanism in α-MnO2 which features wide [2×2] tunnels. Exemplified by the substitution doping of Ni (≈5 at.%) in α-MnO2 that increases the energy density of the electrode by ≈25 %, we reveal a close link between the tetragonal-orthorhombic (TO) distortion of the lattice and the diffusion kinetics of protons in the tunnels. Experimental and theoretical results verify that Ni dopants can exacerbate the TO distortion during discharge, thereby facilitating the hydrogen bond formation in bulk α-MnO2 . The isolated direct hopping mode of proton transport is switched to a facile concerted mode, which involves the formation and concomitant cleavage of O-H bonds in a proton array, namely via Grotthuss proton transport mechanism. Our study provides important insight towards the understanding of proton transport in MnO2 and can serve as a model for the compositional design of cathode materials for rechargeable aqueous batteries.

Boosting the Energy Density of Aqueous Batteries via Facile Grotthuss Proton Transport

AbstractThe recent developments in rechargeable aqueous batteries have witnessed a burgeoning interest in the mechanism of proton transport in the cathode materials. Herein, for the first time, we report the Grotthuss proton transport mechanism in α‐MnO2 which features wide [2×2] tunnels. Exemplified by the substitution doping of Ni (≈5 at.%) in α‐MnO2 that increases the energy density of the electrode by ≈25 %, we reveal a close link between the tetragonal‐orthorhombic (TO) distortion of the lattice and the diffusion kinetics of protons in the tunnels. Experimental and theoretical results verify that Ni dopants can exacerbate the TO distortion during discharge, thereby facilitating the hydrogen bond formation in bulk α‐MnO2. The isolated direct hopping mode of proton transport is switched to a facile concerted mode, which involves the formation and concomitant cleavage of O−H bonds in a proton array, namely via Grotthuss proton transport mechanism. Our study provides important insight towards the understanding of proton transport in MnO2 and can serve as a model for the compositional design of cathode materials for rechargeable aqueous batteries.

Temperature Dependence of Intramolecular Vibrational Bands in Small Water Clusters.

Cyclic water clusters are pivotal for understanding atmospheric reactions as well as liquid water, yet the temperature (T) dependence of their dynamics and spectroscopy is poorly studied. The development of highly accurate water potentials, such as MB-pol, partly rectifies this. It remains to account for the quantum nuclear effects (NQE), because quantum nuclear dynamics become increasingly inaccurate at low temperatures. From a practical point of view, we find that NQE can be accounted for simply by subtracting a constant from the frequencies obtained from the velocity autocorrelation functions (VACF) of classical nuclear dynamics, resulting in unprecedented agreement with experiment, mostly within 5 cm-1. We have performed classical simulations of (H2O)n clusters (n = 2-5) from 20 K and up to their melting temperature, calculating both all-atom and partial VACF, thus generating the temperature dependence of the vibrational frequencies (IR and Raman bands). Focusing on the hydrogen-bonded (HBed) OH stretch and HOH bend, we find opposing T dependencies. The HBed OH modes blue shift linearly with T, attributed to ring expansion rather than any specific conformational change. The lowest-frequency Raman concerted mode is predicted to show the largest such shift. In contrast, the HOH bend undergoes a red-shift, with the highest frequency concerted band undergoing the largest red-shift. These results can be explained by a coupled-oscillator model for n hydrogen atoms on a ring, constrained to move either tangentially (stretch) or perpendicularly (bend) to the ring. With increasing temperature and weakening of HBs, the intrinsic force constant increases (stretch) or remains constant (bend), while the nearest-neighbor coupling constant decreases, and this results in the interesting behavior revealed herein. T-dependent Raman studies are required for testing some of these predictions.

Development of Freeze-Thaw Tolerant Lactobacillus rhamnosus GG by Adaptive Laboratory Evolution.

The industrial application of microorganisms as starters or probiotics requires their preservation to assure viability and metabolic activity. Freezing is routinely used for this purpose, but the cold damage caused by ice crystal formation may result in severe decrease in microbial activity. In this study, adaptive laboratory evolution (ALE) technique was applied to a lactic acid bacterium to select tolerant strains against freezing and thawing stresses. Lactobacillus rhamnosus GG was subjected to freeze-thaw-growth (FTG) for 150 cycles with four replicates. After 150 cycles, FTG-evolved mutants showed improved fitness (survival rates), faster growth rate, and shortened lag phase than those of the ancestor. Genome sequencing analysis of two evolved mutants showed genetic variants at distant loci in six genes and one intergenic space. Loss-of-function mutations were thought to alter the structure of the microbial cell membrane (one insertion in cls), peptidoglycan (two missense mutations in dacA and murQ), and capsular polysaccharides (one missense mutation in wze), resulting in an increase in cellular fluidity. Consequently, L. rhamnosus GG was successfully evolved into stress-tolerant mutants using FTG-ALE in a concerted mode at distal loci of DNA. This study reports for the first time the functioning of dacA and murQ in freeze-thaw sensitivity of cells and demonstrates that simple treatment of ALE designed appropriately can lead to an intelligent genetic changes at multiple target genes in the host microbial cell.

Three-body dissociation of OCS3+: Separating sequential and concerted pathways.

Events from the sequential and concerted modes of the fragmentation of OCS3+ that result in coincident detection of fragments C+, O+, and S+ have been separated using a newly proposed representation. An ion beam of 1.8 MeV Xe9+ is used to make the triply charged molecular ion, with the fragments being detected by a recoil ion momentum spectrometer. By separating events belonging exclusively to the sequential mode of breakup, the electronic states of the intermediate molecular ion (CO2+ or CS2+) involved are determined, and from the kinetic energy release spectra, it is shown that the low lying excited states of the parent OCS3+ are responsible for this mechanism. An estimate of branching ratios of events coming from sequential versus concerted mode is presented.

COAXIAL DISK SHUNT FOR MEASURING IN THE HEAVY-CURRENT CHAIN OF HIGH-VOLTAGE GENERATOR OF STORM DISCHARGES OF IMPULSES OF CURRENT OF ARTIFICIAL LIGHTNING WITH THE INTEGRAL OF ACTION TO 15•106 J/OHM

Purpose. Description of construction and basic technical descriptions developed and created in Research & Design Institute «Molniya» National Technical University «Kharkiv Polytechnic Institute» high-voltage heavy-current coaxial disk shunt of type of SC-300M2, allowing reliably to measure the peak-temporal parameters (PTP) of impulses of current of artificial lightning in wide peak and temporal ranges with the integral of their action to 15·106 J/Ohm. Methodology. Electrophysics bases of high-voltage impulsive technique, scientific and technical bases of development and creation of high-voltage heavy-current impulsive electrical equipment, including the powerful generators of current of lightning (GCL), and also measuring methods in bit chains powerful high-voltage GCL AVP large impulsive currents of micro- and millisecond temporal ranges. Results. Offered and described new construction of measuring high-voltage heavy-current shunt, containing a measuring round disk from stainless steel easily soiled a 12Х18Н10Т thickness 2 mm and external diameter 80 mm. Experimental a way impulsive active resistance of RS≈0,08 mOhm of the indicated measuring disk and on his basis a calculation coefficient transformation is found of SS of coaxial disk shunt of type of SC-300M2, numeral equal in the concerted mode of operations of his coaxial cable line (CCL) SS≈2/RS≈25·103 A/V. It is rotined that it is expedient to use this value SS for measuring in the heavy-current bit chain of GCL ATP impulsive A- and repeated impulsive D- component of current of artificial lightning, and also ATP of aperiodic impulse of current of artificial lightning of temporal form 10 μc/350 μc. It is set that taking into account application in the end CCL of shunt of a co-ordinate divizor of voltage with two output coaxial sockets 1:1 (for SSA≈25·103 A/V) and 1:2 (SSC≈12,5·103 A/V) at measuring of ATP intermediate B-, protracted C- and shortened protracted C*- component of current of artificial lightning in GCL it is expedient to utillize a numeral value SS for the examined shunt, equal 12,5·103 A/V. Practical approbation and verification of capacity of the improved measuring coaxial disk shunt of type of SC-300M2 is executed in the high-voltage heavy-current bit chain of powerful GCL, forming on the actively-inductive loading of A- and C*- the components of current of artificial lightning with rationed ATP. Originality. Developed and created new high-voltage heavy-current measuring shunt of type of SC-300M2, allowing reliably to register rationed ATP of attenuation sinewave and aperiodic impulses of current of artificial lightning in the bit chains of powerful GCL with amplitude to ±220 кА and integral them action to 13,5·106 J/Ohm. On the measuring coaxial disk shunt of type of SC-300M2 from government metrology service of Ukraine the certificate of accordance of the set form is got. Practical value. Application of the created shunt of type of SC-300M2 in composition the high-voltage heavy-current bit chains of powerful GCL will allow in a certain measure to improve the metrology providing of tests of aviation and space-rocket technique, and also objects of electroenergy on stability to lightning.

Multifunctionality of a Picornavirus Polymerase Domain: Nuclear Localization Signal and Nucleotide Recognition

The N-terminal region of the foot-and-mouth disease virus (FMDV) 3D polymerase contains the sequence MRKTKLAPT (residues 16 to 24) that acts as a nuclear localization signal. A previous study showed that substitutions K18E and K20E diminished the transport to the nucleus of 3D and 3CD and severely impaired virus infectivity. These residues have also been implicated in template binding, as seen in the crystal structures of different 3D-RNA elongation complexes. Here, we report the biochemical and structural characterization of different mutant polymerases harboring substitutions at residues 18 and 20, in particular, K18E, K18A, K20E, K20A, and the double mutant K18A K20A (KAKA). All mutant enzymes exhibit low RNA binding activity, low processivity, and alterations in nucleotide recognition, including increased incorporation of ribavirin monophosphate (RMP) relative to the incorporation of cognate nucleotides compared with the wild-type enzyme. The structural analysis shows an unprecedented flexibility of the 3D mutant polymerases, including both global rearrangements of the closed-hand architecture and local conformational changes at loop β9-α11 (within the polymerase motif B) and at the template-binding channel. Specifically, in 3D bound to RNA, both K18E and K20E induced the opening of new pockets in the template channel where the downstream templating nucleotide at position +2 binds. The comparisons of free and RNA-bound enzymes suggest that the structural rearrangements may occur in a concerted mode to regulate RNA replication, processivity, and fidelity. Thus, the N-terminal region of FMDV 3D that acts as a nuclear localization signal (NLS) and in template binding is also involved in nucleotide recognition and can affect the incorporation of nucleotide analogues. The study documents multifunctionality of a nuclear localization signal (NLS) located at the N-terminal region of the foot-and-mouth disease viral polymerase (3D). Amino acid substitutions at this polymerase region can impair the transport of 3D to the nucleus, reduce 3D binding to RNA, and alter the relative incorporation of standard nucleoside monophosphate versus ribavirin monophosphate. Structural data reveal that the conformational changes in this region, forming part of the template channel entry, would be involved in nucleotide discrimination. The results have implications for the understanding of viral polymerase function and for lethal mutagenesis mechanisms.

Rotation of the Allylselenic Intermediate in Moderating the Stereochemical Course of the Selenium Dioxide-Mediated Allylic Oxidation

Allylic oxidation adjacent to C = C bonds to produce allylic alcohols remains a reaction of considerable interest in organic chemistry and various methods for this purpose have been developed. Among those the selenium dioxide-mediated oxidation is regarded as the most reliable and predictable method to introduce a hydroxy group into the allylic position for substituted alkenes regioand stereo-selectively. The key mechanistic basis to induce a high regioand stereo-selectivity in the allylic oxidation is the concerted and pericyclic process through two consecutive steps (an electrophilic ‘ene’ reaction followed by the [2,3]-sigmatropic rearrangement) (Scheme 1) as in a theoretical mechanism proposed by Sharpless and a recent account concerning theoretical and experimental data. We reported the overall stereochemical pathways by elucidating both an ‘ene’ reaction and the [2,3]-sigmatropic rearrangement of the selenium dioxide-mediated oxidation of 2methyl-2-butene. Those efforts seem successful to explain regioand stereo-selective aspects experimentally observed in the selenium dioxide-mediated allylic oxidation of several trisubstituted olefin compounds, particularly those where the concerted nature can be maintained during the whole process. However, modes of selectivity in the allylic oxidation of substituted olefin compounds are found to depend strongly on the geometric features of the alkene substrates. In the case of the allylic oxidation of more general cyclic systems such as 1-tert-butyl-4-alkylidene cyclohexanes, where the system can avoid the concerted mode throughout two steps, an unexpected isomeric compound, cis-5-tert-butyl-2-ethylidenecyclohexanol was obtained. There should be involved a rotation of the allylselenic intermediate between two pericyclic steps. The purpose of this note is to provide a clearer explanation for the mechanism of the selenium dioxide-mediated oxidation in the substituted alkenes how the rotation of the allylselenic intermediate affects the stereochemical mechanism. The Rotation of the Allylselenic Intermediate in the Allylic Oxidation of 1-tert-Butyl-4-alkylidene Cyclohexanes. In the allylic oxidation of 1-tert-butyl-4-alkylidene cyclohexanes, we observed a different stereo-selectivity mode compared to 2-methyl-2-butene. Two important approaches of selenium dioxide toward the olefin function in the pericyclic ‘ene’ step of the allylic oxidation of 1-tert-butyl-4-ethylidene cyclohexane (1) are trans-anti approach (A) and trans-syn (B) approach (Figure 1). Thus, theoretical calculations show significant products obtained from the allylic oxidation of 1-tertbutyl-4-ethylidene cyclohexane should be ones via two approaches (A and B). The relative transition state energy of as shown in Figure 1, the trans-anti approach (A) is predicted moderately preferred than trans-syn approach (B), The TS energy of A has been calculated to be more stable than B by 0.633 and 0.577 kcal/mol in HF/3-21G and B3LYP/6-31G*, respectively. According to the theoretical study of the reaction using HF/3-21G method, the trans-isomer 2a is predicted as a major product (73%). The trans-isomer can be provided from the initial trans-anti approach (A) in the ‘ene’ step and in situ [2,3]-rearrangement. The allylselenic intermediate generated after trans-anti approach proceeds with a concerted mode, i.e., without C3-C4 bond rotation into a [2,3]-sigmatropic rearrangement. In this case, the position where the ‘anti’ hydrogen (Hanti in Scheme 2) originally located is substituted by the OSeOH group after two concerted steps. The dominant option after trans-syn ‘ene’ approach is to

ChemInform Abstract: The Analysis of Enzymic Free Energy Relationships Using Kinetic and Computational Models

AbstractReview: 191 refs.

The analysis of enzymic free energy relationships using kinetic and computational models

Free energy relationships are a ubiquitous means of characterizing trends in rates of reaction with changing molecular structure. They may be used to quantify the extent of progress along a reaction coordinate at a reaction's transition state or alternatively the extent of similarity between a reaction's transition state and some reference transformation. This critical review outlines correlative procedures for the treatment of experimentally-determined free energy relationships with a particular focus on enzyme-catalyzed group transfers. The reasons for observed non-linearities in free energy relationships are considered. Attention is paid to the influences of changes in kinetic mechanism (e.g. general-acid catalyzed versus uncatalyzed reactions, and the competition between associative, dissociative and concerted modes of group transfer), changes in rate-determining step and the choice of an appropriate reference reaction. The relationship between experimental data and physical/theoretical models of reactivity is discussed (191 references).

Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution

Protein dynamics are essential for protein function, and yet it has been challenging to access the underlying atomic motions in solution on nanosecond-to-microsecond time scales. We present a structural ensemble of ubiquitin, refined against residual dipolar couplings (RDCs), comprising solution dynamics up to microseconds. The ensemble covers the complete structural heterogeneity observed in 46 ubiquitin crystal structures, most of which are complexes with other proteins. Conformational selection, rather than induced-fit motion, thus suffices to explain the molecular recognition dynamics of ubiquitin. Marked correlations are seen between the flexibility of the ensemble and contacts formed in ubiquitin complexes. A large part of the solution dynamics is concentrated in one concerted mode, which accounts for most of ubiquitin's molecular recognition heterogeneity and ensures a low entropic complex formation cost.

Structural and Functional Basis for (S)-Allantoin Formation in the Ureide Pathway

The ureide pathway, which mediates the oxidative degradation of uric acid to (S)-allantoin, represents the late stage of purine catabolism in most organisms. The details of uric acid metabolism remained elusive until the complete pathway involving three enzymes was recently identified and characterized. However, the molecular details of the exclusive production of one enantiomer of allantoin in this pathway are still undefined. Here we report the crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU) decarboxylase, which catalyzes the last reaction of the pathway, in a complex with the product, (S)-allantoin, at 2.5-A resolution. The homodimeric helical protein represents a novel structural motif and reveals that the active site in each monomer contains no cofactors, distinguishing this enzyme mechanistically from other cofactor-dependent decarboxylases. On the basis of structural analysis, along with site-directed mutagenesis, a mechanism for the enzyme is proposed in which a decarboxylation reaction occurs directly, and the invariant histidine residue in the OHCU decarboxylase family plays an essential role in producing (S)-allantoin through a proton transfer from the hydroxyl group at C4 to C5 at the re-face of OHCU. These results provide molecular details that address a longstanding question of how living organisms selectively produce (S)-allantoin.

Crystal Structure of the Translocation ATPase SecA from Thermus thermophilus Reveals a Parallel, Head-to-Head Dimer

The mechanism of pre-protein export through the bacterial cytoplasmic membrane, in which the SecA ATPase plays a crucial role as an “energy supplier”, is poorly understood. In particular, biochemical and structural studies provide contradictory data as to the oligomeric state of SecA when it is integrated into the active trans-membrane translocase. Here, we report the 2.8 Å resolution crystal structure of the Thermus thermophilus SecA protein (TtSecA). Whereas the structure of the TtSecA monomer closely resembles that from other bacteria, the oligomeric state of TtSecA is strikingly distinct. In contrast to the antiparallel (head-to-tail) dimerization reported previously for the other bacterial systems, TtSecA forms parallel (head-to-head) dimers that are reminiscent of open scissors. The dimer interface is abundant in bulky Arg and Lys side-chains from both subunits, which stack on one another to form an unusual “basic zipper” that is highly conserved, as revealed by homology modeling and sequence analysis. The basic zipper is sealed on both ends by two pairs of the salt bridges formed between the basic side-chains from the zipper and two invariant acidic residues. The organization of the dimers, in which the two pre-protein binding domains are located proximal to each other at the tip of the “scissors”, might allow a concerted mode of substrate recognition while the opening/closing of the scissors might facilitate translocation.

Tandem Pseudopericyclic Reactions: [1,5]-X Sigmatropic Shift/6π-Electrocyclic Ring Closure ConvertingN-(2-X-Carbonyl)phenyl Ketenimines into 2-X-Quinolin-4(3H)-ones

N-(2-X-Carbonyl)phenyl ketenimines undergo, under mild thermal conditions, [1,5]-migration of the X group from the carbonyl carbon to the electron-deficient central carbon atom of the ketenimine fragment, followed by a 6pi-electrocyclic ring closure of the resulting ketene to provide 2-X-substituted quinolin-4(3H)-ones in a sequential one-pot manner. The X groups tested are electron-donor groups, such as alkylthio, arylthio, arylseleno, aryloxy, and amino. When involving alkylthio, arylthio, and arylseleno groups, the complete transformation takes place in refluxing toluene, whereas for aryloxy and amino groups the starting ketenimines must be heated at 230 degrees C in a sealed tube in the absence of solvent. The mechanism for the conversion of these ketenimines into quinolin-4(3H)-ones has been studied by ab initio and DFT calculations, using as model compounds N-(2-X-carbonyl)vinyl ketenimines bearing different X groups (X = F, Cl, OH, SH, NH(2), and PH(2)) converting into 4(3H)-pyridones. This computational study afforded two general reaction pathways for the first step of the sequence, the [1,5]-X shift, depending on the nature of X. When X is F, Cl, OH, or SH, the migration occurs in a concerted mode, whereas when X is NH(2) or PH(2), it involves a two-step sequence. The order of migratory aptitudes of the X substituents at the acyl group is predicted to be PH(2) > Cl > SH > NH(2) > F> OH. The second step of the full transformation, the 6pi-electrocyclic ring closure, is calculated to be concerted and with low energy barriers in all the cases. We have included in the calculations an alternative mode of cyclization of the N-(2-X-carbonyl)vinyl ketenimines, the 6pi-electrocyclic ring closure leading to 1,3-oxazines that involves its 1-oxo-5-aza-1,3,5-hexatrienic system. Additionally, the pseudopericyclic topology of the transition states for some of the [1,5]-X migrations (X = F, Cl, OH, SH), for the 6pi-electrocyclization of the ketene intermediates to the 4(3H)-pyridones, and for the 6pi-electrocyclization of the starting ketenimines into 1,3-oxazines could be established on the basis of their geometries, natural bond orbital analyses, and magnetic properties. The calculations predict that the 4(3H)-pyridones are the thermodynamically controlled products and that the 1,3-oxazines should be the kinetically controlled ones.

The order of the ring: assembly of Escherichia coli cell division components

Topological cues appear to override temporal events in the assembly of the Escherichia coli cell division ring. When a procedure that allows the recruitment of ring components based on their topological properties is used, a concerted mode of assembly of several components of the divisome, rather than a strict linear mode, is revealed. Three multimolecular complexes, the proto-ring, the periplasmic connector and the peptidoglycan factory, show some degree of concertation for their assembly. In addition, back-recruitment of all late proteins except FtsN into the division ring occurs even in the absence of proteins incorporated at earlier stages, i.e. FtsA or FtsQ.

Allosteric Modulation of the RNA Polymerase Catalytic Reaction Is an Essential Component of Transcription Control by Rifamycins

Rifamycins, the clinically important antibiotics, target bacterial RNA polymerase (RNAP). A proposed mechanism in which rifamycins sterically block the extension of nascent RNA beyond three nucleotides does not alone explain why certain RNAP mutations confer resistance to some but not other rifamycins. Here we show that unlike rifampicin and rifapentin, and contradictory to the steric model, rifabutin inhibits formation of the first and second phosphodiester bonds. We report 2.5 A resolution structures of rifabutin and rifapentin complexed with the Thermus thermophilus RNAP holoenzyme. The structures reveal functionally important distinct interactions of antibiotics with the initiation sigma factor. Strikingly, both complexes lack the catalytic Mg2+ ion observed in the apo-holoenzyme, whereas an increase in Mg2+ concentration confers resistance to rifamycins. We propose that a rifamycin-induced signal is transmitted over approximately 19 A to the RNAP active site to slow down catalysis. Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal.

Insight into Catalytically Relevant Correlated Motions in Human Purine Nucleoside Phosphorylase

The catalytic site of the homotrimeric enzyme human purine nucleoside phosphorylase enzyme (hPNP) features residue F200 and the 241-265 loop directly skirting the purine base and a residue belonging to the adjacent monomer, F159, immediately conterminous to the ribosyl moiety. Crystallographic B-factors of apo human purine nucleoside phosphorylase, and hPNP complexed with substrate/transition state (TS) analogues, show that residue E250 is the centroid of a highly mobile loop region. Furthermore, superimposition of apo hPNP and hPNP complexed with TS analogue Immucillin-H shows a tightening of the active site, caused by the ligand-dependent 241-265 loop rearrangement taking place upon substrate/inhibitor binding, suggesting a putative dynamic role of the loop in binding/catalysis. However, crystallographic structures reveal only average atomic positions, and more detailed information is needed to discern the dynamic behavior of hPNP. The Essential Dynamics (ED) method is used here to investigate the existence of correlated motions in hPNP and consequently proposes mutagenesis assays to estimate the relative importance of these motions in the phosphorolytic efficiency of the reaction catalyzed by hPNP. We compare the concerted motions obtained from multiple molecular dynamics simulations of apo and Michaelis complex of hPNP both in vacuo and in solution. The results of the principal component analysis for the apo hPNP indicate the existence of strong correlations predominantly in the vicinity of residue F159. However, for the Michaelis complex, concerted motions are seen mostly around both active site residue F200 and loop residue E250. Additionally, for a simulation depicting the relaxation of tight complexed hPNP with a TS analogue, toward its relaxed apo form (after removal of the TS analog), a combination of the apo hPNP and Michaelis complex motions is found, with prominent concerted modes centered around neighboring residues F159, F200, and E250. Finally, we probed the extent to which these concerted motions bear an intrinsic catalytic role by performing experimental site-directed mutagenesis on some residues, followed by kinetic analysis. The F159G and F200G mutants displayed a strong increase in K(M) and modest decrease in k(cat), suggesting that these concerted motions may provide dynamical roles in substrate binding and/or catalysis. However, further structural data for the hPNP mutants are needed to confirm our hypothesis.

Evolutionary turnover of two pBuM satellite DNA subfamilies in the Drosophila buzzatii species cluster ( repleta group): From alpha to alpha/beta arrays

The pBuM satellite DNA family was studied in seven Drosophila species from the buzzatii cluster (within the large Drosophila repleta group). The pBuM repeats are slightly AT-rich and show high levels of intraspecific sequence homogeneity. The pBuM family can be divided into two subfamilies. The pBuM-1 subfamily consists of tandemly arranged repetition units of approximately 190 bp, termed alpha. Alpha repeats were found in a high copy number in the genome of D. buzzatii, D. serido and D. antonietae. The pBuM-2 subfamily consists of tandemly arranged repetition units of 370 bp. Its origin is explained by an insertion of an approximately 180 bp foreign sequence (termed beta) in an alpha basic repeat unit, with subsequent homogenization/amplification events increasing its frequency. Alpha/beta repeats were found in a high copy number in the genome of D. serido, D. antonietae, D. seriema and D. gouveai. pBuM sequences were not detected in D. koepferae and D. borborema by hybridization experiments. The nucleotide analysis of 74 pBuM repeats revealed that apart from the beta insertion event, the evolution of the pBuM family has proceeded in a gradual fashion, mainly through accumulation and horizontal spread of nucleotide substitutions. Moreover, the data also indicate a faster evolutionary rate for the pBuM-2 subfamily than the pBuM-1 subfamily. Members of both subfamilies display a greater intraspecific than interspecific homogeneity, indicating a concerted mode of pBuM evolution. A scenario to explain the evolution of both satDNA subfamilies in the seven Drosophila species from the buzzatii cluster is proposed.