Local Steric Effects Research Articles

Association kinetics and equilibrium in solutions of cross-associating chains that contain inactive spacers

Thermodynamic and kinetic characteristics of chemical reactions in soft matter are affected by volume exclusion caused by an inert component (crowder). In previous molecular dynamics simulations we examined the crowding effect on the association equilibrium in solutions of cross-associating macromolecules that contain, as part of the chains, inactive monomers acting as crowders. Here, we extend our studies to association kinetics. For a number of mixtures where one or both chain species contain inert spacers, a simple mean field approximation describes quite well the composition dependence of the association equilibrium in a wide concentration range. Two main factors determine this dependence: the local distribution of the stickers (the relative excess of one kind of stickers in vicinity of the other) and the local steric effects. The kinetic characteristics of dissociation/association show somewhat similar pattern: the bonded pairs dissociate and recombine slower in solutions with higher content of inactive monomer units. However, the dissociation and recombination dynamics also depends on the reactants’ diffusion and its interplay with effects of chain connectivity and chemical structure. Particularly, when one of the associating components does not carry inert spacers, the recombination accelerates because it makes easier for the sticker from the other chain species to find a new partner for bond formation near its previous partner. These local effects and variations in the subdiffusive behavior of chain molecules are important to take into account for advancing the theory of reversible association in macromolecular systems.

Folded alkane chains and the emergence of the lamellar crystal.

The competition between chain stiffness and chain collapse gives rise to complex low temperature morphologies of single polymer chains, in our case alkanes. These structures are characterized by specific sequences of dihedral angles along the chain, i.e., dihedral angle correlations extending beyond local steric effects. To describe and classify these morphologies, one can transfer concepts from protein science, where this creation of dihedral angle correlations underlies the formation of α-helices and β-sheets. We show here by means of flat-histogram Monte Carlo simulations that, although lacking in primary structure being simple homopolymers, short alkane chains fold into non-trivial ground states (tertiary structure) consisting of chain segments of defined secondary structures. The folded lamellar crystal typical for polyethylene chains requires a minimum chain length to occur as the ground state folded structure, which we identify to be around 150 repeat units.

STERIC HINDRANCE OF CRYSTAL GROWTH: NONLINEAR STEP FLOW IN 1+1 DIMENSIONS.

By linking atomistic and mesoscopic scales, we formally show how a local steric effect can hinder crystal growth and lead to a buildup of adsorbed atoms (adatoms) on a supersaturated, (1+1)-dimensional surface. Starting from a many-adatom master equation of a kinetic restricted solid-on-solid (KRSOS) model with external material deposition, we heuristically extract a coarse-grained, mesoscale description that defines the motion of a line defect (i.e., a step) in terms of statistical averages over KRSOS microstates. Near thermodynamic equilibrium, we use error estimates to show that this mesoscale picture can deviate from the standard Burton-Cabrera-Frank (BCF) step flow model in which the adatom flux at step edges is linear in the adatom supersaturation. This deviation is caused by the accumulation of adatoms near the step, which block one another from being incorporated into the crystal lattice. In the mesoscale picture, this deviation manifests as a significant contribution from many-adatom microstates to the corresponding statistical averages. We carry out kinetic Monte Carlo simulations to numerically demonstrate how certain parameters control the aforementioned deviation. From these results, we discuss empirical corrections to the BCF model that amount to a nonlinear relation for the adatom flux at the step. We also discuss how this work could be used to understand the kinetic interplay between accumulation of adatoms and step motion in recent experiments of ice surfaces.

Modulating the Cellular Immune Response of Oligonucleotides by Brush Polymer-Assisted Compaction.

Unwanted stimulation of the innate immune system by foreign nucleic acids has been one of the major barriers preventing bioactive sequences from reaching market. Foreign nucleic acids can be recognized by multiple pattern recognition receptors (PRRs), which trigger a signaling cascade to activate host defense systems, leading to a range of side effects. This study demonstrates that polyethylene glycol (PEG)-modified DNA strands can greatly reduce the activation of the innate immune system, and the extent of reduction is dependent upon polymer architecture. Highly branched brushes with long PEG side chains achieve the best suppression by blocking PRR interactions via a local steric effect. Interestingly, the brush polymer creates little barrier toward DNA-DNA interaction. Quantification of inflammatory cytokines in both mRNA and protein levels as well as the extent of cellular uptake shows a direct correlation between steric congestion and reduction of cellular immune response. These results suggest that the brush architecture offers unique advantages for PEGylating oligonucleotides in the context of minimizing unwanted immune system activation.

지구온난화에 의한 북서태평양 및 한반도 근해의 해수면 상승

지구온난화로 인한 북서태평양 및 한반도 근해의 미래 해수면 상승을 IPCC AR4 기후 예측모델들의 결과를 이용하여 조사하였다. 본 연구에서는 대부분의 기후모델에서 제시하지 않은 지역적인 열팽창에 의한 해수면 상승을 3차원 수온과 염분 자료를 이용한 역학고도의 계산을 통해 분석하였다. 해수면 자료의 분석결과, 열팽창을 고려한 북서태평양 및 한반도 근해의 해수면 상승률은 전 지구 평균보다 최대 두 배까지 높게 나타났다. 특히, 쿠로시오 확장지역에서 가장 높은 해수면 상승 경향을 보였다. 열팽창을 고려한 A1B 시나리오에 의한 MPI_ECHAM5와 GFDL_CM2.1 모델 결과에서는 향후 100년 동안 북서태평양에서 각각 24 cm와 28 cm 그리고 한반도 근해에서 27 cm와 31 cm의 해수면이 상승하는 것으로 예측되었다. 통계분석 결과, 이러한 해수면 상승은 겨울철 시베리아 고기압의 약화와 북서태평양 해역의 기압장 변화 그리고 이로 인한 바람장 및 해류의 변화로 발생한 수온변화가 그 원인으로 분석된다. 특히, 쿠로시오 확장지역의 북상에 따른 수온 변화가 북서태평양에서 가장 큰 해수면 상승을 유발한 것으로 사료된다. This study investigates sea level (SL) rise due to global warming in the Northwestern Pacific (NWP) and Seas around the Korean peninsula (KP) using outputs of IPCC AR4 climate models. Particularly, components of the SL rise induced by a local steric effect, which was not considered in most climate models, were computed using model-projected 3-dimensional temperature and salinity data. Analysis of the SL data shows that the ratio of the SL rise in the NWP and KP was about two times higher than that in global mean and particularly the ratio in the Kuroshio extension region was the highest. The SL rises over 100 years estimated from MPI_ECHAM5 and GFDL_CM2.1 model by A1B scenario considering the thermosteric effect were 24 cm and 28 cm for the NWP and 27 cm and 31 cm for the Seas around the KP, respectively. Statistical analysis reveals that these SL rises are caused by the weakening of the Siberian High in winter as well as variations of pressure system in the NWP and by the resultant change of water temperature. It also found that the highest SL rise in the Kuroshio extension region of the NWP was connected with the large increase of water temperature in this area.

Selective probing of a NADPH site controlled light‐induced enzymatic catalysis

Achieving molecular recognition of NADPH binding sites is a compelling strategy to control many redox biological processes. The NADPH sites recognize the ubiquitous NADPH cofactor via highly conserved binding interactions, despite differences in the regulation of the hydride transfer in redox active proteins. We recently developed a photoactive NADPH substitute, called nanotrigger NT synchronizing the initiation of enzymatic catalysis of the endothelial NO-synthase (eNOS) with a laser pulse. Spatial and temporal control of enzymatic activity by such a designed light-driven activator would benefit from achieving molecular selectivity, i.e. activation of a single NADPH-mediated enzyme.In this work, we probe the ability of NT to discriminate between two NADPH sites with light. The selected NADPH sites belong to dihydrofolate reductase dihydrofolate reductase enzyme (DHFR) and endothelial NO-synthase (eNOS). Ultrafast kinetics showed that NT could not activate DHFR catalysis with a laser pulse in contrast with the observed trigger of eNOS catalysis leading to NO formation. Homology modelling, molecular dynamics simulations showed that NT discriminated between the two NADPH sites by different donor to acceptor distances and by local steric effects hindering light activation of DHFR catalysis. The data suggested that the narrow NADPH site required a tight fit of the nanotrigger at a suitable distance/angle to the electron acceptor for a specific activation of the catalysis. The ability of the nanotrigger to activate eNOS combined with a low reactivity in unfavourable NADPH sites makes NT a highly promising tool for targeting eNOS in endothelial cells with a laser pulse.

Effects of Inorganic Ions on the Binding of Triflupromazine and Chlorpromazine to Bovine Serum Albumin Studied by Spectrometric Methods

The effects of inorganic salts, NaCl, NaBr, NaI, Na2SO4, KCl, KBr, KI, on the binding constants (Ks) of psychotropic phenothiazine drugs, triflupromazine (TFZ) and chlorpromazine, to bovine serum albumin (BSA) were examined by using second-derivative spectrophotometry. All of the salts examined, with the exception of Na2SO4, decreased the K values significantly, depending on the concentration of the salt, e.g., the decrease in the K values of both drugs were about 40% for 0.1 M NaCl. The results obtained with Na2SO4 indicated that neither Na+ nor SO4(2-) had any affect on the binding of the phenothiazines to BSA. Based on the Na2SO4 results and the finding that the effect of each potassium salt on binding was quite similar to that of the corresponding sodium salt, the effects of these halogen salts can be considered to be derived from their anions, although the phenothiazines are positively charged at pH 7.4. The effectiveness of the anions was determined to occur in the following order: I->>Br->Cl-; these results coincided with the published order of the binding affinity of these anions to albumin. The 19F-NMR spectra of TFZ in the presence of each of these halogen salts revealed a concentration-dependent decrease in the intensity of the signal at 13.8 ppm that had previously been assigned to the TFZ bound to Site II. Consequently, the effects of these anions on the binding of positively charged phenothiazine drugs are thought to be local steric effects caused by the binding of these anions to Site II.

The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding.

Using an all-atom representation, we exhaustively enumerate all sterically allowed conformations for short polyalanyl chains. Only intrachain interactions are considered, including one adjustable parameter, a favorable backbone energy (e.g., a peptide hydrogen bond). The counting is used to reevaluate Flory's isolated-pair hypothesis, the simplifying assumption that each phi,psi pair is sterically independent. This hypothesis is a conceptual linchpin in helix-coil theories and protein folding. Contrary to the hypothesis, we find that systematic local steric effects can extend beyond nearest-chain neighbors and can restrict the size of accessible conformational space significantly. As a result, the entropy price that must be paid to adopt any specific conformation is far less than previously thought.

DNA-damaging effects of genotoxins in mixture: modulation of covalent binding to DNA.

Modulation of DNA adduct formation by pre-existing adducts was examined in synthetic oligonucleotides and genomic DNA (calf thymus); genotoxins studied were N-acetoxy-acetylaminofluorene (N-AcO-AAF), aminofluorene (AF), aflatoxin B1-8,9-epoxide (AFB1-8,9-epoxide), and dimethylsulfate (DMS). Oligodeoxynucleotides containing either guanine-C8-AAF (Gua-C8-AAF) or Gua-C8-AF adducts and a neighboring unadducted guanine (G) (target G), located 1, 2, or 4 nucleotides from the adduct, were reacted, as single- (ss) or double-stranded (ds) substrates, with dimethylsulfate (DMS) or AFB1-8,9-epoxide. A modified Maxam-Gilbert technique showed that the presence of the AAF adduct lowered the extent to which AFB1-8,9-epoxide, but not DMS, reacted with target G. Binding of AFB1-8,9-epoxide to the target G was attenuated (> or =5-fold) when the target was located immediately adjacent to an AAF, but not AF, adduct in ds-DNA. Reaction with AFB1-8,9-epoxide increased when the target G was located 2 or 4 nucleotides from the AAF adduct. Pretreatment of calf thymus DNA with AAF (0-1.8% nucleotides modified) reduced levels of Gua-N7-AFB1 adducts formed after subsequent treatment with AFB1-8,9-epoxide. Pretreatment of calf thymus DNA with AFB1 did not alter levels of adducts formed after subsequent treatment with N-AcO-AAF. The supposition that aflatoxin B1-binding to DNA may be altered by conformational changes in the helix, due to the presence of a pre-existing AAF adduct, is supported by the absence of an effect by AF and confirmation of local denaturation of the oligomer helix by use of chemical probes hydroxylamine and diethylpyrocarbonate. Nonetheless, the importance of changes in the nucleophilicity of neighboring nucleotides and local steric effects cannot be ruled out.

Conformational Heterogeneity about Pipecolic Acid Peptide Bonds: Conformational, Thermodynamic, and Kinetic Aspects

Cis−trans isomerization about pipecolic peptide bonds has been studied using a set of designed tetrapeptides of the sequence acetyl-Gly-X-Pip-Gly-carboxamide (GXPipG), where X = A, F, Y, W, or cyclohexylalanine (Cha). The substitution of a pipecolic residue for a proline leads to (1) a significant increase of the population of the cis conformer, (2) a reduction in the Van’t Hoff enthalpy for isomerism, and (3) acceleration of the rates of isomerization. GAPipG and GChaPipG are unstructured, and isomerization is controlled by local steric effects between the α and e positions of the pipecolic ring and the α position of the preceding residue. The fraction of the cis isomer is the same for these two peptides, indicating that the bulk of the preceding amino acid does not play a significant role in influencing the equilibrium. In the trans form of the aromatic containing peptides, an i to i + 2 aromatic−amide interaction is observed, and in the cis form a stabilizing interaction between the aromatic residue an...

Different positioning of the ligand-binding domain helix 12 and the F domain of the estrogen receptor accounts for functional differences between agonists and antagonists.

The estrogen receptor is capable of binding a diverse set of ligands that are broadly categorized as agonists or antagonists, depending on their abilities to induce or interfere with transcriptional responsiveness. We show, using a fusion protein assay for ligand-binding which does not rely on transcriptional responsiveness, that agonists and antagonists differently position the C-terminus of the ligand-binding domain (helix 12) and the F domain. Upon antagonist binding, the F domain interferes with the fusion protein activity. Mutational disruption of helix 12 alters the position of the F domain, imposing interference after agonist or antagonist binding. Genetically selected inversion mutations where only agonists, but not antagonists, induce interference are similarly reliant on helix 12 and F domain positioning. Our results demonstrate that agonists and antagonists differently position helix 12 and implicate the F domain in mechanisms of antagonist action.

Photoemission studies of mixed valence in Yb 3Si 3, YbSi and Yb 5Si 3: Equivalent versus inequivalent Yb sites

We present angle integrated 4ƒ photoemission from Yb 3Si 5, YbSi and Yb 5Si 3 taken with synchrotron radiation ( hv = 80 eV, hv = 450 eV, and hv at the 4d-4ƒ threshold). The Yb valence is determined and Si2 p shifts are also given. Yb 3Si 5 and YbSi are homogeneous mixed valent in the bulk; in Yb 5Si 3, which has inequivalent Yb sites, one Yb specie is divalent and the other is mixed valent. This shows the connection between mixed valence and local steric effects due to crystal structure. In all compounds the Yb is divalent in the surface region.

The Glyceraldehyde 3-Phosphate Dehydrogenases of Liver and Muscle: COOPERATIVE INTERACTIONS AND CONDITIONS FOR FUNCTIONAL REVERSIBILITY

Abstract A method is described for the isolation of glyceraldehyde 3-phosphate dehydrogenase from rabbit liver. The enzyme has been crystallized as the NAD complex and its chemical and physical properties have been compared with those of the muscle enzyme. The kinetics of the reversible reaction catalyzed by the dehydrogenases is sensitive to temperature and ionic strength and has been examined at 37°, pH 7.4, in a solvent of ionic strength 0.1. Under these conditions the outstanding new feature of the reverse reaction, the reductive dephosphorylation of 3-phosphoglyceroyl phosphate, is the positive cooperativity of the response of both enzymes to concentration increments of the acyl phosphate and the increase in this cooperativity as a function of concentration of the cosubstrate, NADH. At low concentrations of the acyl phosphate, the reduced coenzyme exerts an inhibitory function which is abolished by high concentrations of acyl phosphate or by low concentrations of NAD acting as a heterotropic effector. The same concentrations of NAD which activate at low acyl phosphate concentration inhibit at high concentrations of the 3-carbon substrate by competing with NADH. Activation of the reaction by NAD involves a transition of the acyl phosphate saturation function from a sigmoidal to the hyperbolic form and hence sensitizes the enzyme to lower concentrations of acyl phosphate. The substrate inhibition by NADH and the activation by NAD may be accounted for by the binding of the nucleotides to catalytic sites of the tetrameric protein that are not occupied by the acyl enzyme intermediate. Although the competitive advantage in binding to the apoprotein strongly favors NAD over NADH, the competition under reaction conditions tends to be equalized at nonacylated sites of the acylated protein and is drastically reversed at the acylated sites. Thus at kinetic saturation levels of the acyl phosphate Knadh remains in the 10-µm range, but half-maximal inhibition by NAD occurs at concentrations of the latter that are in excess of 1000 µm. These properties involve both ligandinduced conformational transitions of the protein and a local steric effect of the acyl group that interferes with the binding of the oxidized but not the reduced form of the pyridine nucleotide. In the forward or oxidative phosphorylation reaction the reciprocal kinetic plots are entirely linear except under conditions of product inhibition by NADH. The preferential binding of NADH at an acylated site is not strongly expressed in the inhibition by added NADH because such sites are already occupied by product NADH that is released subsequent to the rate-limiting acyl group transfer from enzyme to orthophosphate ion. The acyl phosphate is a strong inhibitor of the forward reaction, noncompetitive with NAD and strictly competitive with aldehyde. Intracellularly, the enzyme always operates in the presence of high concentrations of NAD which are required to provide the driving force for the energy-conserving reaction. Functional reversibility, under the adverse substrate concentration distributions in the aerobic hepatocyte, is maintained by regulatory effects of NAD binding which promote the reaction of extremely low concentrations of acyl phosphate, and by the differential effects of acylation of the protein which allow access of substrate NADH and at the same time eliminate a prohibitive inhibition by the high concentrations of NAD. The catalytic properties of the liver and muscle enzyme are qualitatively similar but exhibit some quantitative differences that would favor the more diversified metabolic requirements of liver. However, no definitive structural differences have been identified.