A suggested chain process for radiation damage

It has been suggested that when an organism is exposed to ionizing radiation the initial damage results from the occurrence of ionization in a so-called sensitive volume due to absorption of radiation quanta. The initial radiation damage is then transmitted or amplified to a level of macroscopic perception. In this paper a mechanism by which this transmission may take place and a finite Markov chain model applicable to this transmission are postulated and discussed. This mechanism is assumed to be the depolymerization of essential chain molecules which are connected to some “central group” associated with the seensitive volume. The depolymerization of the macromolecules following a hit in the sensitive volume is postulated to be determined by a chain mechanism, which acts in a manner inverse to the mechanism controlling the polymerization process. A mathematical study of this problem is made using the theory of Markov chains. The probability of complete degradation of the chain macromolecule, and the probability of recombination of the units to give the intact chain were determined, assuming that the probabilty of successive steps in the degradation increase linearly from the intact state to that of complete breakdown.     

Local dynamics in biological macromolecules

The diffusive approach in the optimized Rouse-Zimm approximation to segment relaxation in the nanosecond time domain (ORZLD) is extended to consider chains of nonequivalent units as occurring in biological macromolecules. The correlation times for second-order time correlation functions of each virtual bond on the chain are calculated for some homopolypeptides, and random and regular copolypeptides. The expected correlation times for biological macromolecules organized in multiple domains are discussed via a simple model of the ORZLD hierarchy. Dynamic bond correlation times are compared with static local persistence lengths.     

Translocation of Rodlike Polymers through Membrane Channels

A theory of channel-facilitated transport of long rodlike macromolecules through thin membranes under the influence of a driving force of arbitrary strength is developed. Analytic expressions are derived for the translocation probability and the Laplace transform of the probability density of time that a macromolecule spends in the channel. We also derive expressions for the (conditional) probability densities of time spent in the channel by translocating and nontranslocating (returning back) macromolecules. These results are used to study how the distribution of the macromolecule lifetime in the channel depends on a polymer chain length and the driving force. It is shown that depending on the values of the parameters, the lifetime probability density may have one or two peaks. Our theory is a generalization of the theory developed by Lubensky and Nelson, who were inspired by recent experiments on driven translocation of single-stranded RNA and DNA molecules through single channels in narrow membranes.     

Enzymatic generation of binary block‐copolymeric structures: Mathematical analysis based on triad frequencies evaluated by NMR

A mathematical model is derived for describing a multiple‐attack pathway for enzymatic generation of block structure in binary linear copolymers having initially a randomized sequential structure. The model is based on sequential information in terms of copolymer monads, diads, and triads estimated by nmr spectroscopy, and is applicable to enzymes attacking next to a reacted unit in the polymer chains. Then the block distribution of unreacted units remains constant and explicit relationships are provided. The probability of triad frequencies as a function of monads, i.e., progress curve of enzyme copolymer sequential structure, allows us to characterize the enzymatic mode of attack independently of enzyme kinetics. The produced fractions of heterogeneous triads centered by reacted units are shown to be affected, to a large extent, by the degree of multiple attack (d) entering into the formula as a variable parameter. The single‐chain, d = ∞, and multiple‐chain mechanisms, d =1, representing the two extremes of the treated mechanism, are very clearly discriminated. © 1999 John Wiley & Sons, Inc. Biopoly 50: 221–226, 1999     

BCL::SAXS: GPU accelerated Debye method for computation of small angle X‐ray scattering profiles

Small angle X‐ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS—an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of hen egg white lysozyme. Using this protein we show how to generate SAXS profiles representing: (1) complete models, (2) models with approximated side chain coordinates, and (3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non‐redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAχS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native. Proteins 2015; 83:1500–1512. © 2015 Wiley Periodicals, Inc.     

Match probability calculations for multi-locus DNA profiles

The paper considers aspects of the match probability calculation for multi-locus DNA profiles and a related calculation which aims to assess the probability that a pair of profiles is concordant for the presence and absence of bands. It is suggested that levels of allelism and linkage for multi-locus profiles may be higher than reported in previous studies, and that comparison of bandsharing values between different studies is problematic. Our view is that the independence assumptions which underpin the calculations have not been established. The effect of ignoring (local) heterogeneities in band frequencies may be non-conservative. Concerns thus raised about the match probability calculation could be important in practical casework. The speculative nature of some aspects of the concordance probability calculation would seem to render it inappropriate for use in court.Editor's commentsThe author continues the investigation of multilocus probes begun introduced by Curnow in this volume. He contrasts bandsharing estimates from Jeffreyset al. (1991) and the UK Forensic Science Service. Much of the difference is attributable to the greater resolving power of Jeffreys' gels (J.S. Buckleton, personal communication). Tests for independence of multilocus probe bands, and studies of the joint possession of subsets of bands within populations, were conducted by the UK Forensic Science Service, but not published (J.S. Buckleton, personal communication). In spite of the complexities of multilocus probe profiles, it is interesting to note that, just as when several single-locus probes are used, the same profiles are not found for unrelated people in large populations.     

Probing binding mechanism of interleukin-6 and olokizumab: in silico design of potential lead antibodies for autoimmune and inflammatory diseases

Computer-aided antibody engineering has been successful in the design of new biologics for disease diagnosis and therapeutic interventions. Interleukin-6 (IL-6), a well-recognized drug target for various autoimmune and inflammatory diseases such as rheumatoid arthritis, multiple sclerosis, and psoriasis, was investigated in silico to design potential lead antibodies. Here, crystal structure of IL-6 along with monoclonal antibody olokizumab was explored to predict antigen–antibody (Ag???Ab)-interacting residues using DiscoTope, Paratome, and PyMOL. Tyr56, Tyr103 in heavy chain and Gly30, Ile31 in light chain of olokizumab were mutated with residues Ser, Thr, Tyr, Trp, and Phe. A set of 899 mutant macromolecules were designed, and binding affinity of these macromolecules to IL-6 was evaluated through Ag???Ab docking (ZDOCK, ClusPro, and Rosetta server), binding free-energy calculations using Molecular Mechanics/Poisson Boltzman Surface Area (MM/PBSA) method, and interaction energy estimation. In comparison to olokizumab, eight newly designed theoretical antibodies demonstrated better result in all assessments. Therefore, these newly designed macromolecules were proposed as potential lead antibodies to serve as a therapeutics option for IL-6-mediated diseases.     

Role of lipids in the structure and function of biological membranes

The concept of biological membranes as vesicular or tubular continua built up of nesting repeating units has been systematically explored and some of the relevant experimental work has been assembled. The bulk of the data have been drawn from studies on the mitochondrion, which is assumed to be a model for membranes generally. The repeating units of membranes are composite macromolecules containing both protein and lipid. The unit of the mitochondrial inner membrane is tripartite; the basepiece is the membrane-forming element. The four complexes of the electron transfer chain represent the different species of basepieces in the inner membrane. The repeating units of the outer mitochondrial membrane have a different form and size and a completely different set of enzymes (the enzymes of the citric and fatty acid oxidation cycles). The repeating units of the inner mitochondrial membrane are capable of forming membranes spontaneously. This membrane-forming capability is absolutely dependent on the presence of lipid. Evidence is presented for the view that lipid restricts the number of binding modalities and thus compels a two-dimensional alignment of repeating units. In absence of lipid three-dimensional stacking takes place, and the aggregates thus formed are, in effect, bulk phases. The membrane may be looked upon as a device for molecularizing repeating units, and it is this molecularization which underlies the essentiality of lipid for electron transfer. The theory of lipid requirement for enzymic activity is developed. The reconstitution of the electron transfer chain is shown to be essentially a membrane phenomenon rather than an expression of direct chemical interaction between the different parts of the electron transfer chain.     

Monte Carlo simulation of photoselective cyclization of azobenzene-containing oligosarcosines

Conformations of (Sar)_n? Azo? (Sar)_n oligomers [Sar = sarcosine (N-methylglycine) unit. Azo = p-aminoazobenzene unit] were computer-simulated for trans and cis states of the azobenzene group. Each part of the oligosarcosine chain was assumed to behave independently and the ring-closure probability, i.e., the probability that the end-to-end distance of the above oligomer is shorter than 4 Å, was evaluated from an overlap integral of the two three-dimensional distribution functions for the left and right halves of the oligosarcosine chain. The ring-closure probability for the cis azobenzene unit was larger than that for trans, indicating the preference of cyclization reaction to the corresponding intermolecular reactions. The prediction agrees qualitatively with the experimental observation reported by us in our companion paper, but the calculated ring-closure probability for the cis state was substantially larger than the experimental value. The difference was explained as a result of intramolecular overlappings of the two halves of the oligosarcosine chain, which is facilitated when the azobenzene group is in the cis state.     

Electrophoretic Plugging of Nuclear Pores by Using the Nuclear Hourglass Technique

The nuclear hourglass technique (NHT) was recently introduced as a novel technique that measures the electrical nuclear envelope (NE) conductance of isolated Xenopus laevis oocyte nuclei. The main conclusion drawn from NHT work so far is that nuclear pore complexes (NPCs) of oocytes are in an electrically open state under physiological conditions, with a mean conductance of 1.7 nS per NPC. Since nuclear patch-clamp data indicate that usually NPCs are electrically closed, our work has been challenged by the notion that NHT cannot assure a high resistance seal (``gigaseal') between glass wall and NE like that required for patch-clamp experiments. Thus, NHT could have dramatically underestimated NE electrical resistance. Here we demonstrate that NHT does not require a gigaseal for accurate NE conductance measurements. In addition, we present experimental conditions where mean single NPC electrical conductance is reduced 26-fold due to electrophoretic plugging by negatively charged nucleoplasmic macromolecules. In addition, data indicate that under physiological conditions (i.e., when macromolecules are offered in the cytosolic solution) the nuclear surface is heavily folded, underestimating ``true' NE surface by a factor of 2.6. When ``true' NE surface area is taken into consideration, modified values of mean single NPC conductances of 654 pS for electrically open conditions and 25 pS for electrically plugged conditions can be calculated. We conclude that the large overall NE conductance detected with the nuclear hourglass technique in intact Xenopus laevis oocyte nuclei can be explained by the sum of single NPC conductances in the pS range, as long as open probability is high. This confirms previous patch-clamp work concerning single NPC conductance, but disagrees with the view that mean open probability of NPC channels is usually low. Received: 27 March 2001/Revised: 3 July 2001     

Adsorption of the polypeptides on a solid surface. III. Behavior of stiff chains in a pore

A strict analytical theory has been developed describing the behavior of a model lattice polymer chain of arbitrary stiffness in a slitlike pore at polymer–adsorbent interaction energies –ε. The thermodynamic characteristics of the system were calculated. It was shown that the transition of the macromolecule from the solution volume inside a pore occurs by the first-order phase transition with evolution of latent heat of adsorption. The transition point –ε = –ε_c is determined by the chain stiffness and is independent of the pore width D. It is shown that in the precritical range, –ε < –ε_c, the free energy ΔF of the macromolecules in the pores is adequately described by the universal dependence ΔF = ΔF(D*/A), where D* is some effective pore width depending on the value of –ε, and A is the length of the Kuhn segment. At high attraction energies, –ε ? –ε_c, the macromolecules are bonded to the pore walls by a great number of units and their free energy depends only on –ε and the chain stiffness, ΔF = ΔF(A, ε). Close to the critical energy –ε ? –ε_c (transition range), ΔF is determined by both the stiffness of the macromolecule and the pore width D: ΔF ～ A²D^?1 for fairly high values of A and D. The possibilities of using porous media as protein stabilizers are discussed, and the value of the stabilizing effect depending on the chain stiffness is estimated.     

Protein design as a challenge for peptide chemists

All efforts to turn the ultimate goal in protein de novo design into reality–the construction of new macromolecules with predetermined three-dimensional structure and well-defined functionality–failed because the mechanism of folding has still to be unravelled. In the present review, various attempts to apply synthetic tools for inducing native-like structural features in peptides in order to bypass the folding problem are described. Besides well-established methods for the nucleation and stabilization of secondary structures, e.g. α-helices, β-sheets and β-turns, topological templates as ‘built-in’ folding devices have more recently become the key elements for the induction of protein-like folding units (template-assembled synthetic proteins, TASP). Progress in the synthetic strategy and structural characterization of this new type of macromolecules opens the way for the design of functional TASP molecules.     

Simultaneous Analysis of Six Microsatellite Markers in Atlantic Cod (<Emphasis Type="Italic">Gadus morhua</Emphasis>): A Novel Multiplex Assay System for Use in Selective Breeding Studies

A novel hexaplex assay system including Gmo8, Gmo19, Gmo35, Gmo37, Tch11, and Tch12 microsatellites from Atlantic cod, consisting of trinucleotide or tetranucleotide repeat units, is introduced. All 6 loci were coamplified in a single reaction employing dye-labeled primers. Alleles from these loci were sized using an internal standard by automated sample processing in an ABI 310 Genetic Analyser. Amplified alleles in profiles containing selected microsatellites were typed clearly, providing easily interpretable results. Sequencing data indicated that alleles at all loci consisted of simple repeat units. This may help minimize the likelihood of stuttering upon polymerase chain reaction amplification. The results suggest that the presented hexaplex assay system may be a useful tool in a selective breeding program in which genetic identification will allow different genotypes to be reared together from fertilization. This should have a great impact as it will make selective breeding more efficient.     

Modeling of α(1–4) chain arrangements in α(1–4)(1–6) glucans: The action and outcome of β-amylase and Pseudomonas stutzeri amylase on an α(1–4)(1–6) glucan model

Simulated enzymic debranching of a β-limit dextrin model, prepared from a computed construct made by random extension and branching, and given the CCL value of w-maize amylopectin (and equal amounts of external chains with ECL values of 2 and 3) has been related to experimental chromatograms of the debranched β-limit dextrin of the amylopectin. The profile was similar to those from gel chromatograms and IEC-PAD chromatography.The equivalent lengths in glucosyl units of grid-links (g-links) of internal and external chains in constructs were calculated from the ICL and ECL values of amylopectin and models produced from the constructs with the appropriate lengths for internal and external chains. These derived models were subjected to simulated hydrolysis by Pseudomonas stutzeri amylase and the products compared with those of the experimental distribution from w-maize amylopectin. With the model the amounts of maltotetraose and maltodextrins released were similar to the experimental values but the distribution of branched maltodextrins was quite different. Unlike w-maize amylopectin – a polymer with the cluster structure – which has given a profile of molecular sizes of maltodextrins with low amounts of single and small numbers of internal chains and with a peak at a M_W of about 14,000 (13 chains), in the model the proportion of maltodextrin with one internal chain was high and as d.p. increased the amounts decreased exponentially. This would be expected if the distribution of internal chains in the core was random. It is suggested that in the core of a model prepared from a construct made with alternating probabilities of extension – one in which this probability is high relative to branching, and a second in which it is low – may give clusters of branched maltodextrins with short internal chains which are joined by longer chains; more closely approximating the distribution of internal chains of different lengths in amylopectin.An arrangement for amylopectin molecules in the starch granule has been proposed. In this, they have a wafer-like, discoidal shape, composed of the amorphous zone overlain with the double helical, crystalline region. The flat macromolecules are concentrically layered with the former on the inside and the latter oriented to the outside of the granule.     

Electrophoretic analysis of the lipopolysaccharides ofBacteroides spp.

Lipopolysaccharide (LPS) extracts of reference strains and isolates ofBacteroides spp. prepared by the proteinase K method were resolved by tricine-sodium-dodecyl-sulphate-polyacrylamide gel electrophoresis and located by silver staining. A considerable diversity of LPS profiles was evident within theBacteroides genus although profiles were essentially species-specific, with some minor interstrain variations apparent among isolates ofB. uniformis, B. ovatus, B. eggerthii andB. thetaiotaomicron. The LPS of most species consisted of a major rough LPS component of 2–5 kDa and a series of higher molecular weight bands which varied with species.B. vulgatus LPS was distinctive in showing an extensive ladder of multiple repeating oligosaccharide units with molecular weights ranging from 4 to >17 kDaB. stercoris LPS included a high molecular weight (>17 kDa) ladder of repeating oligosaccharide units.B. fragilis andB. thetaiotaomicron differed from most other species in producing a short ladder of repeating oligosaccharide units interspersing the rough LPS and a 5.6 kDa (B. fragilis) or 9 kDa (B. thetaiotaomicron) yellow-staining component. The heterogeneity of LPS profiles within theBacteroides genus may reflect the differences in pathogenicity among the species and prove useful for typing.     

The relationship between the structure of plastoquinone derivatives and their biological activity in Photosystem II of spinach chloroplasts

The relationship between the structure of reconstituted plastoquinone derivatives and their ability to recover the Hill reaction was investigated by extraction and reconstitution of lyophilized chloroplasts from spinach, followed by monitoring DCIP photoreduction at 600 nm. The results show that: It is not essential that the plastoquinone side chain be an isoprenoid or a phytol; the activity increases with increasing length of the side chain up to 13–15 carbon atoms; for chains longer than 15 carbon atoms, the activity is practically constant. Lipophilic groups (such as -Br) in the side chain increased the activity, hydrophilic groups (such as -OH) decreased the activity. Conjugated double bonds in the side chain decreased the activity greatly, but non-conjugated double bonds had almost no effect on the activity, indicating a requirement of flexibility of the side chain. The activity is decreased in the order of PQ, UbiQ and MQ, showing a large effect of the ring structure.Abbreviations DCIP 2,6-dichlorophenolindophenol - DCMU 3-(3,4-dichlorophenyl)-1,1-dimethylurea - Q_A primary electron acceptor in PS II reaction centers - Q_B secondary electron acceptor in PS II reaction centers - PQ _n plastoquinones with an isoprenoid side chain (n, number of the isoprenoid units in the side chain) - PQ-n synthetic plastoquinones with alkyl side chain (n, number of the carbon atoms in the alkyl side chain) - PQ-n synthetic plastoquinones with a double bond in the alkyl side chain - UQ _n ubiquinones with an isoprenoid side chain (n, number of the isoprenoid units in the side chain) - UQ-n synthetic ubiquinones with alkyl side chain (n, number of the carbon atoms in the akyl side chain) - MQ-n 2-alkyl-1,4-naphthoquinone (n, number of the carbon atoms in the alkyl side chain)     

Molecular Dynamics of Anthraquinone DNA Intercalators with Polyethylene Glycol Side Chains

Abstract

The interactions of a homologous series of four anthraquinone (AQ) intercalators with increasing lengths of polyethylene glycol (PEG) side chains with DNA have been studied via molecular dynamics (MD) simulations. The geometry, conformation, interactions, and hydration of the complexes were examined. The geometries of the four ligands were similar with parallel stacking to the long axis of the adjacent DNA base pairs. Hydrogen bonding between the AQ amide and DNA led to a preference for the trans-syn conformer. As the side chain lengthened, binding to DNA reduced the conformational space, resulting in an increase in unfavorable entropy. Increased localization of the PEG side chain in the DNA groove, indicating some interaction of the side chain with DNA, also contributed unfavorably to the entropy. The changes in free energy of binding due to entropic considerations (— 3.9 to—6.3 kcal/mol) of AQ I-IV were significant. The hydration of the PEG side chain decreased upon binding to DNA. Understanding of side chain conformations, interactions, and hydration changes that accompany the formation of a ligand-DNA complex may be important in the development of new applications of pegylated small molecules that target biological macromolecules.     

Protein folding and chain collapse

It is currently assumed that the folded structure of a globular protein is controlled in a highly deterministic way by its amino acid sequence. We show here that a very different although not necessarily contrasting viewpoint can be adopted. From statistical treatment of x-ray results, we suggest that the folding pattern essentially follows the collapse to be expected on statistical-mechanical grounds for an ideal chain effectively experiencing self-attraction and comprising identical units, whose conformational properties are obtained as an average over the actual amino acid units. The local details of folding of each protein, obviously dictated byits amino acid sequence, can be regarded as statistical fluctuations. We consider 31 globular fragments belonging to 21 different water-soluble, nonmembrane proteins. By the theory of chain collapse proposed by two of us [G. Allegra and F. Ganazzoli (1985) J. Chem. Phys. 83 , 397], all the average intramolecular distances may be obtained. Accordingly, first an average plot of the mean-square distances between kth neighboring amino acid units is constructed, starting from the observed crystallographic coordinates. Then the plot is basically reproduced with a wormlike chain model undergoing collapse as a result of intramolecular attractive forces. Agreement is especially good for short amino acid sequences (k ? 30), in which case the statistical sampling is more accurate, enabling us to determine the model parameters. The resulting mean-square radius of gyration is also in good agreement with the experimental average, whereas the unperturbed characteristic ratio is roughly consistent with results from conformational calculations by W. L. Mattice [(1977) Macromolecules 10 , 516], based on the rotational isomeric state approach.     

Chiroptical and photochromic properties of stereoregular copolymers of 4-methacryloxyethylenoxyazobenzene with (−)-menthyl methacrylate

Copolymers of the photochromic monomer 4-methacryloxyethylenoxyazobenzene with the optically active comonomer (-)-menthyl methacrylate, having different stereoregularity, were investigated in order to obtain a better understanding of the relationship between microstructure and photochromism in synthetic macromolecules. No appreciable effect was observed by copolymer composition, sequence distribution, and microtacticity on the photoinduced trans → cis isomerization of the azobenzene side chains. This last, however, is reflected in changes of the chiroptical properties, type and entity of the photoinduced variation being dependent on chain structure. The long spacer separating the azo chromophore from the main chain limits the extent of chiroptical properties dependence on irradiation.