Controlling protein molecular dynamics:how to accelerate folding while preserving the native state

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1 micros. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

The impact of visual-verbal relationships on native-nonnative english speakers' reading processes and comprehension

The aim of this study was to comparatively investigate the impact of visual-verbal relationships that exist in expository texts on the reading process and comprehension of readers from different language background: native speakers of English (LI) and speakers of English as a foreign language (EFL). The study focussed, in this respect, on the visual elements (VEs) mainly graphs and tables that accompanied the selected texts. Two major experiments were undertaken. The first, was for the reading process using the post-reading questionnaire technique. Participants were 163 adult readers representing three groups: 77 (LI), 56 (EFL postgraduates); and 30 (EFL undergraduates). The second experiment was for the reading comprehension using cloze procedure. Participants were 123 representing the same above gorups: 50, 33 and 40 respectively. It was hypothesised that the LI readers would make use of VEs in the reading process in ways different from both EFL groups and that use would enhance each group's comprehension in different aspects and to different levels. In the analysis of the data of both experiments two statistical measurements were used. The chi-square was used to measure the differences between frequencies and the t-test was used to measure the differences between means. The results indicated a significant relationship between readers' language background and the impact of visual-verbal relationships on their reading processes and comprehension of such type of texts. The results also revealed considerable similarities between the two EFL groups in the reading process of texts accompanied by VEs. In the reading comprehension, however, the EFL undergraduates seemed to benefit from the visual-verbal relationships in their comprehension more than the postgraduates, suggesting a weak relationship of this impact for older EFL readers. Furthermore, the results showed considerable similarities between the reading process of texts accompanied by VEs and of whole prose texts. Finally an evaluation of this study was undertaken as well as practical implications for EFL readers and suggestions for future research.

Coherence and understanding in informal conversations between native and non-native speakers of English

This study investigates informal conversations between native English speakers and international students living and studying in the UK. 10 NNS participants recorded themselves during conversations with native speakers. The audio-recordings were transcribed and a fine-grained, qualitative analysis was employed to examine how the participants jointly achieved both coherence and understanding in the conversations, and more specifically how the NNSs contributed to this achievement. The key areas of investigation focused on features of topic management, such as topic initiations, changes and transitions, and on the impact which any communicative difficulties may have on the topical continuity of the conversations. The data suggested that these conversations flowed freely and coherently, and were marked by a relative scarcity of the communicative difficulties often associated with NS-NNS interactions. Moreover, language difficulties were found to have minimal impact on the topic development of the conversations. Unlike most previous research in the field, the data further indicated that the NNSs were able to make active contributions to the initiation and change of topics, and to employ a range of strategies to manage these effectively and coherently. The study considers the implications which the findings may have for teaching and learning, for second language acquisition research, and for non-native speakers everywhere.

Surfactant-free purification of membrane proteins with intact native membrane environment

In order to study the structure and function of a protein, it is generally required that the protein in question is purified away from all others. For soluble proteins, this process is greatly aided by the lack of any restriction on the free and independent diffusion of individual protein particles in three dimensions. This is not the case for membrane proteins, as the membrane itself forms a continuum that joins the proteins within the membrane with one another. It is therefore essential that the membrane is disrupted in order to allow separation and hence purification of membrane proteins. In the present review, we examine recent advances in the methods employed to separate membrane proteins before purification. These approaches move away from solubilization methods based on the use of small surfactants, which have been shown to suffer from significant practical problems. Instead, the present review focuses on methods that stem from the field of nanotechnology and use a range of reagents that fragment the membrane into nanometre-scale particles containing the protein complete with the local membrane environment. In particular, we examine a method employing the amphipathic polymer poly(styrene-co-maleic acid), which is able to reversibly encapsulate the membrane protein in a 10 nm disc-like structure ideally suited to purification and further biochemical study.

Topic continuity in informal conversations between native and non-native speakers of English

Topic management by non-native speakers (NNSs) during informal conversations has received comparatively little attention from researchers, and receives surprisingly little attention in second language learning and teaching. This article reports on one of the topic management strategies employed by international students during informal, social interactions with native-speaker peers, exploring the process of maintaining topic continuity following temporary suspensions of topics. The concept of side sequences is employed to illustrate the nature of different types of topic suspension, as well as the process of jointly negotiating a return to the topic. Extracts from the conversations show that such sequences were not exclusively occasioned by language difficulties, and that the non-native speaker participants were able to effect successful returns to the main topic of the conversations.

A description of the french passive for non-native speakers

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Degradation, receptor binding, insulin secreting and antihyperglycaemic actions of palmitate-derivatised native and Ala8-substituted GLP-1 analogues

The hormone glucagon-like peptide-1(7-36)amide (GLP-1) is released in response to ingested nutrients and acts to promote glucose-dependent insulin secretion ensuring efficient postprandial glucose homeostasis. Unfortunately, the beneficial actions of GLP-1 which give this hormone many of the desirable properties of an antidiabetic drug are short lived due to degradation by dipeptidylpeptidase IV (DPP IV) and rapid clearance by renal filtration. In this study we have attempted to extend GLP-1 action through the attachment of palmitoyl moieties to the E-amino group in the side chain of the LyS26 residue and to combine this modification with substitutions of the Ala 8 residue, namely Val or amino-butyric acid (Abu). In contrast to native GLP-1, which was rapidly degraded, [Lys(pal) 26]GLP-1, [Abu8,Lys(pal)26]GLP-1 and [Val8,Lys-(pal)26]GLP-1 all exhibited profound stability during 12 h incubations with DPP IV and human plasma. Receptor binding affinity and the ability to increase cyclic AMP in the clonal β-cell line BRIN-BD11 were decreased by 86- to 167-fold and 15- to 62-fold, respectively compared with native GLP-1. However, insulin secretory potency tested using BRIN-BD11 cells was similar, or in the case of [Val8,Lys(pal)26]GLP-1 enhanced. Furthermore, when administered in vivo together with glucose to diabetic (ob/ob) mice, [Lys(pal)26]GLP-1, [Abu8,Lys(pal) 26]GLP-1 and [Val8,Lys(pal) 26]GLP-1 did not demonstrate acute glucose-lowering or insulinotropic activity as observed with native GLP-1. These studies support the potential usefulness of fatty acid linked analogues of GLP-1 but indicate the importance of chain length for peptide kinetics and bioavailability. Copyright © by Walter de Gruyter.

From Spanish paintings to murder:topic transitions in casual conversations between native and non-native speakers of English

This article explores some of the strategies used by international students of English to manage topic shifts in casual conversations with English-speaking peers. It therefore covers aspects of discourse which have been comparatively under-researched, and where research has also tended to focus on the problems rather than the communicative achievements of non-native speakers. A detailed analysis of the conversations under discussion, which were recorded by the participants themselves, showed that they all flowed smoothly, and this was in large measure due to the ways in which topic shifts were managed. The paper will focus on a very distinct type of topic shift, namely that of topic transitions, which enable a smooth flow from one topic to another, but which do not explicitly signal that a shift is taking place. It will examine how the non-native speakers achieved coherence in the topic transitions which they initiated, which strategies or procedures they employed, and show how their initiations were effective in enabling the proposed topic to be understood, taken up and developed. It therefore adds to our understanding of the interactional achievements of international speakers in informal, social contexts. © 2013 Elsevier B.V.

Native language identification (NLID) for forensic authorship analysis of weblogs

This chapter introduces Native Language Identification (NLID) and considers the casework applications with regard to authorship analysis of online material. It presents findings from research identifying which linguistic features were the best indicators of native (L1) Persian speakers blogging in English, and analyses how these features cope at distinguishing between native influences from languages that are linguistically and culturally related. The first chapter section outlines the area of Native Language Identification, and demonstrates its potential for application through a discussion of relevant case history. The next section discusses a development of methodology for identifying influence from L1 Persian in an anonymous blog author, and presents findings. The third part discusses the application of these features to casework situations as well as how the features identified can form an easily applicable model and demonstrates the application of this to casework. The research presented in this chapter can be considered a case study for the wider potential application of NLID.

Negotiating topic changes:native and non-native speakers of English in conversation

There is a tendency to view conversations involving non-native speakers (NNSs) as inevitably fraught with problems, including an inability to handle topic management. This article, in contrast, will focus on effective topic changes made by non-native speakers during informal conversations with native speakers of English. A micro-analysis of ten conversations revealed several ways of shifting conversational topics; however, the article concentrates on those strategies which the participants used to effect a particular type of topic move, namely 'marked topic changes', where there is no connection at all with previous talk. The findings show how these topic changes were jointly negotiated, and that the non-native speakers' contributions to initiating new topics were competently managed.

Action Plan to Conserve the Native Plants of Florida

In this document, a strategy aimed at conserving the native flora of Florida is presented. The strategy is developed in a four-step sequence. Following the Introduction (Part I), The Florida Native Plant Resource (Part II) describes the resource and the threats to it. That section includes a brief description of the vegetation of Florida prior to the demographic explosion of the last century, a report on the current status of plants in the state, and discussion of some factors responsible for the evident and continuing decline in the quality and quantity of the vegetation resource. In Part III (The Florida Plant Conservation Process), an explicit goal for plant conservation in Florida is expressed, a model describing the plant conservation process is presented, and activities included with each component of the model are examined and evaluated for the state as a whole. Finally, in Part IV (Recommendations To Improve The Process), changes are presented that we believe would help create a more effective plant conservation environment in Florida.

Wayside Trees of Tropical Florida : a guide to the native and exotic trees and palms of Miami and tropical south Florida

Wayside Trees is an beautifully illustrated guide to Florida trees growing south of Lake Okeechobee. It covers both native and exotic species in the areas of Miami to Palm Beach on the east coast, and Naples to Fort Meyers on the west. The introduction describes environmental, cultural and economic importance of trees, while a non-technical key provides a means for even non-specialists to identify the 167 most common species. The bulk of the book consists of illustrated descriptions of the trees, arranged by plant family, and includes ecological and cultural information on each species. Lavishly illustrated with over 1200 color photographs and diagrams, the book is designed to serve homeowners, gardeners, teachers and students, as well as environmental professionals. It is also a useful guide to urban tropical trees growing outside south Florida. The authors, a botanist and a graphic artist, have 70 collective years of experience living, working, and loving the trees of south Florida.

Proton nuclear magnetic resonance investigation of the native and modified active site structure of heme proteins

Hemoproteins are a very important class of enzymes in nature sharing the essentially same prosthetic group, heme, and are good models for exploring the relationship between protein structure and function. Three important hemoproteins, chloroperoxidase (CPO), horseradish peroxidase (HRP), and cytochrome P450cam (P450cam), have been extensively studied as archetypes for the relationship between structure and function. In this study, a series of 1D and 2D NMR experiments were successfully conducted to contribute to the structural studies of these hemoproteins. ^ During the epoxidation of allylbenzene, CPO is converted to an inactive green species with the prosthetic heme modified by addition of the alkene plus an oxygen atom forming a five-membered chelate ring. Complete assignment of the NMR resonances of the modified porphyrin extracted and demetallated from green CPO unambiguously established the structure of this porphyrin as an NIII-alkylated product. A novel substrate binding motif of CPO was proposed from this concluded regiospecific N-alkylation structure. ^ Soybean peroxidase (SBP) is considered as a more stable, more abundant and less expensive substitute of HRP for industrial applications. A NMR study of SBP using 1D and 2D NOE methods successfully established the active site structure of SBP and consequently fills in the blank of the SBP NMR study. All of the hyperfine shifts of the SBP-CN- complex are unambiguously assigned together with most of the prosthetic heme and all proximal His170 resonances identified. The active site structure of SBP revealed by this NMR study is in complete agreement with the recombinant SBP crystal structure and is highly similar to that of the HRP with minor differences. ^ The NMR study of paramagnetic P450cam had been greatly restricted for a long time. A combination of 2D NMR methods was used in this study for P450cam-CN - complexes with and without camphor bound. The results lead to the first unequivocal assignments of all heme hyperfine-shifted signals, together with certain correlated diamagnetic resonances. The observed alternation of the assigned novel proximal cysteine β-CH2 resonances induced by camphor binding indicated a conformational change near the proximal side.^