Protein structure

The rate of exchange of pep- tide group NH hydrogens with the hydrogens of aqueous solvent is sensitive to neighboring side chains. To evaluate the effects of protein side chains, all 20 naturally occurring amino acids were studied using dipeptide models. Both inductive and steric blocking effects are appar- ent. The additivity of nearest-neighbor block- ing and inductive effects was

The purpose of this paper is to determine the effects of usage of sequential teaching method on the academic achievement and retention level of students. Three student groups of biology students in University “Goce Delcev”, Faculty of Natural and Technical Sciences, Institute of Biology, - Stip, R. Macedonia were offered a topic on general characteristics of Proteins: Their Biological Functions and Primary Structure with different sequences of 3 teaching methods. The teaching methods were Laboratory method (student experiment), slide demonstration and lecture method. The first group started to course with experiments in the laboratory, then the relevant theory of proteins was given lecture method, and then the slides was shown (Group I). The sequence of these three teaching methods used in the first group was changed in both second and third group as follow: The lecture methods, slide show and experiment in Group II, and slide show, experiment and lecture method in Group III, respectively. Laboratory method used in the study was focused on the topic of This diversity and abundance reflect the central role of proteins in virtually all aspects of cell structure and function. An extraordinary diversity of cellular activity is possible only because of the versatility inherent in proteins, each of which is specifically tailored to its biological role. The pattern by which each is tailored resides within the genetic information of cells, encoded in a specific sequence of nucleotide bases in DNA proteins activity, a student experiment was designed for this reason, and including to examine its features, effective factors, and relation between the structure and function of the proteins. This experiment was carried out by students. Slide demonstration method included slides about protein structure and function. The slides were shown by teachers. Lecture method was performed by teachers as usual. Effectiveness of different sequential teaching methods was measured quantitatively by an achievement test. Achievement test contained 20 questions, testing the knowledge of facts as well as the ability to transfer the knowledge and problem solving ability. This test was used as pre-test before methods’ application, post-test after the methods’ application and retention test after 30 days from methods’ applied.

The biological literature databases continue to grow rapidly with vital information that is important for conducting sound biomedical research and development. The current practices of manually searching for information and extracting pertinent knowledge are tedious, time-consuming tasks even for motivated biological researchers. Accurate and computationally efficient approaches in discovering relationships between biological objects from text documents are important for biologists to develop biological models. The term "object" refers to any biological entity such as a protein, gene, cell cycle, etc. and relationship refers to any dynamic action one object has on another, e.g. protein inhibiting another protein or one object belonging to another object such as, the cells composing an organ. This paper presents a novel approach to extract relationships between multiple biological objects that are present in a text document. The approach involves object identification, reference resolution, ontology and synonym discovery, and extracting object-object relationships. Hidden Markov Models (HMMs), dictionaries, and N-Gram models are used to set the framework to tackle the complex task of extracting object-object relationships. Experiments were carried out using a corpus of one thousand Medline abstracts. Intermediate results were obtained for the object identification process, synonym discovery, and finally the relationship extraction. For the thousand abstracts, 53 relationships were extracted of which 43 were correct, giving a specificity of 81 percent. These results are promising for multi-object identification and relationship finding from biological documents.

Extreme environments are those that fall outside the limited range in which we and most other eukaryotes can survive, and are inhabited by the extremophiles, which include thermophiles and psychrophiles. Psycrophilic organisms are living at temperatures close to the freezing point of water, while in the other end of the scale the hyperthermophilic can function perfectly at temperatures above the boiling point. It is of great interest to understand how these organisms can function at "the limits of life". Few structural comparison studies between psychrophiles and mesophiles and/or thermophiles have been done, the first in 1998 (1). Citrate synthase from a psychrophile, a mesophile and a thermophile were compared sequentially and structurally. The results from the study confirm only a few observations reported in earlier sequence comparison and homology studies in the structural features of psychrophile enzymes, and many questions are still left unanswered. This project con...

Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Glucose oxidase (GOX) from Aspergillus niger is a well-characterised glycoprotein consisting of two identical 80-kDa subunits with two FAD co-enzymes bound. Both the DNA sequence and protein structure at 1.9 Ǻ have been determined and reported previously. GOX catalyses the oxidation of d-glucose (C6H12O6) to d-gluconolactone (C6H10O6) and hydrogen peroxide. GOX is produced naturally in some fungi and insects where its catalytic product, hydrogen peroxide, acts as an anti-bacterial and anti-fungal agent. GOX is Generally Regarded As Safe, and GOX from A. niger is the basis of many industrial applications. GOX-catalysed reaction removes oxygen and generates hydrogen peroxide, a trait utilised in food preservation. GOX has also been used in baking, dry egg powder production, wine production, gluconic acid production, etc. Its electrochemical activity makes it an important component in glucose sensors and potentially in fuel cell applications. This paper will give a brief background on the natural occurrence, functions as well as the properties of glucose oxidase. A good coverage on the diverse uses of glucose oxidase in the industry is presented with a brief outline on the working principles in the various settings. Furthermore, food grade GOX preparations are relatively affordable and widely available; the readers may be encouraged to explore other potential uses of GOX. One example is that GOX-catalysed reaction generates significant amount of heat (∼200 kJ/mol), and this property has been mostly neglected in the various applications described so far.

Fourier transform infrared (FTIR) spectroscopy was conducted on type A gelatins derived from skins and bones of young and adult Nile perch (Lates niloticus) by a sequential extraction process. Spectra for gelatins were compared to each other and to that of acid soluble collagen from young Nile perch skins, in order to elucidate changes in protein secondary structure during collagen to gelatin transformation. The first gelatin extracts showed diminished amide III bands while the last gelatin extracts showed distinct amide III bands and their amide I bands consisted of a higher percent area of a component around 1690 cm−1. The differences suggested that the collagen to gelatin transition leads to loss of molecular order. The later gelatin extracts exhibited higher molecular order than earlier gelatin extracts, probably because the former contained surviving crosslinks or/and because renaturation of the low molecular weight gelatin fractions (later gelatin extracts) led to formation of more protein–protein linkages.