Narrow Results

Protein sequences are typical complex systems and the knowledge of their local features is very important to predict their secondary structures and biological function. In the present paper a compositional complexity is used to measure the local features of the protein sequences. We found that the transition segments between the regular secondary structures (α-helices and β-strands) and irregular secondary structures (loops and turns) usually have higher complexity than the neighboring segments. This result may be useful to identify the locations of irregular secondary structures which usually are active sites.

The stability of α-helices in proteins depends on both their compositions and environments. To see how these two factors match with each other, we selected three typical α-helices from real proteins each of them has different compositions of hydrophobic and hydrophilic amino acids. We simulated the dynamics of the three helices in vacuum and in water using molecular dynamics. The results show that the stabilities of the three α-helices are different in vacuum and in water, which are consistent with their locations in the proteins. We also found some interesting behaviors of these α-helices.

We discuss the results of a computer simulation of the biopolymer crystal growth and aggregation based on the 2D lattice Monte Carlo technique and the HP approximation of the biopolymers. As a modeled molecule (growth unit) we comparatively consider the previously studied non-mutant lysozyme protein, Protein Data Bank (PDB) ID: 193L, which forms, under a certain set of thermodynamic-kinetic conditions, the tetragonal crystals, and an amyloidogenic variant of the lysozyme, PDB ID: 1LYY, which is known as fibril-yielding and prone-to-aggregation agent. In our model, the site-dependent attachment, detachment and migration processes are involved. The probability of growth unit motion, attachment and detachment to/from the crystal surface are assumed to be proportional to the orientational factor representing the anisotropy of the molecule. Working within a two-dimensional representation of the truly three-dimensional process, we also argue that the crystal grows in a spiral way, whereby one or more screw dislocations on the crystal surface give rise to a terrace. We interpret the obtained results in terms of known models of crystal growth and aggregation such as B-C-F (Burton-Cabrera-Frank) dislocation driven growth and M-S (Mullins-Sekerka) instability concept, with stochastic aspects supplementing the latter. We discuss the conditions under which crystals vs non-crystalline protein aggregates appear, and how the process depends upon difference in chemical structure of the protein molecule seen as the main building block of the elementary crystal cell.

The fractal method has been successfully used to study many problems in physics, mathematics, engineering, finance, even in biology till now. In the past decade or so there has been a ground swell of interest in unravelling the mysteries of DNA. How to get more bioinformations from these DNA sequences is a challenging problem. The problem of classification and evolution relationship of organisms are the central problems in bioinformatics. And it is also very hard to predict the secondary and space structure of a protein from its amino acid sequence. In this paper, some recent results related these problems obtained through multifractal analysis and iterated function system (IFS) model are introduced.

Sum frequency generation (SFG) vibrational spectroscopy has been employed to study a variety of interesting biological phenomena occurring at interfaces. This review summarizes recent SFG studies on proteins, lipid monolayers and bilayers, and other biological molecules. Molecular level details revealed by SFG in these studies show that SFG is a powerful technique for characterizing conformation, orientation and ordering of biological molecules at interfaces.

We simulate numerically the dynamic properties of new soliton with quasi-coherent two quanta in the improved model by fourth-order Runge–Kutta way. We observed that the window of formation of new soliton is shifted toward smaller values of coupling constants when compared with the Davydov's soliton with one quantum and Förner's soliton with two quantum model. The new soliton formation starts at (χ₁+χ₂)=20 PN, and pinning starts from (χ₁+χ₂)=86 PN. The pinned solitons are also observed if both quanta are on the same end of the chain in the initial state. The behaviors of new soliton are varied under influences for variations of characteristic parameters arising from the structure nonuniformity of protein molecules. Although the new soliton is also sensitive to the dipole-dipole interaction and diagonal disorder, the sensitivity to the impurity is weaker than that of the Davydov's and Förner's solitons. Therefore, the new soliton is robust against the fluctuations of coupled constant, dipole-dipole interaction and diagonal disorder arising from the impurity or structure nonuniformity, when compared with that of the Davydov's and Förner's solitons.

In this contribution biomolecular systems are analyzed in a framework of differential geometry in order to derive important condensed matter physics information. In the first section lipid bi-layer membranes are examined with respect to statistical properties and topology, e.g. a relation between vesicle formation and the proliferation of genus number. In the second section differential geometric methods are used for analyzing the surface structure of proteins and thereby understanding catalytic properties of larger proteins.

The effects of long-range interactions between peptides on the protein–DNA dynamics in the long-wave limit are studied. The investigation, done at the physiological temperature, is based on a coupled spin system of DNA molecule which includes the helicoidal geometry of DNA molecule and the Kac–Baker long-range interaction between the peptides of the protein molecule. By using the Holstein–Primakoff bosonic representation of the spin operators, we show that the original discrete equations for the protein–DNA interaction dynamics can be reduced to the nonlinear Schrödinger (NLS) equation of which the dispersive and the nonlinear coefficients depend among other things on the protein long-range interaction parameter and on the helicoidal coupling coefficient. Furthermore, we find that the amplitude and the width of the resulting breather solution, in the form of the bubble moving along the DNA molecule, are strongly influenced by the long-range and helicoidal interactions. This result shows a relevant length scale for real protein–DNA interaction.

The self-consistent cluster-embedding (SCCE) calculation method reduces the computational effort from M³ to about M¹ (M is the number of atoms in the system) with precise calculations. Thus the ab initio, all-electron calculation of the electronic structure and biological function of protein molecule has become a reality, which will promote new proteomics considerably. The calculated results of two real protein molecules, the trypsin inhibitor from the seeds of squash Cucurbita maxima (CMTI-I, 436 atoms) and the ascaris trypsin inhibitor (912 atoms, two three-dimensional structures), will be presented in this paper. The reactive sites of the inhibitors are determined and explained. The accuracy of structure determination of the inhibitors are tested theoretically.

We studied numerically the influences of damping and temperature of medium on the properties of the soliton transported bio-energy in the α-helix protein molecules with three channels by using the dynamic equations in the improved Davydov theory and fourth-order Runge–Kutta method. From the simulation experiments, we see that the new solitons can move along the molecular chains without dispersion at a constant speed, in which the shape and energy of the soliton can remain in the cases of motion, whether short-time at T=0 or long time at T=300 K. In these motions, the soliton can travel over about 700 amino acid residues, thus its lifetime is, at least, 120 ps at 300 K. When the two solitons undergo a collision, they can also retain themselves forms to transport towards. These results are consistent with the analytic result obtained by quantum perturbed theory in this model. However, the amplitudes of the solitons depress along with increase of temperature of the medium, and it begins to disperse at 320 K. In the meanwhile, the damping of the medium can influence the states and properties of the soliton excited in α-helix protein molecules. The investigation indicates that the amplitude and propagated velocity of the soliton decrease, when the damping of medium increases. The soliton is dispersed at the large damping coefficient Γ=4 Γ₀ at 300 K. The results show that the soliton excited in the α-helix protein molecules with three channels is very robust against the damping and thermal perturbation of medium at biological temperature of 300 K. Thus we can conclude that the soliton can play important part in the bio-energy transport and the improved model is possibly a candidate for the mechanism of the energy transport in the α-helix proteins.

An n-string tangle is a three-dimensional ball with n-strings properly embedded in it. In the late 1980s, Ernst and Sumners introduced a tangle model for protein-DNA complexes. The protein is modeled by a three-dimensional ball and the protein-bound DNA is modeled by strings embedded inside the ball. Originally the tangle model was applied to proteins such as Tn3 resolvase which binds two DNA segments. This protein breaks and rejoins two DNA segments and can create knotted DNA. A 2-string tangle model can be used for this complex. More recently, Pathania, Jayaram and Harshey determined that the topological structure of DNA within a Mu protein complex consists of three DNA segments containing five crossings. Since Mu binds DNA sequences at three sites, this Mu protein-DNA complex can be modeled by a 3-string tangle. Darcy, Leucke and Vazquez analyzed Pathania et al.'s experimental results by using 3-string tangle analysis. There are protein-DNA complexes that involve four or more DNA sites. When a protein binds circular DNA at four sites, a protein-DNA complex can be modeled by a 4-string tangle with four loops outside of the tangle. We determine a biologically relevant 4-string tangle model. We also develop mathematics for solving 4-string tangle equations to determine the topology of DNA within a protein complex.

The interfacial surface activity of a protein, ovalbumin (OVA) at bare air/water interface in presence and also in absence of electrolyte (KCl) in subphase has been investigated. The surface activity was measured as a function of time. It has been found that, the presence of KCl in aqueous subphase enhances the adsorption rate of the protein. The changes of area/molecule, compressibility, rigidity and unfolding of OVA are trivial up to 10 mM KCl concentration. These properties of OVA, above 10 mM KCl concentration are significant and have been explained in the perspective of DLVO theory and many-body ion–protein dispersion potentials. The presence of high concentration of electrolyte increases the β-structure of OVA, resulting into larger unfolding as well as larger intermolecular aggregates. The overall study indicates that KCl perturbs the OVA monolayer.

Was it SARS?

Eli Lilly's Bid to Curb Tuberculosis.

Fountain-Pen Nanochemistry Enables Writing of Microscipic Patterns of Protein.

The article starts of with an overview of the Institute of Bioengineering and Nanotechnology. It describes the focus of the institution. There are two research articles after the summary. One of it touches on non-cytotoxic and photostable quantum dots for bioimaing applications and the other is on silica-coated nanocomposites of magnetic nanoparticles and quantum dots.

AUSTRALIA – Mosquito Parasite Could Control Dengue

CHINA – China has Twice the Global Average of Drug-Resistant Tuberculosis

CHINA – 80 000 Antibiotics Abuse-related Deaths Annually

CHINA – Bird Flu Found in Chicken from China

CHINA – China on Alert following Bird Flu Death

CHINA – Chinese Dairies to Compensate Tainted Milk Victims' Families

CHINA – New Insulin Resistance Tricks Found

CHINA – World's First Plant Chromosome Atlas

CHINA – Project Launched to Study Structure of Proteins

CHINA – Fake Diabetes Drug Linked to Two Deaths

CHINA – Birth Defects Rising in Polluted China

INDIA – India Culls Poultry in Darjeeling After Bird Flu

INDIA – India Introduces Second-Line Anti-retroviral Treatment in Eight States

INDIA – Indian Medical Tourism to Reach US$1.9 billion by 2015

INDIA – Canadian and Indian Ministers Sign Pact on Agriculture Cooperation

INDIA – 6000 year-old Rice Species Discovered in Meghalaya

INDIA – Genetics to Help Conserve Rare Bird Species

JAPAN – Coating the Protein Enhances Disease-fighting Capability

JAPAN – Scientists Isolate Genes that Made 1918 Flu Lethal

JAPAN – Researchers in Japan Develop All-round Flu Vaccine

PHILIPPINES – Ebola Reston Virus Found in Filipino Farm Worker

SINGAPORE – New Method to Create iPS Cells

SINGAPORE – Ray of Hope for Liver Cancer Sufferers

SINGAPORE – Bacteria Improve Energy and Cost Efficiency in Water Treatment

TAIWAN – Secrets of “Speciation” Gene Unravelled

TAIWAN – Initial Breakthrough in Poultry Vaccine Development

TAIWAN – Taiwan Gains Direct Access to WHO

VIETNAM – Doctors Report First Drug Hypersensitivity Syndrome

VIETNAM – Public Advised Serious Caution Against Bird Flu

NORTH AMERICA – Kids of Pregnant Drinking Mums will Like Booze

NORTH AMERICA – High Functional Diversity in Mycobacterium Tuberculosis Driven By Genetic Drift And Human Demography

NORTH AMERICA – Newly Discovered Tuberculosis Protein May Help Explain Bacterium's Resilience

NORTH AMERICA – U.S. Patent For Diagnostic Technology Awarded To URMC, Lighthouse Biosciences

EUROPE – Structure Mediating Spread of Antibiotic Resistance Discovered

EUROPE – New EU Pesticide Regulations Could Undermine Battle against Malaria

EUROPE – iPill – The Smart Drug Delivery that can “Call” the Doctor

EUROPE – What Drives Locusts to Swarm

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Benitec MOU with Biomics Biotechnologies China.

Arkema & Aussie Chemeq Sign Manufacturing Cooperation Agreement.

AstraZeneca and Mental Health Research Institute in Australia Announce Collaboration to Improve Early Detection of Alzheimer's Disease.

Avexa Gets CSIRO Investment.

Living Cell Technologies' Encapsulated Choroid Plexus Cells May Be Used To Treat Hearing Loss.

Sundia MediTech Acquires Protein Folding Technology.

Beijing Cancer Hospital Introduces Fast and Precise RapidArc Radiotherapy Cancer Treatments.

Zydus Cadila and Karo Bio's Research Collaboration has Generated Promising Lead Compounds.

ICON Acquires Veeda Laboratories Limited.

Novavax-Cadila to Conduct Swine Flu Clinical Trials.

Axygen & Astellas form JV to Develop Protein Drugs.

Rexahn, KRICT to Develop Anti-Cancer Drugs.

Japan's Largest Pharmaceutical Firm Opens Regional HQ in Singapore.

Mesoblast to Acquire Angioblast Systems.

Ansell Unveils First Antimicrobial Surgical Glove.

OriGene to Build World's Largest MAb Facility in China.

Zydus Cadila to Launch India's First H1N1 Vaccine.

Abbott Acquires India's Piramal Health for $3.72 bn.

Mantrax Ventures and TCG Lifesciences Collaborate.

Protox Therapeutics, Kissei Pharmaceutical in Prostate Cancer Deal.

First Transcatheter Valve Clinical Trial in Japan Treats Patients with Edwards SAPIEN XT Valve.

South Korean Firm Develops Drug to Kill Leukemia Stem Cells.

GSK Extends Presence in Asia with New Strategic Alliance in South Korea.

World's Most Comprehensive Nanoparticle System Unveiled.

*BIO, Onyx Pharmaceuticals Expand Development, Commercialization Collaboration for JAK2 Inhibitors.

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Discovery of Crucial Protein Interaction Sheds Light on Mental Retardation.

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AUSTRALIA – Australian Researcher Finds Radical Technique to Save MAS Babies.

AUSTRALIA – Austrian Scientists Discover Enzyme Function in Cancer.

CHINA – Domestic Dengue Fever Cases Breaks 1,000.

CHINA – China Experts Design Gel to Protect Women from HIV.

INDIA – India, South Africa to Team up on HIV Vaccine Research.

MALAYSIA – Malaysia to use Lab Mosquitoes to Fight Dengue

NEW ZEALAND – Plant Derived Foods can Keep us Feeling Full.

SINGAPORE – Singapore Hosts First "Decade of the Mind" Conference in Asia and Expands Efforts in Brain & Cognition Research.

SINGAPORE – Drugs May Replace Chemo in Leukemia Therapy.

SINGAPORE – Singapore Scientists First to Perform Genome-Wide study of Human Stem Cells.

SINGAPORE – Singapore Babies in Waste-disease Trial.

SINGAPORE – New Technology a Shot in the Arm for Biofuels.

SINGAPORE – S$3.7 Billion for Singapore Biomedical Sciences R&D.

TAIWAN – Medical Tourism Booms in Taiwan.

OTHER REGIONS — EUROPE – Gene that Triggers Human Cancer Identified.

OTHER REGIONS — EUROPE – Painfully Potent Pepper.

OTHER REGIONS — NORTH AMERICA – 2 Dads and No Mum make 10 Mice.