Determining the Conformational Stability of a Protein from Urea and Thermal Unfolding Curves.

This article contains protocols for determining the conformational stability of a globular protein from either urea or thermal unfolding curves. Circular dichroism is the optical spectroscopic technique most commonly used to monitor protein unfolding. These protocols describe how to analyze data from an unfolding curve to obtain the thermodynamic parameters necessary to calculate conformational stability, and how to determine differences in stability between protein variants.

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace.

Cooked Chickpea Consumption Inhibits Colon Carcinogenesis in Mice Induced with Azoxymethane and Dextran Sulfate Sodium.

Scope: The objective of the study was to evaluate the effect of daily consumption of cooked chickpea (2% and 10%) in ICR male mice in which colon cancer was induced with azoxymethane and dextran sulfate sodium.

Methods And Results: The effect of consumption of 2% or 10% cooked chickpeas on carcinogenesis-induced colon azoxymethane (AOM)/dextran sulfate sodium (DSS) in ICR mice was determined. Protein oxidation and lipids were determined by colorimetric methods and oxidation of DNA through the identification of adducts 8-hydroxy-2'-desoxiguanosine and proliferation markers (proliferating cell nuclear antigen [PCNA], Ki-67, and β-catenin), and inflammation (cyclooxygenase [COX]-2 and inducible nitric oxide synthase [iNOS]) were identified by immunohistochemistry reactions.

Contribution of hydrogen bonds to protein stability.

Our goal was to gain a better understanding of the contribution of the burial of polar groups and their hydrogen bonds to the conformational stability of proteins. We measured the change in stability, Δ(ΔG), for a series of hydrogen bonding mutants in four proteins: villin headpiece subdomain (VHP) containing 36 residues, a surface protein from Borrelia burgdorferi (VlsE) containing 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa (RNase Sa) and T1 (RNase T1). Crystal structures were determined for three of the hydrogen bonding mutants of RNase Sa: S24A, Y51F, and T95A.

Determining the conformational stability of a protein from urea and thermal unfolding curves.

This unit contains basic protocols for determining the conformational stability of a globular protein from either urea or thermal unfolding curves. Circular dichroism is the optical spectroscopic technique most commonly used to monitor protein unfolding. The protocols describe how to analyze data from an unfolding curve to obtain the thermodynamic parameters necessary to calculate conformational stability, and how to determine differences in stability between protein variants.

Accuracy of intraoperative fluoroscopy with and without laser guidance in foot and ankle surgery.

Background: The use of intraoperative fluoroscopy in orthopedic surgery involves frequent exposure to ionizing radiation in the operating room. Although a number of studies have found radiation exposure to orthopedic surgeons to be well below recommended doses, the long-term effects of low-dose radiation are not well known. Thus, all effective practical methods should be undertaken to reduce the exposure to radiation.

First web space soft tissue release in bunion surgery: functional outcomes of a new technique.

Background: The current approach to soft tissue release in bunion surgery is through an incision in the dorsum of the first web space between the first and second metatarsals. However, the soft tissue release through this approach can be excessive or inadequate for the correction required. In addition, it leaves a visible scar.

Contribution of hydrophobic interactions to protein stability.

Our goal was to gain a better understanding of the contribution of hydrophobic interactions to protein stability. We measured the change in conformational stability, Δ(ΔG), for hydrophobic mutants of four proteins: villin headpiece subdomain (VHP) with 36 residues, a surface protein from Borrelia burgdorferi (VlsE) with 341 residues, and two proteins previously studied in our laboratory, ribonucleases Sa and T1. We compared our results with those of previous studies and reached the following conclusions: (1) Hydrophobic interactions contribute less to the stability of a small protein, VHP (0.

Use of a patient-controlled stretching device to improve the ankle range of motion.

Background: Ankle and subtalar stiffness are widely associated with many foot and ankle conditions and functional deficits. Loss of range of motion, particularly dorsiflexion, results in significant gait dysfunction. A variety of methods have been evaluated to address this problem, including yoga, manipulation, dance training, jogging and static stretching exercises.

Ethnic radiographic foot differences.

Background: The prevalence of foot and ankle conditions varies among different ethnic groups. It is not known if this difference is due to any distinctive skeletal morphological characteristics of the foot. The purpose of this study was to determine if ethnic differences exist in the morphometric measurements on radiographs of the weightbearing foot.

The use of a kickstand modification for the prevention of heel decubitus ulcers in trauma patients with lower extremity external fixation.

External fixation is frequently used to manage patients with lower extremity trauma. Excessive pressure from contact surfaces must be avoided to prevent added morbidity from heel ulcers. The purpose of this article is to present a simple solution to off-load the heel by adding a "kickstand" to the external fixator.

Measuring and increasing protein solubility.

High concentration protein delivery is difficult to achieve for several protein pharmaceuticals due to low solubility. In this review, we discuss different types of low protein solubility, including low in vitro solubility, which is relevant to the formulation of protein pharmaceuticals. We also discuss different methods of measuring protein solubility with an emphasis on the method of inducing amorphous precipitation using ammonium sulfate.

Increasing protein conformational stability by optimizing beta-turn sequence.

Protein conformational stability is an important concern in many fields. Here, we describe a strategy for significantly increasing conformational stability by optimizing beta-turn sequence. Proline and glycine residues are statistically preferred at several beta-turn positions, presumably because their unique side-chains contribute favorably to conformational stability in certain beta-turn positions.

The "kick-off" position: a new sign for early diagnosis of complex regional pain syndrome in the leg.

Background: Complex regional pain syndrome (CRPS) is a clinical entity that develops after a precipitating injury. It involves dysfunction of the sensory, autonomic, and motor systems and frequently is missed on initial presentation. The purpose of this report was to describe a simple clinical sign that can aid in its diagnosis.

Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa.

Poor protein solubility is a common problem in high-resolution structural studies, formulation of protein pharmaceuticals, and biochemical characterization of proteins. One popular strategy to improve protein solubility is to use site-directed mutagenesis to make hydrophobic to hydrophilic mutations on the protein surface. However, a systematic investigation of the relative contributions of all 20 amino acids to protein solubility has not been done.

Asp79 makes a large, unfavorable contribution to the stability of RNase Sa.

The two most buried carboxyl groups in ribonuclease Sa (RNase Sa) are Asp33 (99% buried; pK 2.4) and Asp79 (85% buried; pK 7.4).

Evaluation of results of endoscopic gastrocnemius recession.

Background: Gastrocnemius recession is traditionally done as an open procedure. The aim of this retrospective study was to evaluate the safety and efficacy of gastrocnemius recession performed endoscopically.

Methods: The procedure was done in 28 patients (17 men and 11 women), ranging in age from 16 to 72 years (average 47.

Comparison between manual and computer-assisted measurements of hallux valgus parameters.

Background: The aim of this study was to determine if there are intraobserver and interobserver differences in reliability when measuring hallux valgus angles (HVA), 1-2 intermetatarsal angles (IMA), and distal metatarsal articular angles (DMAA) manually compared to computer-assisted means. Our hypothesis was that the measurements taken by computer-assisted methods of these three forefoot angles would be superior in consistency and accuracy compared to manual measurements.

Methods: Four examiners studied 20 weightbearing anteroposterior radiographs of patients with hallux valgus.

Use of a Torque-Range-of-Motion device for objective differentiation of diabetic from normal feet in adults.

Background: The ability of the foot and ankle complex to act as an energy absorber is reflected in its viscoelastic properties. The Torque-Range-of-Motion (TROM) device was designed to provide an effective objective assessment of foot and ankle passive mechanical function. The hypothesis of this study was that mechanical parameters derived from passive TROM curves of otherwise normal feet of adults with diabetes would be significantly different from those of adults without diabetes.

Protein structure, stability and solubility in water and other solvents.

Proteins carry out the most difficult tasks in living cells. They do so by interacting specifically with other molecules. This requires that they fold to a unique, globular conformation that is only marginally more stable than the large ensemble of unfolded states.

Contribution of active site residues to the activity and thermal stability of ribonuclease Sa.

We have used site-specific mutagenesis to study the contribution of Glu 74 and the active site residues Gln 38, Glu 41, Glu 54, Arg 65, and His 85 to the catalytic activity and thermal stability of ribonuclease Sa. The activity of Gln38Ala is lowered by one order of magnitude, which confirms the involvement of this residue in substrate binding. In contrast, Glu41Lys had no effect on the ribonuclease Sa activity.