Macromolecular Crowding Effects In The Mechanical Unfolding Forces Of Proteins

Macromolecules can occupy a large fraction of the volume of a cell and this crowded environment influences the behavior and properties of the proteins, such as mechanical unfolding forces, thermal stability and rates of folding and diffusion. Although much is already known about molecular crowding, it is not well understood how it affects a protein's resistance to mechanical stress in a crowded environment and how the size of the crowders affect those changes. An atomic force microscope-based single molecule method was used to measure the effects of the crowding on the mechanical stability of a model protein, in this case I-27. As proteins tend to aggregate, single molecule methods provided a way to prevent aggregation because of the very low concentration of proteins in the solution under study. Dextran was used as the crowding agent with three different molecular weights 6kDa, 10 kDa and 40 kDa, with concentrations varying from zero to 300 grams per liter in a pH neutral buffer solution at room temperature. Results showed that the forces required to unfold biomolecules were increased when a high concentration of crowder molecules were added to the buffer solution and that the maximum force required to unfold a domain was when the crowder size was 10 kDa, which is comparable to the protein size. Unfolding rates obtained from Monte Carlo simulations showed that they were also affected in the presence of crowders. As a consequence, the energy barrier was also affected. These effects were most notable when the size of the crowder was 10 kDa, comparable to the size of the protein. On the other hand, distances to the transition state did not seem to change when crowders were added to the solution. The effect of Dextran on the energy barrier was modeled by using established theories such as Ogston's and scaled particle theory, neither of which was completely convincing at describing the results. It can be hypothesized that the composition of Dextran plays a role in the deviation of the predicted behavior with respect to the experimental data.

Mechanical Unfolding Response of Proteins is a thermodynamically motivated overview of when, why, and how proteins respond to mechanical perturbations and the experimental techniques used to probe single protein biophysics. Relative newcomers to the field (new graduate students), and those starting from a biological background hoping for an introduction to the physics behind protein behavior, will benefit from reading this primer.

From the Introduction: Nanotechnology and its underpinning sciences are progressing with unprecedented rapidity. With technical advances in a variety of nanoscale fabrication and manipulation technologies, the whole topical area is maturing into a vibrant field that is generating new scientific research and a burgeoning range of commercial applications, with an annual market already at the trillion dollar threshold. The means of fabricating and controlling matter on the nanoscale afford striking and unprecedented opportunities to exploit a variety of exotic phenomena such as quantum, nanophotonic and nanoelectromechanical effects. Moreover, researchers are elucidating new perspectives on the electronic and optical properties of matter because of the way that nanoscale materials bridge the disparate theories describing molecules and bulk matter. Surface phenomena also gain a greatly increased significance; even the well-known link between chemical reactivity and surface-to-volume ratio becomes a major determinant of physical properties, when it operates over nanoscale dimensions. Against this background, this comprehensive work is designed to address the need for a dynamic, authoritative and readily accessible source of information, capturing the full breadth of the subject. Its six volumes, covering a broad spectrum of disciplines including material sciences, chemistry, physics and life sciences, have been written and edited by an outstanding team of international experts. Addressing an extensive, cross-disciplinary audience, each chapter aims to cover key developments in a scholarly, readable and critical style, providing an indispensible first point of entry to the literature for scientists and technologists from interdisciplinary fields. The work focuses on the major classes of nanomaterials in terms of their synthesis, structure and applications, reviewing nanomaterials and their respective technologies in well-structured and comprehensive articles with extensive cross-references. It has been a constant surprise and delight to have found, amongst the rapidly escalating number who work in nanoscience and technology, so many highly esteemed authors willing to contribute. Sharing our anticipation of a major addition to the literature, they have also captured the excitement of the field itself in each carefully crafted chapter. Along with our painstaking and meticulous volume editors, full credit for the success of this enterprise must go to these individuals, together with our thanks for (largely) adhering to the given deadlines. Lastly, we record our sincere thanks and appreciation for the skills and professionalism of the numerous Elsevier staff who have been involved in this project, notably Fiona Geraghty, Megan Palmer and Greg Harris, and especially Donna De Weerd-Wilson who has steered it through from its inception. We have greatly enjoyed working with them all, as we have with each other.

In Single Molecule Studies of Proteins, expert researchers discuss the successful application of single-molecule techniques to a wide range of biological events, such as the imaging and mapping of cell surface receptors, the analysis of the unfolding and folding pathways of single proteins, the analysis interaction forces between biomolecules, the study of enzyme catalysis or the visualization of molecular motors in action. The chapters are aimed at established investigators and post-doctoral researchers in the life sciences wanting to pursue research in the various areas in which single-molecule approaches are important; this volume also remains accessible to advanced graduate students seeking similar research goals.

Nucleic acids are the fundamental building blocks of DNA and RNA and are found in virtually every living cell. Molecular biology is a branch of science that studies the physicochemical properties of molecules in a cell, including nucleic acids, proteins, and enzymes. Increased understanding of nucleic acids and their role in molecular biology will further many of the biological sciences including genetics, biochemistry, and cell biology. Progress in Nucleic Acid Research and Molecular Biology is intended to bring to light the most recent advances in these overlapping disciplines with a timely compilation of reviews comprising each volume. Follow the new editor-in-chief, P. Michael Conn, as he introduces this second thematic volume in the series – an in-depth aid to researchers who are looking for the best techniques and tools for understanding the complexities of protein folding Understand the advantages of protein folding over other therapeutic approaches and see how protein folding plays a critical role in the development of diseases such as Alzheimer’s and diabetes Decipher the rules of protein folding through compelling and timely reviews combined with chapters written by international authors in engineering, biochemistry, physics and computer science

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