Download or read book Calcualtion of the Relative Stabilities of Proteins as a Function of Temperature Pressure and Chemical Potentials in Subcellular and Geochemical Environments written by Jeffrey Michael Dick and published by . This book was released on 2007 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Calculation of the Relative Chemical Stabilities of Proteins as a Function of Temperature and Redox Chemistry in a Hot Spring written by Jeffrey M. Dick and published by . This book was released on 2011 with total page 21 pages. Available in PDF, EPUB and Kindle. Book excerpt: Uncovering the chemical and physical links between natural environments and microbial communities is becoming increasingly amenable owing to geochemical observations and metagenomic sequencing. At the hot spring known as Bison Pool in Yellowstone National Park, the cooling of the water in the outflow channel is associated with an increase in oxidation potential estimated from multiple field-based measurements. Representative groups of proteins whose sequences were derived from metagenomic data also exhibit an increase in average oxidation state of carbon in the protein molecules with distance from the hot-spring source. The energetic requirements of reactions to form selected proteins used in the model were computed using amino-acid group additivity for the standard molal thermodynamic properties of the proteins, and the relative chemical stabilities of the proteins were investigated by varying temperature, pH and oxidation state, expressed as activity of dissolved hydrogen. The relative stabilities of the proteins were found to track the locations of the sampling sites when the calculations included a function for hydrogen activity that increases with temperature and is higher, or more reducing, than values consistent with measurements of dissolved oxygen, sulfide and oxidation-reduction potential in the field. These findings imply that spatial patterns in the amino acid compositions of proteins can be linked, through energetics of overall chemical reactions representing the formation of the proteins, to the environmental conditions at this hot spring, even if microbial cells maintain considerably different internal conditions. Further applications of the thermodynamic calculations are possible for other natural microbial ecosystems.
Download or read book Protein Stability and Folding written by Wolfgang Pfeil and published by Springer Science & Business Media. This book was released on 2013-06-29 with total page 524 pages. Available in PDF, EPUB and Kindle. Book excerpt: In 1998, we published the data compilation PROTEIN STABILITY AND FOLDING which covered the data from the early beginnings of thermodynamic studies of protein folding until 1996. Since then, the amount of available thermodynamic data has increased nearly twice. The data constitute very important additions to the information on the protein folding problem, the construction of mutant protein, and the practical application of proteins in various fields. The Supplement covers the period 1997-1999 and is designed to make the vast amount of present data accessible to multidisciplinary research where chemistry, physics, biology, and medicine are involved and also biotechnology, pharmaceutical and food research. At the same time the data could be helpful to identify problems unsolved so far, and to avoid unnecessary duplication of scientific work. The structure of the Supplement is the same as in the previous data compilation. However, some additional data characterizing protein-denaturant interaction and protein unfolding by trifluoroethanol have been added. In that context, some previous data have been reconsidered. The author wishes to thank everyone who provided data, ideas, or even unpublished results. Furthermore, support by the Deutsche Forschungsgemeinschaft (INK 16 BI-I) is gratefully acknowledged. Finally, I would like to thank the staff of Springer Verlag for their efforts and for excellent assistance during the production of the data collections.
Download or read book Thermostable Proteins written by Srikanta Sen and published by CRC Press. This book was released on 2011-10-10 with total page 190 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thermostable Proteins: Structural Stability and Design provides a comprehensive, updated account of the physical basis of enhanced stability of thermophilic proteins and the design of tailor-made thermostable proteins, paving the way for their possible industrial applications. This book is devoted to understanding the survival mechanisms of "thermophilic life forms" at the molecular level with an emphasis on design strategies. The review chapters presented in Thermostable Proteins span a wide range of protein thermostability research. Basic structural, thermodynamic, and kinetic principles are explained and molecular strategies for the adaptation to high temperatures are delineated. In addition, this book covers: Computing and simulation methods in current and future thermostability research, especially in nonempirical situations How rigidity theory is used to improve the thermal adaptation of mesophiles Subtilisin-like serine proteases and their significant engineering applications The state of knowledge concerning structure–function relations and the origins of their structural stability Computational and experimental approaches for the design of proteins with increased thermal stability based on sequences or three-dimensional structures Understanding the molecular basis of how thermostable and hyperthermostable proteins gain and maintain their stability and biological function at high temperatures remains an important scientific challenge. A more detailed knowledge of protein stability not only deepens our understanding of protein structure but also helps in obtaining insights into processes that drive protein activities—folding, unfolding, and misfolding—essential to biological function.
Download or read book Protein Stability and Folding written by Wolfgang Pfeil and published by Springer Science & Business Media. This book was released on 2012-12-06 with total page 662 pages. Available in PDF, EPUB and Kindle. Book excerpt: Protein folding remains one of the most exclusive problems of modern biochemistry. Structure analysis has given access to the wealth of the molecular architecture of pro teins. As architecture needs static calculations, protein structure is always related to thermodynamic factors that govern folding and stability of a particular folded protein over the non-organized polypeptide chain. During the past decades a huge amount of thermodynamic data related to protein folding and stability has been accumulated. The data are certainly of importance in dechiffring the protein folding problem. At the same time, the data can guide the con struction of modified and newly synthesized proteins with properties optimized for particular application. The intention of this book is a generation of a data collection which makes the vast amount of present data accessible for multidisciplinary research where chemistry, phy sics, biology, and medicine are involved and also pharmaceutical and food research and technology. It took several years to compile all the data and the author wishes to thank everyone who provided data, ideas or even unpublished results. The author is, in particular, indebted to Prof. Wadso (Lund, Sweden) and IUPAC's Steering Committee on Bio physical Chemistry. Furthermore, support by the Deutsche Forschungsgemeinschafi (INK 16 AI-I) is acknowledged.
Download or read book Thermostable Proteins written by and published by . This book was released on 2012 with total page 175 pages. Available in PDF, EPUB and Kindle. Book excerpt: Thermostable Proteins: Structural Stability and Design provides a comprehensive, updated account of the physical basis of enhanced stability of thermophilic proteins and the design of tailor-made thermostable proteins, paving the way for their possible industrial applications. This book is devoted to understanding the survival mechanisms of thermophilic life forms at the molecular level with an emphasis on design strategies.The review chapters presented in Thermostable Proteins span a wide range of protein thermostability research. Basic structural, thermodynamic, and kinetic principles are explained and molecular strategies for the adaptation to high temperatures are delineated. In addition, this book covers: computing and simulation methods in current and future thermostability research, especially in nonempirical situations, how rigidity theory is used to improve the thermal adaptation of mesophiles Subtilisin-like serine proteases and their significant engineering applications. The state of knowledge concerning structure function relations and the origins of their structural stability. Computational and experimental approaches for the design of proteins with increased thermal stability based on sequences or three-dimensional structures. Understanding the molecular basis of how thermostable and hyperthermostable proteins gain and maintain their stability and biological function at high temperatures remains an important scientific challenge. A more detailed knowledge of protein stability not only deepens our understanding of protein structure but also helps in obtaining insights into processes that drive protein activities folding, unfolding, and misfolding essential to biological function--Provided by publisher.
Download or read book Protein Stability and Folding written by Wolfgang Pfeil and published by . This book was released on 2001 with total page 521 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Water Interactions written by Vladimir A. Sirotkin and published by Nova Science Publishers. This book was released on 2014 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book is aimed at understanding which molecular parameters control the thermodynamics, structure, and functions of the protein-water systems. Proteins are one of the most important classes of biological molecules. Water binding (hydration or biological water) plays a crucial role in determining the structure, stability, and functions of proteins. Knowledge of processes occurring upon hydration or dehydration of protein macromolecules is very important in biotechnological and pharmaceutical applications of proteins such as their use as biocatalysts, biosensors, and selective adsorbents. There are essential differences between hydration and bulk water surrounding a protein. This means that a characterisation of the hydration of protein macromolecules requires elucidating the effects of both the protein on water and vice versa. Therefore, a quantitative estimation of the protein and water contributions to the thermodynamic functions of binary protein-water systems is of considerable fundamental importance and practical interest. This book describes the basic principles of a novel methodology to investigate the protein-water interactions. This methodology is based on the analysis of the excess thermodynamic functions of mixing. The thermodynamic properties (volume V, enthalpy H, entropy S, heat capacity Cp, and Gibbs free energy G) of a real binary water-protein system can be expressed in terms of the excess functions. They are the difference between the thermodynamic function of mixing in a real system and the value corresponding to an ideal system at the same temperature, pressure and composition. For an ideal system, all excess functions are zero. Deviations of the excess functions from zero indicate the extent to which the studied binary system is non-ideal due to strong specific interactions between components (ie: hydrogen bonding and charge-charge interactions).
Download or read book Protein Stability and Folding written by Bret A. Shirley and published by Taylor & Francis US. This book was released on 1995-03-24 with total page 392 pages. Available in PDF, EPUB and Kindle. Book excerpt: In Protein Stability and Folding: Theory and Practice, world-class scientists present in a single volume a comprehensive selection of hands-on recipes for all of the major techniques needed to understand the conformational stability of proteins, as well as their three-dimensional folding. The distinguished contributors provide clear, step-by-step instructions along with many troubleshooting tips, alternative procedures, and informative explanations about why certain steps are necessary. Even highly skilled researchers will find many time-saving methods. Among the techniques discussed are fluorescent, ultraviolet, and infrared spectroscopy; HPLC peptide mapping; differential scanning calorimetry; and hydrogen exchange. Shirley's Protein Stability and Folding: Theory and Practice will ensure a significant difference in the outcome of your experiments, producing the result desired even for beginners.
Download or read book Stabilizing Protein Function written by Ciarán ÓFágáin and published by Springer. This book was released on 1997-10-17 with total page 224 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides an account of our current knowledge of protein stability. It demonstrates how an understanding of protein stability has emerged from investigations of protein denaturation/inactivation and from studies on stabilizing interactions in proteins. It also describes the stability characteristics of enzymes in nonaqueous media and the special adaptations of thermophilic proteins. Manipulation of protein stability is outlined in chapters on the use of additives, chemical modification of proteins in solution, immobilization, protein engineering and long-term storage of proteins. The book includes numerous case studies and copious references to original research papers and relevant reviews and monographs.
Download or read book Protein Stability and Stabilization Through Protein Engineering written by Yoshiaki Nosoh and published by Ellis Horwood. This book was released on 1991 with total page 234 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Molecular Thermodynamics of Proteins in Aqueous Solutions of Concentrated Electrolyte written by Robin Andrew Curtis and published by . This book was released on 2000 with total page 568 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Protein Structure Stability and Folding written by Kenneth P. Murphy and published by Springer Science & Business Media. This book was released on 2001-04 with total page 272 pages. Available in PDF, EPUB and Kindle. Book excerpt: Stabilization of protein structure (Kenneth P. Murphy). Protein stabilization by naturally occurring osmolytes (D. Wayne Bolen). The thermodynamic linkage between protein structure, stability, and function (Ernesto Freire). Measuring the conformational stability of a protein by Hydrogen Exchange (Beatrice M.P. Huyghues-Despointes, C. Nick Pace, S Walter Englander, and J. Martin Scholtz). Modeling the native state ensemble (Vincent J. Hilser). Conformational entropy in protein folding: a guide to estimating conformational entropy via modeling and computational (Trevor P. Creamer). Turn scanning: experimental and theoretical approaches to the role of turns (Carl Frieden, Enoch S. Huang, and Jay W. Ponder). Laser temperature-jump methods for studying folding dynamics (James Hofrichter). Kinetics of conformational fluctuations by EX1 hydrogen exchange in native proteins (T. Sivaraman and Andrew D. Robertson). Molecular dynamics simulations of protein unfolding/folding (Valerie Daggett).
Download or read book Thermophilic Proteins written by Marina Katava and published by . This book was released on 2016 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Temperature is one of the major factors governing life as demonstrated by the fine tuning of stability and activity of the molecular machinery, proteins in particular. The structural stability and activity of proteins have been often presented as equivalent. However, the thermophilic proteins are stable at ambient condition, but lack activity, the latter recovered only when the temperature increases to match that of the optimal growth condition for the hosting organism. In discussing the protein stability and activity, mechanical rigidity is often used as a relevant parameter, offering a simple and appealing explanation of both the extreme thermodynamic stability and the lack of activity at low temperature. The reality, however, illustrates the complexity of the rigidity/flexibility trade off in ensuring stability and activity through intricate thermodynamic and molecular mechanisms. Here we investigate the problem by studying three study cases. These are used to relate the thermal effects on mechanical properties and the stability and activity of the proteins. For instance, we have probed the thermal activation of functional modes in EF G-domain and Lactate/Malate dehydrogenase mesophilic and thermophilic homologues and verified a “universal” scaling of atomistic fluctuation of the Lysozyme approaching the melting in different environmental conditions. Our conclusions largely rest on an in silico approach, where molecular dynamics and enhanced sampling techniques are utilized, and are often complemented with neutron scattering experiments.
Download or read book Characterization of Pressure and Temperature related Determinants of the Stability of Proteins and Nucleic Acids microform written by David N. (David Noah) Dubins and published by National Library of Canada = Bibliothèque nationale du Canada. This book was released on 2003 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Exploring Kinetic Controlled Protein Solubility Under Physiologically Relevant Conditions written by Hung Hoang Dang and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Proteins are responsible for driving a vast majority of biological processes in the cell. Therefore, it is important that proteins remain mostly folded to carry out their important functions, after transcription-translation. Prior proteome-wide studies showed that proteins in the Escherichia coli proteome are at risk of misfolding and extensive aggregation after translation, especially under cellular or environmental stresses. In addition, aggregates have been shown to be more thermodynamically stable than the native states, for many proteins. Therefore, if misfolding and aggregation in the cell were thermodynamically driven processes, many proteins in the E. coli proteome would spontaneously form aggregates in the cell. Despite a plethora of protein quality control and degradation systems employed by E. coli, it is clear that these systems are energetically expensive and can be overwhelmed, especially if many proteins in the proteome are at risk of thermodynamically driven aggregation. One popular proposed concept in the folding field is that the proteome is kinetically protected from aggregation, avoiding significant reliance on ATP-expensive protein quality control and degradation systems, under cellular conditions. However, there have not been experiments directly proving kinetic stability of proteins relative to aggregation on a proteome-wide scale. Moreover, aggregates are initially formed as soluble non-native oligomers, or soluble aggregates. These soluble aggregates may cause impairments of important biological processes in the cell and can eventually form larger insoluble assemblies. Yet, little is known about how soluble aggregates fit in the life cycle of E. coli proteins. To address the above fascinating biological questions, in this thesis, I will explore the kinetic stability and aggregation of a representative E. coli proteome (A19 cell strain). This Ph.D. thesis includes three Chapters. Chapter 1 includes background information on protein folding and aggregation in the cellular context. In addition, it discusses the importance of proteome-wide studies and the important findings on aggregation from current proteomic analyses and introduces the hypothesis of proteome kinetic stability relative to aggregation. This Chapter serves as the conceptual basis for the subsequent Chapters. Chapter 2 explores the proteome-wide kinetic stability of proteins in E. coli under physiologically relevant conditions. Here, I demonstrate that the free-energy landscape of the E. coli proteome includes extensive insoluble aggregates under physiologically relevant conditions. Further, the soluble and insoluble aggregates can exchange reversibly among each other and the apparent critical concentration for soluble-aggregate formation on a proteome-wide scale is very low (c.a., 0.04 [mu]g/mL). I demonstrate that over 80% of the proteome is kinetically protected from forming these soluble and insoluble aggregates on timescales longer than this organism's doubling time. Using bottom-up proteomics, I report that over 800 E. coli proteins are kinetically stable relative to aggregation regardless of structure, function, and cellular location. Finally, my results show that cytoplasmic/periplasmic molecular chaperones are amongst the most soluble proteins, both at higher temperature and under physiologically relevant conditions. This finding demonstrates that molecular chaperones are extremely robust members of the proteome. Chapter 3 focuses on the development of a novel isotopolog of tryptophan to enhance the sensitivity of NMR spectroscopy and enable monitoring protein behaviors in complex environments. Here, a novel selectively isotopic-labeled tryptophan was synthesized and successfully detected at very low concentrations in buffer and in a complex S30 cell extract (c.a., 20 nM and 1 [mu]M respectively) by low-concentration photochemically induced dynamic nuclear polarization (LC-photo-CIDNP) NMR. Our new selective labeling approach to LC-photo-CIDNP, in combination with existing biophysical analyses, can be utilized to study the effect of heterologous expression. For instance, this Trp isotopolog will enable the monitoring of folding and aggregation of model recombinant proteins within in complex cell-like environments. Overall, I propose that proteome-wide kinetic stability is an effective strategy to maintain a healthy and aggregation-free cellular environment in living systems, without reliance on energetically expensive degradation and disaggregation processes. These results also provide insights into the structural and functional determinants of bacterial kinetic stability and aggregation. In conclusion, it is hoped that the knowledge gained from this work will ultimately benefit the design and discovery of new strategies to prevent protein aggregation in the cell and to improve the shelf life of many protein-based biologics (e.g., monoclonal antibodies, etc).
Download or read book Advances in protein chemistry written by and published by . This book was released on 1959 with total page 520 pages. Available in PDF, EPUB and Kindle. Book excerpt:
