Gotowe bibliografie tematyczne / Biomolecular systems

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Gotowa bibliografia na temat „Biomolecular systems”

Autor: Grafiati

Data publikacji: 6 września 2023

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Artykuły w czasopismach na temat "Biomolecular systems"

Miró, Jesús M., and Alfonso Rodríguez-Patón. "Biomolecular Computing Devices in Synthetic Biology." International Journal of Nanotechnology and Molecular Computation 2, no. 2 (2010): 47–64. http://dx.doi.org/10.4018/978-1-59904-996-0.ch014.

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Synthetic biology and biomolecular computation are disciplines that fuse when it comes to designing and building information processing devices. In this chapter, we study several devices that are representative of this fusion. These are three gene circuits implementing logic gates, a DNA nanodevice and a biomolecular automaton. The operation of these devices is based on gene expression regulation, the so-called competitive hybridization and the workings of certain biomolecules like restriction enzymes or regulatory proteins. Synthetic biology, biomolecular computation, systems biology and standard molecular biology concepts are also defined to give a better understanding of the chapter. The aim is to acquaint readers with these biomolecular devices born of the marriage between synthetic biology and biomolecular computation.

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Katrusiak, Andrzej, Michalina Aniola, Kamil Dziubek, Kinga Ostrowska, and Ewa Patyk. "Biomolecular systems under pressure." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C1188. http://dx.doi.org/10.1107/s2053273314088111.

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Biological systems are often regarded as the ultimate goal of all knowledge in this respect that they can provide the clue for understanding the origin of life and the means for improving the life conditions and healthcare. Hence the interest in high-pressure behavior of organic and biomolecular systems. Such simple organic systems were among the first structural studies at high pressure at all. They included chloroform by Roger Fourme in 1968 [1] and benzene by Piermarini et al. in 1969, still with the use of photographic technique. The efficient studies on bio-macromolecular crystals had to wait for several decades till synchrotron radiation became more accessible and Roger Fourme again stood in the avant-garde of these studies [2]. At the turn of centuries his innovations in the laboratory equipment and experimental setup let him exploring high-pressure conformations of proteins, viral capsids and the double-helix molecular architecture in nucleic acids. These directions of high-pressure studies are continued for simple and macromolecular systems of biological importance. Recently new surprising facts were revealed about the compression of urea, sucrose, and other organic compounds, as well as of macromolecular crystals. Sugars are the main energy carriers for animals as well as building blocks in the living tissue, they are also ideal models for studying pressure-induced changes of OH···O and CH···O interactions. Different types of transformations occur in compressed urea, the first organic compound synthesized in laboratory. Hen egg-white lysozyme was investigated at moderate pressure in a beryllium vessel and the compression of both tetragonal and orthorhombic modifications were measured to 1.0 GPa in a DAC; the high-pressure structure of the tetragonal form was determined and refined at still higher pressure by Fourme et al. [3] Can high pressure provide information about the remarkable polymorphism of lysozyme?

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Niranjan, Vidya, Purushotham Rao, Akshay Uttarkar, and Jitendra Kumar. "Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS." PLOS ONE 18, no. 8 (2023): e0288264. http://dx.doi.org/10.1371/journal.pone.0288264.

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Coarse-grained simulations have emerged as a valuable tool in the study of large and complex biomolecular systems. These simulations, which use simplified models to represent complex biomolecules, reduce the computational cost of simulations and enable the study of larger systems for longer periods of time than traditional atomistic simulations. GROMACS is a widely used software package for performing coarse-grained simulations of biomolecules, and several force fields have been developed specifically for this purpose. In this protocol paper, we explore the advantages of using coarse-grained simulations in the study of biomolecular systems, focusing specifically on simulations performed using GROMACS. We discuss the force fields required for these simulations and the types of research questions that can be addressed using coarse-grained simulations. We also highlight the potential benefits of coarse-grained simulations for the development of new force fields and simulation methodologies. We then discuss the expected results from coarse-grained simulations using GROMACS and the various techniques that can be used to analyze these results. We explore the use of trajectory analysis tools, as well as thermodynamic and structural analysis techniques, to gain insight into the behavior of biomolecular systems.

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Emenecker, Ryan J., Alex S. Holehouse, and Lucia C. Strader. "Biological Phase Separation and Biomolecular Condensates in Plants." Annual Review of Plant Biology 72, no. 1 (2021): 17–46. http://dx.doi.org/10.1146/annurev-arplant-081720-015238.

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A surge in research focused on understanding the physical principles governing the formation, properties, and function of membraneless compartments has occurred over the past decade. Compartments such as the nucleolus, stress granules, and nuclear speckles have been designated as biomolecular condensates to describe their shared property of spatially concentrating biomolecules. Although this research has historically been carried out in animal and fungal systems, recent work has begun to explore whether these same principles are relevant in plants. Effectively understanding and studying biomolecular condensates require interdisciplinary expertise that spans cell biology, biochemistry, and condensed matter physics and biophysics. As such, some involved concepts may be unfamiliar to any given individual. This review focuses on introducing concepts essential to the study of biomolecular condensates and phase separation for biologists seeking to carry out research in this area and further examines aspects of biomolecular condensates that are relevant to plant systems.

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Wang, Li, Coucong Gong, Xinzhu Yuan, and Gang Wei. "Controlling the Self-Assembly of Biomolecules into Functional Nanomaterials through Internal Interactions and External Stimulations: A Review." Nanomaterials 9, no. 2 (2019): 285. http://dx.doi.org/10.3390/nano9020285.

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Biomolecular self-assembly provides a facile way to synthesize functional nanomaterials. Due to the unique structure and functions of biomolecules, the created biological nanomaterials via biomolecular self-assembly have a wide range of applications, from materials science to biomedical engineering, tissue engineering, nanotechnology, and analytical science. In this review, we present recent advances in the synthesis of biological nanomaterials by controlling the biomolecular self-assembly from adjusting internal interactions and external stimulations. The self-assembly mechanisms of biomolecules (DNA, protein, peptide, virus, enzyme, metabolites, lipid, cholesterol, and others) related to various internal interactions, including hydrogen bonds, electrostatic interactions, hydrophobic interactions, π–π stacking, DNA base pairing, and ligand–receptor binding, are discussed by analyzing some recent studies. In addition, some strategies for promoting biomolecular self-assembly via external stimulations, such as adjusting the solution conditions (pH, temperature, ionic strength), adding organics, nanoparticles, or enzymes, and applying external light stimulation to the self-assembly systems, are demonstrated. We hope that this overview will be helpful for readers to understand the self-assembly mechanisms and strategies of biomolecules and to design and develop new biological nanostructures or nanomaterials for desired applications.

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Smith, Paul E., and B. Montgomery Pettitt. "Modeling Solvent in Biomolecular Systems." Journal of Physical Chemistry 98, no. 39 (1994): 9700–9711. http://dx.doi.org/10.1021/j100090a002.

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Rhodes, William. "Coferent dynamics in biomolecular systems." Journal of Molecular Liquids 41 (October 1989): 165–80. http://dx.doi.org/10.1016/0167-7322(89)80076-5.

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Rowe, Rhianon K., and P. Shing Ho. "Relationships between hydrogen bonds and halogen bonds in biological systems." Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials 73, no. 2 (2017): 255–64. http://dx.doi.org/10.1107/s2052520617003109.

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The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds.

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Wang, Yue, Lei Ren, Hongzhen Peng, Linjie Guo, and Lihua Wang. "DNA-Programmed Biomolecular Spatial Pattern Recognition." Chemosensors 11, no. 7 (2023): 362. http://dx.doi.org/10.3390/chemosensors11070362.

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Molecular recognition based on non-covalent interactions between two or more molecules plays a crucial role in biological systems. Specific biological molecule recognition has been widely applied in biotechnology, clinical diagnosis, and treatment. The efficiency and affinity of molecular recognition are greatly determined by the spatial conformation of biomolecules. The designability of DNA nanotechnology makes possible the precise programming of the spatial conformation of biomolecules including valency and spacing, further achieving spatial pattern recognition regulation between biomolecules. This review summarizes recent achievements with DNA-based molecular spatial pattern recognition systems, the important factors affecting spatial pattern recognition, and their applications in biosensing, bioimaging, and targeted therapy. The future challenges in and development of this field are discussed and prospected. This review will provide valuable guidance for the creation of new DNA tools to enhance the efficiency and specificity of biomolecular recognition.

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Ren, Pengyu, Jaehun Chun, Dennis G. Thomas, et al. "Biomolecular electrostatics and solvation: a computational perspective." Quarterly Reviews of Biophysics 45, no. 4 (2012): 427–91. http://dx.doi.org/10.1017/s003358351200011x.

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AbstractAn understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

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