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With the huge increase in available data on the DNA sequences of proteins, there is a growing need to understand and characterize how proteins fold into their biologically active native states and the basis for the stability of these states. In Protein Structure, Stability, and Folding, Kenneth P. Murphy and a panel of internationally recognized investigators describe some of the newest experimental and theoretical methods for investigating these critical events and processes. Among the techniques discussed are the many methods for calculating aspects of protein stability and dynamics from knowledge of the structure, for calculating conformational entropy, and for performing molecular dynamics simulations of protein unfolding. New experimental approaches presented include the use of co-solvents, novel applications of hydrogen exchange techniques, temperature-jump methods for looking at folding events, and new strategies for mutagenesis experiments. Unique in its powerful combination of theory and practice, Protein Structure, Stability, and Folding offers protein and biophysical chemists the means to gain a more comprehensive understanding of this complex area by detailing many of the major innovative techniques in use today.

Protein folding. --- Proteins --- Conformation. --- Protein conformation --- Folding of proteins --- Folding --- Conformation --- Biochemistry. --- Biochemistry, general. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Composition --- Protein folding --- Protein Conformation --- Protein Folding --- Structure-Activity Relationship --- 577.122 --- Protein Folding, Globular --- Folding, Globular Protein --- Folding, Protein --- Foldings, Globular Protein --- Foldings, Protein --- Globular Protein Folding --- Globular Protein Foldings --- Protein Foldings --- Protein Foldings, Globular --- Proteostasis --- Protein Multimerization --- Intrinsically Disordered Proteins --- Conformation, Protein --- Conformations, Protein --- Protein Conformations --- 577.122 Protein metabolism --- Protein metabolism --- Relationship, Structure-Activity --- Relationships, Structure-Activity --- Structure Activity Relationship --- Structure-Activity Relationships --- chemistry --- PROTEINS --- PROTEIN FOLDING --- CONFORMATION

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Recent major advances in our understanding of modulating protein functions has led to the development of new methods and algorithms to predict and decipher how amino acid sequences shape three-dimensional structures. Protein Design: Methods and Applications presents the most up-to-date protein design and engineering strategies so that readers can undertake their own projects with a maximum chance of success. The authors present integrated computational approaches that require various degrees of computational complexity, and the major accomplishments that have been achieved in the design and structural characterization of helical peptides and proteins. Other topics of discussion include: design of structural elementary motifs, entire proteins, and interfaces of protein complexes, and of amyloidogenic polypeptides and amyloid inhibitors. Authoritative and cutting-edge, Protein Design: Methods and Applications will be of major interest to protein scientists, biochemists, and all experimentalists selecting the strategy most adaptable for their design problem.

Protein engineering --- Protein Engineering --- Proteins --- Protein Conformation --- Protein Folding --- methods --- chemistry --- Protein engineering. --- Biophysical Processes --- Biophysical Phenomena --- Engineering, Protein --- Protein design --- Proteins. --- Proteids --- Biomolecules --- Polypeptides --- Proteomics --- Biochemical engineering --- Genetic engineering --- Design --- Biochemistry. --- Biochemistry, general. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Biology --- Chemistry --- Medical sciences --- Composition --- 577.122 --- 577.122 Protein metabolism --- Protein metabolism --- Protein Folding, Globular --- Folding, Globular Protein --- Folding, Protein --- Foldings, Globular Protein --- Foldings, Protein --- Globular Protein Folding --- Globular Protein Foldings --- Protein Foldings --- Protein Foldings, Globular --- Proteostasis --- Protein Multimerization --- Intrinsically Disordered Proteins --- Conformation, Protein --- Conformations, Protein --- Protein Conformations --- Protein Engineering - methods --- Proteins - chemistry

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Disordered proteins are relatively recent newcomers in protein science. They were first described in detail by Wright and Dyson, in their J. Mol. Biol. paper in 1999. First, it was generally thought for more than a decade that disordered proteins or disordered parts of proteins have different amino acid compositions than folded proteins, and various prediction methods were developed based on this principle. These methods were suitable for distinguishing between the disordered (unstructured) and structured proteins known at that time. In addition, they could predict the site where a folded protein binds to the disordered part of a protein, shaping the latter into a well-defined 3D structure. Recently, however, evidence has emerged for a new type of disordered protein family whose members can undergo coupled folding and binding without the involvement of any folded proteins. Instead, they interact with each other, stabilizing their structure via “mutual synergistic folding” and, surprisingly, they exhibit the same residue composition as the folded protein. Increasingly more examples have been found where disordered proteins interact with non-protein macromolecules, adding to the already large variety of protein–protein interactions. There is also a very new phenomenon when proteins are involved in phase separation, which can represent a weak but functionally important macromolecular interaction. These phenomena are presented and discussed in the chapters of this book.

Research & information: general --- Biology, life sciences --- intrinsically disordered proteins --- epiproteome --- disordered protein platform --- molecular recognition feature --- post-translational modifications --- physiological homeostasis --- stress response --- RIN4 --- p53 --- molecular machines --- intrinsically disordered protein --- membrane-less organelle --- neurodegenerative disease --- p300 HAT acetylation --- post-translational modification --- protein aggregation --- Tau fibrillation --- intrinsically disorder proteins --- disorder-to-order regions --- protein–RNA interactions --- unstructured proteins --- conformational plasticity --- disordered protein --- folding --- ribosomal protein --- spectroscopy --- protein stability --- temperature response --- protein thermostability --- salt bridges --- meta strategy --- dual threshold --- significance voting --- decision tree based artificial neural network --- protein intrinsic disorder --- intrinsic disorder --- intrinsic disorder prediction --- intrinsically disordered region --- protein conformation --- transcriptome --- RNA sequencing --- Microarray --- differentially regulated genes --- gene ontology analysis --- functional analysis --- intrinsically disordered --- structural disorder --- correlated mutations --- co-evolution --- evolutionary couplings --- residue co-variation --- interaction surface --- residue contact network --- dehydron --- homodimer --- hydrogen bond --- inter-subunit interaction --- ion pair --- mutual synergistic folding --- solvent-accessible surface area --- stabilization center --- MLL proteins --- MLL4 --- lncRNA --- HOTAIR --- MEG3 --- leukemia --- histone lysine methyltransferase --- RNA binding --- protein --- hydration --- wide-line 1H NMR --- secretion --- immune --- extracellular --- protein-protein interaction --- structural domain --- evolution --- transcription factors --- DNA-protein interactions --- Sox2 sequential DNA loading --- smFRET --- DNA conformational landscape --- sequential DNA bending --- transcription factor dosage --- oligomer --- N-terminal prion protein --- copper binding --- prion disease mutations --- Nuclear pore complex --- FG-Nups --- phosphorylation --- coarse-grained --- CABS model --- MC simulations --- statistical force fields --- protein structure --- intrinsically disordered proteins (IDPs) --- neurodegenerative diseases --- aggregation --- drugs --- drug discovery --- plant virus --- eIF4E --- VPg --- potyvirus --- molten globule --- fluorescence anisotropy --- protein hydrodynamics

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Fuzzy Logic is a good model for the human ability to compute words. It is based on the theory of fuzzy set. A fuzzy set is different from a classical set because it breaks the Law of the Excluded Middle. In fact, an item may belong to a fuzzy set and its complement at the same time and with the same or different degree of membership. The degree of membership of an item in a fuzzy set can be any real number included between 0 and 1. This property enables us to deal with all those statements of which truths are a matter of degree. Fuzzy logic plays a relevant role in the field of Artificial Intelligence because it enables decision-making in complex situations, where there are many intertwined variables involved. Traditionally, fuzzy logic is implemented through software on a computer or, even better, through analog electronic circuits. Recently, the idea of using molecules and chemical reactions to process fuzzy logic has been promoted. In fact, the molecular word is fuzzy in its essence. The overlapping of quantum states, on the one hand, and the conformational heterogeneity of large molecules, on the other, enable context-specific functions to emerge in response to changing environmental conditions. Moreover, analog input–output relationships, involving not only electrical but also other physical and chemical variables can be exploited to build fuzzy logic systems. The development of “fuzzy chemical systems” is tracing a new path in the field of artificial intelligence. This new path shows that artificially intelligent systems can be implemented not only through software and electronic circuits but also through solutions of properly chosen chemical compounds. The design of chemical artificial intelligent systems and chemical robots promises to have a significant impact on science, medicine, economy, security, and wellbeing. Therefore, it is my great pleasure to announce a Special Issue of Molecules entitled “The Fuzziness in Molecular, Supramolecular, and Systems Chemistry.” All researchers who experience the Fuzziness of the molecular world or use Fuzzy logic to understand Chemical Complex Systems will be interested in this book.

Research & information: general --- Biology, life sciences --- fuzzy logic --- complexity --- chemical artificial intelligence --- human nervous system --- fuzzy proteins --- conformations --- photochromic compounds --- qubit --- protein dynamics --- conformational heterogeneity --- promiscuity --- fuzzy complexes --- higher-order structures --- protein evolution --- fuzzy set theory --- artificial intelligence --- GCN4 mimetic --- peptides-DNA --- E:Z photoisomerization --- conformational fuzziness --- photoelectrochemistry --- wide bandgap semiconductor --- artificial neuron --- in materio computing --- neuromorphic computing --- intrinsically disordered protein --- intrinsically disordered protein region --- liquid-liquid phase transition --- protein-protein interaction --- protein-nucleic acid interaction --- proteinaceous membrane-less organelle --- fuzzy complex. --- d-TST --- activation energy --- Transitivity plot --- solution kinetic --- Maxwell-Boltzmann path --- Euler's formula for the exponential --- activation --- transitivity --- transport phenomena --- moonlighting proteins --- intrinsically disordered proteins --- metamorphic proteins --- morpheeins --- fuzzy logic --- complexity --- chemical artificial intelligence --- human nervous system --- fuzzy proteins --- conformations --- photochromic compounds --- qubit --- protein dynamics --- conformational heterogeneity --- promiscuity --- fuzzy complexes --- higher-order structures --- protein evolution --- fuzzy set theory --- artificial intelligence --- GCN4 mimetic --- peptides-DNA --- E:Z photoisomerization --- conformational fuzziness --- photoelectrochemistry --- wide bandgap semiconductor --- artificial neuron --- in materio computing --- neuromorphic computing --- intrinsically disordered protein --- intrinsically disordered protein region --- liquid-liquid phase transition --- protein-protein interaction --- protein-nucleic acid interaction --- proteinaceous membrane-less organelle --- fuzzy complex. --- d-TST --- activation energy --- Transitivity plot --- solution kinetic --- Maxwell-Boltzmann path --- Euler's formula for the exponential --- activation --- transitivity --- transport phenomena --- moonlighting proteins --- intrinsically disordered proteins --- metamorphic proteins --- morpheeins

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Protein folding --- RNA --- Biomolecules --- Protein Engineering. --- Protein Folding. --- Proteins --- Protéines --- ARN --- Biomolécules --- Conformation --- Design --- analysis. --- Repliement --- Protein Folding, Globular --- Folding, Globular Protein --- Folding, Protein --- Foldings, Globular Protein --- Foldings, Protein --- Globular Protein Folding --- Globular Protein Foldings --- Protein Foldings --- Protein Foldings, Globular --- Genetic Engineering, Protein --- Proteins, Genetic Engineering --- Genetic Engineering of Proteins --- Engineering, Protein --- Engineering, Protein Genetic --- Protein Genetic Engineering --- Biological molecules --- Ribonucleic acid --- Ribose nucleic acid --- Folding of proteins --- Folding --- Protein Engineering --- Protein Folding --- analysis --- Gene Products, Protein --- Gene Proteins --- Protein Gene Products --- Proteins, Gene --- Molecular Mechanisms of Pharmacological Action --- Proteostasis --- Protein Multimerization --- Intrinsically Disordered Proteins --- Genetic Engineering --- Directed Molecular Evolution --- DNA Shuffling --- Molecular Farming --- Molecules --- Molecular biology --- Nucleic acids --- Ribose --- Protéines --- Biomolécules --- Protein folding. --- Protein --- Protein engineering. --- Technologie des protéines. --- Protein design --- Biochemical engineering --- Genetic engineering --- Conformació de proteïnes. --- Enginyeria de proteïnes. --- Revistes electròniques. --- Enginyeria de proteïnes --- Proteïnes --- Biomolècules --- Anàlisi --- Disseny --- Conformació