The book contains articles highlighting the rapidly evolving field of protein nucleic acid interactions. Since then, researchers have used a variety of in vitro and in vivo assays to demonstrate that proteins interact with dna and rna to influence the structure and. Overview of proteinnucleic acid interactions thermo. Steitz skip to main content accessibility help we use cookies to distinguish you from other users and to provide you with a better experience on our websites. Other molecules can modulate the conversion of the normal prpc into the pathological conformer prpsc, but the identity and mechanisms of action of the key physiological factors remain unclear.
The structural biology of protein nucleic acid interactions is in some ways a mature field and in others in its infancy. Despite this wide variation, the interfaces in complexes of transcription factors with doublestranded dna could be broken up. Buy proteinnucleic acids interactions volume 91 advances in protein chemistry and structural biology volume 91 on free shipping on qualified orders. No standard method of depicting these interactions has existed until now, often making it difficult to compare interactions in different structures. One of the main concerns in the applications of the sfm to study biological structures in general, and proteinnucleic acid assemblies. Correll, dept of biochemistry and molecular biology, rosalind franklin university, north chicago, il, usa quadruplex nucleic acids. Changlin liu, yong zhang, in advances in protein chemistry and structural biology, 2011. Structural studies of proteinnucleic acid interactions. Proteinnucleic acids interactions, volume 91 1st edition. Current opinion in structural biology catalysis and. Prospective graduate students should have adequate training in chemistry and biology. Dept of structural and chemical biology at icahn school of. The program can be used by both the crystallographer or nmr spectroscopist for analysing a newly solved structure and by other investigators studying protein nucleic acid structures in general. Structures of cas9 orthologs reveal both the conserved and.
The new scowlp comprises its previous structural classification of all protein binding regions of the pdb at protein family level, including protein peptide and watermediated interactions, which has been enhanced by the inclusion of protein nucleic acid and protein saccharide interactions. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those. The proteins featured in this issue face challenges that are different from those of simply reading the dna sequence. A good understanding on the mechanisms of both nucleic acid proteins interactions and nucleic acidmediated protein oligomerization or aggregation will help us not only further explore many important biological processes including selfassembly of viral nanoparticles and virus infection, but also manipulate selfassembly of protein nanostructures. Feb 01, 2001 read proteinnucleic acid interactions, current opinion in structural biology on deepdyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips. Structural biology chapter 3 structural basis for sequencespecific dna recognition by transcription factors and their complexes. Proteinnucleic acid interactions by helen berman overdrive. Recent developments in force fields, simulations of enzyme catalysis, protein ligand, protein protein, and protein nucleic acid noncovalent interactions wei wang, oreola donini, carolina m. A detailed computational analysis of 32 proteinrna complexes is presented. Individual chapters demonstrate the diversity of biological systems to which protein nucleic recognition is of central importance.
Elucidating the roles that proteinnucleic acid complexes play in the regulation of transcription, translation, dna replication, repair and recombination, rna processing and translocation continues to revolutionize our understanding of cell biology, normal cell development and the mechanisms of disease. Proteinnucleic acid interactions thermo fisher scientific uk. Proteinnucleic acid complex structure prediction raymond zhang department of computer science and engineering department of biology university of washington december 16th, 20 1. The database provides various physicochemical features of proteinnucleic acid interface such as size, shape, residue propensity, secondary structure composition and intermolecular interactions. Proteinnucleic acid interactions journal of biological chemistry. Dept of structural and chemical biology at icahn school of medicine at mount sinai, new york. We summarize important information for designing novel potent drugs and for targeting nucleic acids and protein nucleic acid complexes to treat cancers and overcome the drugresistant problems. There are chapters on the interaction of small proteins with dna and rna as well as on chromatin organization. Proteinnucleic acid interactions catalysis and regulation. Proteinprotein interaction and quaternary structure. Sequencespecific dnabinding proteins play key roles in several different dna regulatory activities, including replication, recombination, repair and transcription.
Proteinnucleic acid interactions the expanding role of. A structural analysis article pdf available in nucleic acids research 294. Feb 26, 2020 nucleic acid, naturally occurring chemical compound that is capable of being broken down to yield phosphoric acid, sugars, and organic bases. Structural studies of proteinnucleic acid interaction. The infectious agent of transmissible spongiform encephalopathies tse is believed to comprise, at least in part, the prion protein prp. Protein nucleic acid interactions, edited by fred allain, martin jinek. Proteinnucleic acid interaction edited by wolfram saenger and udo heinemann, macmillan press, 1989. Proteinnucleic acid interactions, edited by stephen cusack and christoph muller.
Structural biology of supramolecular assemblies by magicangle spinning nmr spectroscopy caitlin m. The structural biology of proteinnucleic acid interactions is in some ways a mature field and in others in its infancy. Proteinnucleic acid interactions structural biology. Prp can bind to nucleic acids with relatively high affinity. Dnaprotein interactions, structural studies of protein. Catalysis and regulation, edited by philip cole, andrea mattevi. Thermo scientific offers complete and easytouse for nonradioactive labeling of dna and rna probes in 0. We analyzed the atomic models of 75 xray structures of protein. Chemical and structural biology of nucleic acids and protein. Proteinnucleic acid interactions article in current opinion in structural biology 121. For more complex assemblies, using a different approach, it is possible to gain information about subcomplexes and even the spatial arrangement of proteins in macromolecular machines.
Structure and function analysis of proteinnucleic acid. Abstract this paper describes the design and construction of a program called pna, short for proteinnucleic acid interactions. Proteinnucleic acid interactions are the basis for the regulation of transcription, translation, replication, virus. Highresolution structures of protein dna complexes have been studied since the mid 1980s and a vast array of such structures has now been determined, but surprising and novel structures still appear quite frequently. The distribution of h bonds between dna and aminoacid atoms in proteindna crystal complexes depends upon sequence. A computational analysis of chemical and physical properties of nucleic acid binding sites on proteins, including the size, polarity and packing is described. Dnaprotein interactions, structural studies of proteinnucleic acid interactions by andrew travers. Proteinnucleic acid interactions, current opinion in. Overview of proteinnucleic acid interactions thermo fisher. Current opinion in structural biology proteinnucleic acid. Pdf our knowledge of interactions between proteins and nucleic acids is still rather limited.
Folding and bindingproteinnucleic acid interactions. Volume 22, issue 1, pages 1126 february 2012 download full issue. Structural biology of supramolecular assemblies by magic. Protein nucleic acid interaction an overview sciencedirect topics. Structural insights into the interaction between prion. Chapter 3 proteinnucleic acid interactions rsc publishing. Proteinnucleic acids interactions volume 91 advances. While each of these specific aspects of protein nucleic acid interactions has been studied previously, these different aspects have just recently begun to be considered together. A program to generate schematic diagrams of protein. One of the largest and most diverse classes of dnabinding proteins are the transcriptional regulators that bind dna to initiate mrna. Protein nucleic acid interactions protein nucleic acid interactions phillips, simon e. Articles in press latest issue article collections all issues. Bipa is a database for proteinnucleic acid interactions in 3d structures.
Proteins interact with dna and rna through similar physical forces, which include electrostatic interactions salt bridges, dipolar interactions hydrogen bonding, hbonds, entropic effects hydrophobic interactions and dispersion forces base stacking. Iv selfassembly of protein nanostructures in the presence of. By mass measuring complexes a direct determination of the stoichiometry of protein nucleic acid interactions is revealed. Purchase proteinnucleic acids interactions, volume 91 1st edition. In addition the distribution of observed atomatom contacts in the protein nucleic acid complexes have been calculated and compared to expected values. The interface area measured the extent of contact between the protein and nucleic acid. Specific noncovalent interactions stabilize the structure of macromolecular assemblies.
Highresolution structures of proteindna complexes have been studied since the mid 1980s and a vast array of such structures has now been determined, but surprising and novel structures still appear quite frequently. Such important cellular processes, as replication, transcription, translation, repair and transport of nucleic acids from the nucleus to the cytoplasm, involve specific protein nucleic acid complexes. Proteinnucleic acid interactions article in current opinion in structural biology 111. Nucleic acids are the main informationcarrying molecules of the cell and play a central role in determining the inherited characteristics of every living thing. Structural biology of telomerase and its interaction at telomeres. Folding and bindingprotein nucleic acid interactions. As elsewhere in structural biology, the trend is towards ever larger, more. Protein nucleic acid interactions i 354pos board b140 singlemolecule in vitro and livecell studies of allostery through dna shasha chong 1, sangjin kim, erik brostrmer, dong xing2, hao ge,3, xiaodong su 2, yujie sun, x.
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