| Título: | Measuring the shapes of macromolecules – and why it matters |
| Autores: |
Li, Jie; University of California, Davis Mach, Paul; University of California, Davis Koehl, Patrice; University of California, Davis |
| Fecha: | 2013-12-09 |
| Publicador: | Computacional and structural biotechnology journal |
| Fuente: |
 |
| Tipo: |
info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion Peer-reviewed Article |
| Tema: | No aplica |
| Descripción: | The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing numerical and analytical approaches that solve these problems. We cover in more details our own work in this field, focusing on the alpha shape theory as it provides a unifying mathematical framework that enable the analytical calculations of the surface area and volume of a macromolecule represented as a union of balls, the detection of pockets and cavities in the molecule, and the quantification of contacts between the atomic balls. We have shown that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity. We conclude with a brief description of new challenges for the alpha shape theory in modern structural biology. |
| Idioma: | Inglés |
1 Systems biology and metabolic engineering of Arthrospira cell factories por Klanchui, Amornpan,Vorapreeda, Tayvich,Vongsangnak, Wanwipa,Kannapho, Chiraphan,Cheevadhanarak, Supapon,Meechai, Asawin | 6 The Role of INDY in Metabolic Regulation por Willmes, Diana M; Charité University School of Medicine Berlin,Birkenfeld, Andreas L; Charité University School of Medicine Berlin |
2 Structure-based Methods for Computational Protein Functional Site Prediction por KC, Dukka B; North Carolina A&T State University | 7 The Biochemistry of Vitreoscilla hemoglobin por Stark, Benjamin C.; Illinois Institute of Technology,Dikshit, Kanak L.; Institute of Microbial Technology,Pagilla, Krishna R.; Illinois Institute of Technology |
3 Computer-Aided Protein Directed Evolution: a Review of Web Servers, Databases and other Computational Tools for Protein Engineering por Verma, Rajni; Jacobs University Bremen,Schwaneberg, Ulrich; RWTH Aachen University,Roccatano, Danilo; Jacobs University Bremen | 8 A method to predict edge strands in beta-sheets from protein sequences por Guilloux, Antonin,Caudron, Bernard,Jestin, Jean-Luc |
4 MD simulation studies to investigate iso-energetic conformational behaviour of modified nucleosides m2G and m22G present in tRNA por Bavi, Rohit S,Sambhare, Susmit B,Sonawane, Kailas D; Structural Bioinformatics Unit,
Department of Biochemistry,
Shivaji University, Kolhapur 416 004,
Maharashtra (M.S.), India. | 9 Conformational Sampling in Template-Free Protein Loop Structure Modeling: An Overview por Li, Yaohang; Old Dominion University |
5 Metabolomics in the identification of biomarkers of dietary intake por O’Gorman, Aoife,Gibbons, Helena,Brennan, Lorraine | 10 Development of microorganisms for cellulose-biofuel consolidated bioprocessings: metabolic engineers’ tricks por Mazzoli, Roberto; University of Torino, Italy. |