Affiliation: University of California
- Relative pKa values from first-principles molecular dynamics: the case of histidine deprotonationIvaylo Ivanov
Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104 6323, USA
J Phys Chem B 110:6365-71. 2006..Additional analysis in terms of electron localization functions provided valuable insight into the nature of the deprotonation reaction...
- Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IVIvaylo Ivanov
Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093 0365, USA
Proc Natl Acad Sci U S A 104:1465-70. 2007..This qualitative finding supports the notion that structural rearrangements in the active sites of multinuclear enzymes are integral to biological function...
- Characterization of nonbiological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all-atom molecular dynamicsIvaylo Ivanov
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
J Am Chem Soc 128:1778-9. 2006..Our results indicate sensitive dependence of the overall shape on the sequence, suggesting that experimentally observed changes in activity can be correlated with particular sequences, providing an avenue for rational design...
- Proliferating cell nuclear antigen loaded onto double-stranded DNA: dynamics, minor groove interactions and functional implicationsIvaylo Ivanov
Department of Chemistry and Biochemistry, Howard Hughes Medical Institute and Center for Theoretical Biological Physics, University of California San Diego, 9500 Gilman Drive La Jolla, CA 92093 0365, USA
Nucleic Acids Res 34:6023-33. 2006....
- Barriers to ion translocation in cationic and anionic receptors from the Cys-loop familyIvaylo Ivanov
Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093 0365, USA
J Am Chem Soc 129:8217-24. 2007..Thus, the overall electrostatics and the presence of rings of charged residues at the entrance and exit of the channels were sufficient to explain the experimentally observed anion and cation selectivity...
- Controlling the shape and flexibility of arylamides: a combined ab initio, ab initio molecular dynamics, and classical molecular dynamics studyVojislava Pophristic
Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania 19104, USA
J Phys Chem B 110:3517-26. 2006..Ab initio molecular dynamics simulation of the arylamide independently confirms the degree of flexibility we obtain by classical molecular dynamics when newly developed torsional potentials are used...
- Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptorXiaolin Cheng
Howard Hughes Medical Institute, National Science Foundation Center for Theoretical Biophysics, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
Biophys J 93:2622-34. 2007..The resulting concerted motion causes a downward shift of the M2 helices that disrupts a hydrophobic girdle formed by 9' and 13' residues...
- Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain molecular dynamicsSteve O Nielsen
Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Biophys J 87:2107-15. 2004..This mechanism appears to be a viable pathway for the experimentally observed Lalpha-to-inverse hexagonal (HII) peptide-induced phase transition...
- The design and evaluation of heparin-binding foldamersSungwook Choi
Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104 6323, USA
Angew Chem Int Ed Engl 44:6685-9. 2005
- Characterizing loop dynamics and ligand recognition in human- and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculationsRommie E Amaro
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, California 92093 0365, USA
J Am Chem Soc 131:4702-9. 2009..We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains...
- Ab initio calculations of intramolecular parameters for a class of arylamide polymersSatyavani Vemparala
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
J Comput Chem 27:693-700. 2006..The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers...
- Dynamics of the acetylcholinesterase tetramerAlemayehu A Gorfe
Department of Chemistry and Biochemistry, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92093 0365, USA
Biophys J 94:1144-54. 2008....
- Dynamical flexibility and proton transfer in the arginase active site probed by ab initio molecular dynamicsIvaylo Ivanov
Center for Molecular Modeling, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104 6323, USA
J Am Chem Soc 127:4010-20. 2005..In addition, constrained molecular dynamics permitted us to compare the deprotonation free energy of the bridging nucleophile in the case of native versus metal-depleted arginase...
- Deprotonation of a histidine residue in aqueous solution using constrained ab initio molecular dynamicsIvaylo Ivanov
Center for Molecular Modeling and Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia 19104 6323, USA
J Am Chem Soc 124:13380-1. 2002..A possible transition state for the deprotonation has also been identified. Analysis of the electron localization function indicates that the proton transfer along the selected reaction path is not a fully concerted process...
- Recognition of the ring-opened state of proliferating cell nuclear antigen by replication factor C promotes eukaryotic clamp-loadingJohn A Tainer
Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB4, La Jolla, California 92037, USA
J Am Chem Soc 132:7372-8. 2010..RFC does not appreciably destabilize the closed state of PCNA. Instead, the function of the clamp loader is dependent on the selective stabilization of the open conformation of the clamp...
- Molecular-dynamics simulations of ELIC-a prokaryotic homologue of the nicotinic acetylcholine receptorXiaolin Cheng
Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
Biophys J 96:4502-13. 2009..Finally, the simulation of an ELIC mutant substantiates the important role of F246 on the stability, hydration and possibly function of the ELIC channel...
- First principles computational study of the active site of arginaseIvaylo Ivanov
Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
Proteins 54:1-7. 2004..This is reflected in certain structural variability present in our models and is also consistent with recent experimental findings. Finally, implications of our findings for the biological function of the enzyme are delineated...
- Kinetic studies and molecular modelling attribute a crucial role in the specificity and stereoselectivity of penicillin acylase to the pair ArgA145-ArgB263Maya Guncheva
Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
Eur J Biochem 271:2272-9. 2004..This indicates a crucial role of the specified arginine pair in the substrate- and stereoselectivity of penicillin acylase...
- Escherichia coli mRNAs with strong Shine/Dalgarno sequences also contain 5' end sequences complementary to domain # 17 on the 16S ribosomal RNAAshkan Golshani
Department of Biology, College of Natural Sciences, Carleton University, 1125 Colonel By Drive, Ottawa, Ont, Canada K1S 5B6
Biochem Biophys Res Commun 316:978-83. 2004..The results suggest that mRNA sequences with complementarity to box-17 of 16S rRNA may function as enhancers for translation in E. coli...
- Synthetic mimics of antimicrobial peptidesAbhigyan Som
Department of Polymer Science and Engineering, University of Massachusetts, Amherst, 120 Governors Drive, Amherst, MA 01003, USA
Biopolymers 90:83-93. 2008..The results on SMAMPs are not only extremely promising for novel antibiotics, but also provide an optimistic picture for the greater challenge of general proteomimetics...
- Non-Shine-Dalgarno initiators of translation selected from combinatorial DNA librariesVihren Kolev
Department of Gene Regulations, Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
J Mol Microbiol Biotechnol 5:154-60. 2003..70, 2.06, 2.12 and 1.32 times, respectively, higher than that of the SD-bearing construct...