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November 2014
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Biophysics and Biophysical Chemistry Archives

1. Miller MS, Schmidt-Kittler O, Bolduc DM, Brower ET, Chaves-Moreira D, Allaire M, Kinzler KW, Jennings IG, Thompson PE, Cole PA, Amzel LM, Vogelstein B, Gabelli SB. Structural basis of nSH2 regulation and lipid binding in PI3K?. Oncotarget. 2014 Jul 30;5(14):5198-208.

1. Vos SM, Lyubimov AY, Hershey DM, Schoeffler AJ, Sengupta S, Nagaraja V, Berger JM. Direct control of type IIA topoisomerase activity by a chromosomally encoded regulatory protein. Genes Dev. 2014 Jul 1;28(13):1485-97
Key words: Topoisomerase, Enzyme inhibitors, Antibiotics, Gene Regulation, Transcription, Supercoiling, Energy metabolism
http://www.ncbi.nlm.nih.gov/pubmed/24990966

2. Nicola J, Carrasco N, Amzel LM. Physiological sodium concentrations enhance the iodide affinity of the Naþ/I_ symporter. Nature Communications. 2014 June 3. doi:10.1038/ncomms4948
Key words: sodium, iodide
No PMID available

1. Berndsen CE, Wolberger C. New insights into ubiquitin E3 ligase mechanism. Nat Struct Mol Biol. 2014 Apr 4;21(4):301-7. doi: 10.1038/nsmb.2780.
Key words: ubiquitin, E3 ligase, E2 enzyme
http://www.ncbi.nlm.nih.gov/pubmed/24699078

2. Wolberger C. Mechanisms for regulating deubiquitinating enzymes. Protein Sci. 2014 Apr;23(4):344-53. doi: 10.1002/pro.2415.
Key words: deubiquitinating enzymes; UB, UBL, ubiquitin
http://www.ncbi.nlm.nih.gov/pubmed/24403057

1. Harden BJ, Frueh DP. SARA: a software environment for the analysis of relaxation data acquired with accordion spectroscopy. J Biomol NMR. 2014 Feb;58(2):83-99.
Key words: software, accordion spectroscopy
http://www.ncbi.nlm.nih.gov/pubmed/24408364

2. Frueh DP. Practical aspects of NMR signal assignment in larger and challenging proteins. Prog Nucl Magn Reson Spectrosc. 2014 Apr;78C:47-75.
Key words: NMR, proteins
http://www.ncbi.nlm.nih.gov/pubmed/24534088

3. Mustaev A, Malik M, Zhao X, Kurepina N, Luan G, Oppegard LM, Hiasa H, Marks KR, Kerns RJ, Berger JM, Drlica K. Fluoroquinolone-Gyrase-DNA complexes: two modes of drug binding. J Biol Chem. 2014 Feb 4 [Epub ahead of print].
Key words: Antibiotics action, Bacteria, DNA topoisomerase, Enzyme inhibitors, Escherichia coli, Mycobacterium smegmatis, bacterium, cleaved complexes, crosslinking, resistance mutations
http://www.ncbi.nlm.nih.gov/pubmed/24497635

4. Strycharska MS, Arias-Palomo E, Lyubimov AY, Erzberger JP, O'Shea VL, Bustamante CJ, Berger JM. Nucleotide and partner-protein control of bacterial replicative helicase structure and function. Mol Cell. 2013 Dec 26;52(6):844-54.
Key words: DNA replication, Helicase, Primase, Clamp Loader, AAA+ ATPase, RecA
http://www.ncbi.nlm.nih.gov/pubmed/24373746

1. Bleichert F, Balasov M, Chesnokov I, Nogales E, Botchan MR, Berger JM. A Meier-Gorlin syndrome mutation in a conserved C-terminal helix of Orc6 impedes origin recognition complex formation. Elife. 2013 Oct 8;2:e00882.
Key words: DNA replication, Meier-Gorlin syndrome, ORC, origin licensing, origin recognition complex, MCM
http://elife.elifesciences.org/content/2/e00882
PMID: 24137536

2. Vos SM, Lee I, Berger JM. Distinct regions of the Escherichia coli ParC C-terminal domain are required for substrate discrimination by topoisomerase IV. J Mol Biol. 2013 Sep 9;425(17):3029-45.
Key words: DNA topology, topoisomerase, DNA binding
http://www.sciencedirect.com/science/article/pii/S0022283613004208
PMID: 23867279

3. Vos SM, Stewart NK, Oakley MG, Berger JM. Structural basis for the MukB-topoisomerase IV interaction and its functional implications in vivo. EMBO J. 2013 Oct 4. doi:
10.1038/emboj.2013.218. [Epub ahead of print]
Key words: DNA topology, topoisomerase, chromosome segregation, chromosome partitioning, SMC, condensin, cohesin
http://www.nature.com/emboj/journal/vaop/ncurrent/full/emboj2013218a.html
PMID:24097060

1. Wiener R, Dibello AT, Lombardi PM, Guzzo CM, Zhang X, Matunis MJ, Wolberger C.
E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1.
Nat Struct Mol Biol. 2013 Sep;20(9):1033-9. doi: 10.1038/nsmb.2655.
Key words: ubiquitin, enzymes, OTUB1
http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2655.html
PMID: 23955022

2. Yao Y, Belcher J, Berger AJ, Mayer ML, Lau AY. Conformational analysis of NMDA receptor GluN1, GluN2, and GluN3 ligand-binding domains reveals subtype-specific characteristics. Structure. 2013 Oct 8; 21(10):1788-1799.
Key words: Glutamate receptor, NMDA, Computational modeling, X-ray crystallography
http://www.ncbi.nlm.nih.gov/pubmed/23972471

1. Wiener R, Dibello AT, Lombardi PM, Guzzo CM, Zhang X, Matunis MJ, Wolberger C. E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1. Nat Struct Mol Biol. 2013 Sep;20(9):1033-9. doi: 10.1038/nsmb.2655.
Key words: ubiquitin, e2, deubiquitinating enzymes
http://www.nature.com/nsmb/journal/v20/n9/full/nsmb.2655.html
PMID: 23955022

1. Buss JA, Coltharp C, Huang T, Pohlmeyer C, Wang SC, Hatem C, Xiao J. In vivo organization of the FtsZ-ring by ZapA and ZapB revealed by quantitative super-resolution microscopy. Mol Micro. 2013; doi:10.1111/mmi.12331
Key words: FtsZ-ring, ZapA, ZapB, PALM, division
http://onlinelibrary.wiley.com/doi/10.1111/mmi.12331/
abstract;jsessionid=738A4905CB30DCCCE2855CAEED3667BA.d04t02
PMID: 23859153

2. Hensel Z, Weng X, Lagda AC, Xiao J. Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells. PLoS Biol. 2013 Jun;11(6):e1001591.
Key words: Single-Molecule imaging, DNA looping
PMID: 23853547
http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001591

3. Lau AY, Salazar H, Blachowicz L, Ghisi V, Plested AJ, Roux B. A conformational intermediate in glutamate receptor activation. Neuron 2013;79:492-503.
Key words: Glutamate receptor, AMPA, Structural biology, Computational modeling, Electrophysiology
http://www.ncbi.nlm.nih.gov/pubmed/23931998

4. Feng C, Ghosh A, Amin MN, Giomarelli B, Shridhar S, Banerjee A, Fernández-Robledo JA, Bianchet MA, Wang LX, Wilson IB, Vasta GR. The galectin CvGal1 from the eastern oyster (Crassostrea virginica) binds to blood group A oligosaccharides on the hemocyte surface. J. Biol Chem. 2013 Aug 23;288(34):24394-409.
Key words: Animal Lectin, Lectin structure, Glycobiology
http://www.jbc.org/content/early/2013/07/03/jbc.M113.476531.long
PMID: 23824193

1. Armstrong A, Hildreth JE, Amzel LM. Structural and thermodynamic insights into the recognition of native proteins by anti-peptide antibodies. J Mol Biol. 2013 Mar 6. doi:pii: S0022-2836(13)00146-0. 10.1016/j.jmb.2013.02.031. [Epub ahead of print]
Key words: native proteins, anti-peptide antibodies
http://www.ncbi.nlm.nih.gov/pubmed/23473830

2. Rudzka K, Moreno DM, Eipper B, Mains R, Estrin DA, Amzel LM. Coordination of peroxide to the Cu(M) center of peptidylglycine ?-hydroxylating monooxygenase (PHM): structural and computational study. J Biol Inorg Chem. 2013 Feb;18(2):223-32. doi: 10.1007/s00775-012-0967-z. Epub 2012 Dec 18.
Key words: peptidylglycine ?-hydroxylating monooxygenase, peroxide
http://www.ncbi.nlm.nih.gov/pubmed/23247335

3. Zhang P, Yang X, Zhang F, Gabelli SB, Wang R, Zhang Y, Bhat S, Chen X, Furlani M, Amzel LM, Liu JO, Ma D. Pyridinylpyrimidines selectively inhibit human methionine aminopeptidase-1. Bioorg Med Chem. 2013 Feb 21. doi:pii: S0968-0896(13)00147-8. 10.1016/j.bmc.2013.02.023. [Epub ahead of print]
Key words: pyridinylpyrimidines, human methionine aminopeptidase-1
http://www.ncbi.nlm.nih.gov/pubmed/23507151

1. Berndsen CE, Wiener R, Yu IW, Ringel AE, Wolberger C. A conserved asparagine
has a structural role in ubiquitin-conjugating enzymes. Nat Chem Biol. 2013 Mar;9(3):154-6.
Key words: asparagine, ubiquitin, enzymes
http://www.ncbi.nlm.nih.gov/pubmed/?term=23292652

2. Erdemli SB, Gupta R, Bishai WR, Lamichhane G, Amzel LM, Bianchet MA. Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2. Structure. 2012 Dec 5;20(12):2103-15.
Key words: Mycobacterium tuberculosis, L,D-transpeptidase 2, cell wall
http://linkinghub.elsevier.com/retrieve/pii/S0969-2126(12)00350-4

3. Guzzo CM, Berndsen CE, Zhu J, Gupta V, Datta A, Greenberg RA, Wolberger C,
Matunis MJ. RNF4-dependent hybrid SUMO-ubiquitin chains are signals for RAP80 and
thereby mediate the recruitment of BRCA1 to sites of DNA damage. Sci Signal. 2012
Dec 4;5(253):ra88. doi: 10.1126/scisignal.2003485.
Key words: BRCA1, DNA, SUMO-ubiquitin, RNF4
http://www.ncbi.nlm.nih.gov/pubmed/?term=23211528

1. Chan, W, Schaeffer TB, Pomerantz JL. A quantitative signaling screen identifies CARD11 mutations in the CARD and LATCH domains that induce Bcl10 ubiquitination and human lymphoma cell survival. Mol Cell Biol. 2013. 33(2):429-443.
Key words: lymphoma, signaling, NF-kappaB, CARD11, Bcl10
http://www.ncbi.nlm.nih.gov/pubmed/23149938

2. Coyer SR, Singh A, Dumbauld DW, Calderwood DA, Craig SW, Delamarche E, Garcia AJ. Nanopatterning reveals an ECM area threshold for focal adhesion assembly and force transmission that is regulated by integrin activation and cytoskeletal tension. J of Cell Sci. 2012; 25:5110-5123. Epub 2012 Aug 16.
Key words: Cell-adhesion, Fibronectin, Vinculin, Talin, Focal adhesion
http://www.ncbi.nlm.nih.gov/pubmed/22899715

3. Pedersen PL. Mitochondria in relation to cancer metastasis: introduction to a mini-review series. J Bioenerg Biomembr 2012 Dec 44(6):615-7.
Key words: cancer, metastasis, "Warburg", 3-brompyruvate, hexokinase 2
http://www.ncbi.nlm.nih.gov/pubmed/22926290

4. Tu-Sekine B, Raben DMJ. Dual regulation of diacylglycerol kinase (DGK)-?: polybasic proteins promote activation by phospholipids and increase substrate affinity. Biol. Chem. 2012;287:41619-41627.
Key words: Diacylglycerol kinase, Interfacial Enzymology, Enzyme Regulation, Polybasic Proteins
http://www.ncbi.nlm.nih.gov/pubmed/23091060

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