2,942 Hits in 2.4 sec

Water permeability of chloroplast envelope membranes

Douglas C. McCain, John L. Markley
1985 FEBS Letters  
previously [l] .  ...  Table 1 1 Results of relaxation time and saturation transfer measurements of 8 L. tdipifera samples at 20°C.  ...  ., the time required for a water molecule to diffuse a distance half the mean diameter of a chloroplast [l] .  ... 
doi:10.1016/0014-5793(85)80809-7 pmid:3987894 fatcat:qdyprxswpzahhjp7w6phcvqobq

Databases and Software for NMR-Based Metabolomics

James J. Ellinger, Roger A. Chylla, Eldon L. Ulrich, John L. Markley
2012 Current Metabolomics  
L-alanine as an example of an interactive 1 H-NMR session in the MQMCD.  ...  , specific information acquired from the literature and other databases such as tissue location, average concentrations and associated disorders (for an example of this compilation of information for L-alanine  ... 
doi:10.2174/2213235x11301010028 pmid:24260723 pmcid:PMC3832261 fatcat:umhinkhvavfsjeyhkpqylbjnly

Biomolecular NMR: Past and future

John L. Markley, William Milo Westler
2017 Archives of Biochemistry and Biophysics  
We thank Eldon L. Ulrich for critical comments on the manuscript and the National Institutes of Health for continuous support over 46 years.  ...  Bill Horsely, who worked with John Markley, is sitting at the NMR spectrometer.  ...  Our early experience with NMR John Markley grew up in Colorado and was a chemistry major and member of the ski team at Carleton College (Northfield, Minnesota).  ... 
doi:10.1016/ pmid:28495511 pmcid:PMC5701516 fatcat:2aw6oo3wcfa3peq3prb76ananq

Nuclear Magnetic Resonance Studies of Spherical Plant Viruses

R. Virudachalam, John L. Markley
1986 Biophysical Journal  
VIRUDACHALAM AND JOHN L. MARKLEY Department ofBiochemistry, University of Wisconsin at Madison, Madison, Wisconsin 53706.  ...  L. Markley, unpublished results; see reference 1.) Sauer, R. T., and R. Anderegg. 1978. Primary structure of the X repressor. Biochemistry. 17:1092-1100. 8. Shih, H. H.-L., J. Brady, and M.  ... 
doi:10.1016/s0006-3495(86)83582-2 pmid:19431638 pmcid:PMC1329566 fatcat:b5kbpsozyjcflaxwcfasezzahy

Sliding mode control using modified Rodrigues parameters

John L. Crassidis, F. L. Markley
1996 Journal of Guidance Control and Dynamics  
doi:10.2514/3.21798 fatcat:g2nn5r66crh4tnilgw4zj5dj54

Solution structure of human sorting nexin 22

Jikui Song, Kate Qin Zhao, Carrie L. Loushin Newman, Dmitriy A. Vinarov, John L. Markley
2007 Protein Science  
The sorting nexins (SNXs) constitute a large group of PX domain-containing proteins that play critical roles in protein trafficking. We report here the solution structure of human sorting nexin 22 (SNX22). Although SNX22 has <30% sequence identity with any PX domain protein of known structure, it was found to contain the a/b fold and compact structural core characteristic of PX domains. Analysis of the backbone dynamics of SNX22 by NMR relaxation measurements revealed that the two walls of the
more » ... igand binding cleft undergo internal motions: on the picosecond timescale for the b1/b2 loop and on the micro-to millisecond timescale for the loop between the polyproline motif and helix a2. Regions of the SNX22 structure that differ from those of other PX domains include the loop connecting strands b1 and b2 and the loop connecting helices a1 and a2, which appear to be more mobile than corresponding loops in other known structures. The interaction of dibutanoyl-phosphatidylinositol-3-phosphate (dibutanoyl-PtdIns(3)P) with SNX22 was investigated by an NMR titration experiment, which identified the binding site in a basic cleft and indicated that ligand binding leads only to a local structural rearrangement as has been found with other PX domains. Because motions in the loops are damped out when dibutanoyl-PtdIns(3)P binds, entropic effects could contribute to the lower affinity of SNX22 for this ligand compared to other PX domains.
doi:10.1110/ps.072752407 pmid:17400918 pmcid:PMC2206652 fatcat:5i35wn3tbndu3diflefxhjmgmi

NMR Solution Structure of ATTp, anArabidopsis thalianaTrypsin Inhibitor†,‡

Qin Zhao, Young Kee Chae, John L. Markley
2002 Biochemistry  
L. Markley, manuscript in preparation) .  ...  L. Markley, manuscript in preparation).  ... 
doi:10.1021/bi025702a pmid:12369816 fatcat:w3zaptk5tngtlpldum7ukyui5m

High Pressure Effects on Protein Structure [chapter]

Kenneth E. Prehoda, Ed S. Mooberry, John L. Markley
1998 Protein Dynamics, Function, and Design  
L. Markley, unpublished).  ...  L. Markley, unpublished).  ... 
doi:10.1007/978-1-4615-4895-9_5 fatcat:fvb6a7ke5jbshopj6vxdwcsrqe

The future of the protein data bank

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley
2012 Biopolymers  
The Worldwide Protein Data Bank (wwPDB) is the international collaboration that manages the deposition, processing and distribution of the PDB archive. The wwPDB's mission is to maintain a single archive of macromolecular structural data that are freely and publicly available to the global community. Its members [RCSB PDB (USA), PDBe (Europe), PDBj (Japan), and BMRB (USA)] host data-deposition sites and mirror the PDB ftp archive. To support future developments in structural biology, the wwPDB
more » ... artners are addressing organizational, scientific, and technical challenges.
doi:10.1002/bip.22132 pmid:23023942 pmcid:PMC3684242 fatcat:tkdo6ykibnhebfbavqjb55nhsq

Coupling betweentrans/cisproline isomerization and protein stability in staphylococcal nuclease

Dagmar M. Truckses, Kenneth E. Prehoda, Stephen C. Miller, John L. Markley, John R. Somoza
1996 Protein Science  
In both P117G mutants, the loop formed by residues 112-1 17 is located closer to the adjacent loop formed by residues 77-85, and residues 115-1 18 adopt a type I' p-turn conformation with the L y~"~-G  ...  l y "~ peptide bond in the trans configuration, as compared with the parent protein in which these residues have a typeVI, p-turn conformation with the Ly~"~-Pro'" peptide bond in the cis configuration  ...  As expected, H124L+P1 17G exhibits only one peptide bond configuration at L y~l '~-P r o l '~ , but maintains heterogeneity at the peptide bond.  ... 
doi:10.1002/pro.5560050917 pmid:8880915 pmcid:PMC2143535 fatcat:xhzgbbyh25d3noculexxb32sgi

Predictive Filtering for Nonlinear Systems

John L. Crassidis, F. Landis Markley
1997 Journal of Guidance Control and Dynamics  
, , , , 1 2 (7) S x t m q ∈ × R is a matrix with each i th row given by s L L c L L c i m i g f p i g f p i i q i = = − − 1 1 1 1 2 , , , , , , (8) where the Lie derivative with respect to L g j in Equation  ...  L t Q L y z f f f ≤ − + + − − + − − 2 4 4 1 2 2 2 2 2 ξ ξ ∆ ∆ (43) Substituting 4 1 z Q = − ξ leads to V Q V b ≤ − + − ξ 1 (44) where b Q y L L t Q L y f f f ≡ − − + − −1 2 2 2 2 1 ξ ξ ∆ ∆ (45) Numerical  ... 
doi:10.2514/2.4078 fatcat:6qnpa4fycfaxnmtt6zmggo5fhm

Safeguarding the integrity of protein archive

Helen M. Berman, Gerard J. Kleywegt, Haruki Nakamura, John L. Markley, Stephen K. Burley
2010 Nature  
doi:10.1038/463425c pmid:20110969 pmcid:PMC4456675 fatcat:xgb4narv2vaklpvrndym6eyrgi

Biophysical characterization of α-synuclein and its controversial structure

T Reid Alderson, John L Markley
2013 Intrinsically Disordered Proteins  
In the crowded intracellular environment (~400 g of macromolecules/L), folded globular proteins experience the increased viscosity of the bacterial cytoplasm, which greatly affects rotational diffusion  ... 
doi:10.4161/idp.26255 pmid:24634806 pmcid:PMC3908606 fatcat:pnqfye3mvbfcdaj24tjcs6rlmq

Solution Structure and Backbone Dynamics of Component IVGlycera dibranchiataMonomeric Hemoglobin−CO†,‡

Brian F. Volkman, Steve L. Alam, James D. Satterlee, John L. Markley
1998 Biochemistry  
73 -70 +60 16 H 72 -L 73 +60 +70 13 H 97 -I 98 +60 -70 22 H 97 -I 98 -80 +60 7 G 119 -G 120 -30 +120 24 G 119 -G 120 +110 -120 5 a Table 4 : 4 Average Values for S 2 , Backbone  ...  structures. b Number of structures out of 29 that contain the conformational subpopulation specified by ψi and φi+1. the 15 N-1 H HSQC spectrum prevented the determination of residues ψi φi+1 n b H 72 -L  ... 
doi:10.1021/bi980810b pmid:9692983 fatcat:a7sztpbb2fbl3pu4h4bs4lrqa4

PINE-SPARKY.2 for automated NMR-based protein structure research

Woonghee Lee, John L Markley, Alfonso Valencia
2017 Bioinformatics  
Nuclear magnetic resonance (NMR) spectroscopy, along with X-ray crystallography and cryoelectron microscopy, is one of the three major tools that enable the determination of atomiclevel structural models of biological macromolecules. Of these, NMR has the unique ability to follow important processes in solution, including conformational changes, internal dynamics and protein-ligand interactions. As a means for facilitating the handling and analysis of spectra involved in these types of NMR
more » ... es, we have developed PINE-SPARKY.2, a software package that integrates and automates discrete tasks that previously required interaction with separate software packages. The graphical user interface of PINE-SPARKY.2 simplifies chemical shift assignment and verification, automated detection of secondary structural elements, predictions of flexibility and hydrophobic cores, and calculation of three-dimensional structural models. Availability and implementation: PINE-SPARKY.2 is available in the latest version of NMRFAM-SPARKY from the National Magnetic Resonance Facility at Madison ( download_packages.html), the NMRbox Project ( and to subscribers to the SBGrid ( For a detailed description of the program, see http://www.nmrfam.wisc. edu/pine-sparky2.htm.
doi:10.1093/bioinformatics/btx785 pmid:29281006 pmcid:PMC5925765 fatcat:xxagdsyjarad7a577o2d34gsii
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