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1. NMR‐assisted protein structure prediction with MELDxMD

Author

Robertson, James C, Nassar, Roy, Liu, Cong, Brini, Emiliano, Dill, Ken A, and Perez, Alberto

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Algorithms, Computational Biology, Magnetic Resonance Spectroscopy, Molecular Dynamics Simulation, Protein Conformation, Proteins, Reproducibility of Results, CASP13, MELD, NMR, molecular dynamics, protein structure prediction, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences
Abstract

We describe the performance of MELD-accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR-data-assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next-best groups by a factor of ~4 in z-score. MELDxMD gives ensembles, not single structures; succeeds on a 326-mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR-derived data used in the simulations was NOE-based ambiguous atom-atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.

Published
2019

2. MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.

Author

Robertson, James C, Perez, Alberto, and Dill, Ken A

Subjects
Generic health relevance, Amino Acid Sequence, Bayes Theorem, Computational Biology, Molecular Dynamics Simulation, Protein Conformation, Protein Folding, Proteins, Theoretical and Computational Chemistry, Biochemistry and Cell Biology, Computer Software, Chemical Physics
Abstract

A current challenge is to compute the native structures of proteins from their amino acid sequences. A main approach of bioinformatics is threading, in which a protein to be predicted is computationally threaded onto protein fragments of similar sequence having an already known structure. However, ∼15% of proteins cannot be folded in this way; this has been called the glass ceiling, and the proteins are called nonthreadables. For these, physical molecular dynamics (MD) modeling is promising because it does not require templates. We find that MD, when used with an accelerator called MELD, can fold many nonthreadables. For 41 nonthreadable proteins with fewer than 125 residues, MELD-accelerated MD (MELD × MD) folds 20 of them to better than 4 Å error. In 10 cases, MELD × MD succeeds even when the force field does not properly encode the native state. In 11 cases, MELD × MD foretells its own success; seeing large Boltzmann populations in the simulations predicts it has converged to the correct native state. MELD × MD acceleration can be applied to a broad physical protein modeling range.

Published
2018

8. Introduction

Author

RAMPERSAD, SABRINA R. and ROBERTSON, JAMES C.

Published
2009

14. Discovery of a Novel, First-in-Class Bfl-1 BH3 Mimetic with Pro-Apoptotic Activity

Author

Derks, Maarten, Bryan, Marian C., Rockx, Cindy, Schults, Tamara, Verhulst, Tinne, Pietrak, Beth, Maehigashi, Tatsuya, Robertson, James C., DeMaria, Andrew H., Holt, Kimberly, Ji, Shaofei, Wong, Victoria, Bueters, Ruud, Koo, Seong Joo, Masure, Stefan, Bhogal, Balpreet, Kelly, Christopher B., Mitra, Kaushik, Luistro, Leopoldo, Shaffer, Paul L., Szewczuk, Lawrence, Elsayed, Yusri, and Philippar, Ulrike

Published
2023
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15. Appendix A: Methological details from Impacts of stormwater on coastal ecosystems: the need to match the scales of management objectives and solutions

Author

Levin, Phillip S., Howe, Emily, and Robertson, James C.

Abstract

Despite their limited area relative to the global ocean, coastal zones—the region where land meets the sea-play a disproportionately important role in generating ecosystem services. However, coastal ecosystems are under increasing pressure from human populations. In particular, urban stormwater is an increasingly important threat to the integrity of coastal systems. Urban catchments exhibit altered flow regimes that impact ecosystem processes and coastal foodwebs. In addition, urban stormwater contains complex and unpredictable mixtures of chemicals that result in a multitude of lethal and sublethal impacts on species in coastal systems. Along the western coast of the United States, we estimate that hundreds of billions of kilograms of suspended solids flow off land surfaces and enter the Northern California Current each year. However, 70% of this pollution could be addressed by treating only 1.35% of the land area. Determining how to prioritize treatment of stormwater in this region requires a clear articulation of objectives—spatial distribution of appropriate management actions is dependent on the life histories of species, and management schemes optimized for one species may not achieve desired objectives for other species. In particular, we highlight that the scale of stormwater interventions must match the ecological scale relevant to species targeted by management. In many cases, management and policy will require mechanisms in order to ensure that local actions scale-up to efficiently and effectively achieve management objectives. In the face of rapid urbanization of coastal zones, failure to consider the match of management and ecological scales will result in the continued decline of coastal ecosystems and the species they support.This article is part of the theme issue ‘Integrative research perspectives on marine conservation’.

Published
2020
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17. Particle selection using CsI(Ti) crystals and associated experiments on the luminescence of alkali halide crystals

Author

Robertson, James C.

Abstract

The study of n-alpha reactions has been greatly impeded by the lack of suitable counting techniques. The major experimental difficulty in making such a study is to discriminate between the alpha particles and protons which are emitted simultaneously from n-p reactions. Also, measurements on n-p reactions using electronic techniques have been limited to protons of energy greater than 4 MeV due to the very intense electron backgrounds produced in the detector. It is desirable to make measurements on n-alpha reactions and to extend the measurements on n-p reactions to lower energies, since such measurements would yield important information about the mechanism of such neutron induced reactions. Part I of this thesis entitled:- "Particle Selection using CsI(T1) Crystals", gives a description of a novel form of scintillation counting which makes such measurements possible. This technique utilises the fact that the decay time of the luminescence produced in a CsI(T1) crystal is dependent on the ionization density produced by the particle giving rise to the luminescence, and hence on the nature of the particle. Electronic circuits have been designed and constructed which effectively inspect the decay time of the luminescence produced in a OsI(T1) crystal and thereby effect discrimination between the different types of particle producing the luminescence. In this way the elimination of the unwanted backgrounds produced in a CsI(T1) crystal, when it is used as the detector in neutron experiments, has been achieved. In Part II of this thesis entitled:- "Associated Experiments on the Luminescence of Alkali Halide Crystals", several experiments are described which it was hoped might have improved the technique described in Part I. Firstly a systematic search was made in the hope of finding a crystal in which the decay time of the luminescence was more dependent on ionization density. The decay times of the luminescence produced in LiI(Eu), NaI(T1), KI(T1) and CsBr(T1) by particles producing different ionization densities were measured. The dependence of the luminescent efficiencies, Ealpha,p,e, on ionization density was also examined. (The subscripts denote alpha particles, protons and electrons respectively). In a second experiment, the dependence on thallium concentration in CsI(T1) of the luminescent efficiencies, Ealpha,p,e, and the decay times of the luminescence produced by different particles has been examined.

Published
1961

24. Seating The Disabled

Author

Crewe, Romy, Ferguson-Pell, Martin, Robertson, James C., and Glanville, Hugh J.

Published
1980

25. Graduated Elastic Stockings

Author

Swain, Ian, Robertson, James C., Shaban, Ragai, Fentem, Peter, Blair, S. D., Backhouse, C. M., and McCollum, C. N.

Published
1986

28. Calligraphy and Architecture in the Muslim World

Author

Gharipour, Mohammad, Robertson, James C., Gharipour, Mohammad, and Robertson, James C.

Subjects
Islamic architecture, Islamic decoration and ornament, Decoration and ornament, Architectural, Islamic calligraphy, Architectural inscriptions
Abstract

This major reference work covers all aspects of architectural inscriptions in the Muslim world: the artists and their patrons, what inscriptions add to architectural design, what materials were used, what their purpose was and how they infuse buildings with meaning.

Published
2013

34. High-resolution mapping of the world’sreservoirs and dams for sustainableriver-flow management

Author

Lehner, Bernhard, Reidy Liermann, Catherine, Revenga, Carmen, Vörösmarty, Charles, Fekete, Balazs, Crouzet, Philippe, Döll, Petra, Endejan, Marcel, Frenken, Karen, Magome, Jun, Nilsson, Christer, Robertson, James C, Rödel, Raimund, Sindorf, Nikolai, Wisser, Dominik, Lehner, Bernhard, Reidy Liermann, Catherine, Revenga, Carmen, Vörösmarty, Charles, Fekete, Balazs, Crouzet, Philippe, Döll, Petra, Endejan, Marcel, Frenken, Karen, Magome, Jun, Nilsson, Christer, Robertson, James C, Rödel, Raimund, Sindorf, Nikolai, and Wisser, Dominik

Abstract

Despite the recognized importance of reservoirs and dams, global datasets describing their characteristics and geographical distribution are largely incomplete. To enable advanced assessments of the role and effects of dams within the global river network and to support strategies for mitigating ecohydrological and socioeconomic costs, we introduce here the spatially explicit and hydrologically linked Global Reservoir and Dam database (GRanD). As of early 2011, GRanD contains information regarding 6862 dams and their associated reservoirs, with a total storage capacity of 6197 km3. On the basis of these records, we estimate that about 16.7 million reservoirs larger than 0.01 ha – with a combined storage capacity of approximately 8070 km3 – may exist worldwide, increasing Earth's terrestrial surface water area by more than 305 000 km2. We find that 575 900 river kilometers, or 7.6% of the world's rivers with average flows above 1 cubic meter per second (m3 s−1), are affected by a cumulative upstream reservoir capacity that exceeds 2% of their annual flow; the impact is highest for large rivers with average flows above 1000 m3 s−1, of which 46.7% are affected. Finally, a sensitivity analysis suggests that smaller reservoirs have substantial impacts on the spatial extent of flow alterations despite their minor role in total reservoir capacity. Read More: http://www.esajournals.org/doi/abs/10.1890/100125

Published
2011
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47. Viewpoints

Author

Bullock, Jan, Robertson, James C., Corbell, John, Keefer, Martin J., Beaux, Tim, Hurlbert, R.B., Gorrell, Donald B., and Wells, Jim

Subjects
General interest, News, opinion and commentary
Published
1999

49. Improved Coiled-Coil Design Enhances Interaction with Bcr-Abl and Induces Apoptosis

Author

Dixon, Andrew S., Miller, Geoffrey D., Bruno, Benjamin J., Constance, Jonathan E., Woessner, David W., Fidler, Trevor P., Robertson, James C., Cheatham, Thomas E., and Lim, Carol S.

Abstract

The oncoprotein Bcr-Abl drives aberrant downstream activity through trans-autophosphorylation of homo-oligomers in chronic myelogenous leukemia (CML).(1, 2) The formation of Bcr-Abl oligomers is achieved through the coiled-coil domain at the N-terminus of Bcr.(3, 4) We have previously reported a modified version of this coiled-coil domain, CCmut2, which exhibits disruption of Bcr-Abl oligomeric complexes and results in decreased proliferation of CML cells and induction of apoptosis.(5) A major contributing factor to these enhanced capabilities is the destabilization of the CCmut2 homodimers, increasing the availability to interact with and inhibit Bcr-Abl. Here, we included an additional mutation (K39E) that could in turn further destabilize the mutant homodimer. Incorporation of this modification into CCmut2 (C38A, S41R, L45N, E48R, Q60E) generated what we termed CCmut3, and resulted in further improvements in the binding properties with the wild-type coiled-coil domain representative of Bcr-Abl. A separate construct containing one revert mutation, CCmut4, did not demonstrate improved oligomeric properties and indicated the importance of the L45D mutation. CCmut3 demonstrated improved oligomerization via a two-hybrid assay as well as through colocalization studies, in addition to showing similar biologic activity as CCmut2. The improved binding between CCmut3 and the Bcr-Abl coiled-coil may be used to redirect Bcr-Abl to alternative subcellular locations with interesting therapeutic implications.

Published
2012
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50. CORRESPONDENCE.

Author

Swain, Ian, Robertson, James C., Shaban, Ragai, Fentem, Peter, Blair, S.D., Backhouse, C.M., McCollum, C.N., Briggs, J.E., Das, G., Watkins, S.J., Cohen, H.N., Clee, M.D., Todd, W.T.A., Ashworth, J., Gilbert, Ruth, Morrison, M.C.T., Peters, J.H., and Clitherow, N.R.

Subjects
*MEDICAL care, *INFLAMMATORY bowel diseases, *ESTRADIOL, *PREMENSTRUAL syndrome treatment, *AIDS, *PHYSIOLOGY
Abstract

Focuses on the health care issues in Europe. Use of technetium-99m autologous phagocyte scanning for inflammatory bowel disease; Effect of subcutaneous estradiol implants and cyclical oral norethisterone on the treatment of the premenstrual syndrome; Length of survival of patients with AIDS.

Published
1986

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