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Article ; Online: IMProv: A Resource for Cross-link-Driven Structure Modeling that Accommodates Protein Dynamics.

Ziemianowicz, Daniel S / Saltzberg, Daniel / Pells, Troy / Crowder, D Alex / Schräder, Christoph / Hepburn, Morgan / Sali, Andrej / Schriemer, David C

Molecular & cellular proteomics : MCP

2021 Volume 20, Page(s) 100139

Abstract: Proteomics methodology has expanded to include protein structural analysis, primarily through cross-linking mass spectrometry (XL-MS) and hydrogen-deuterium exchange mass spectrometry (HX-MS). However, while the structural proteomics community has ... ...

Abstract	Proteomics methodology has expanded to include protein structural analysis, primarily through cross-linking mass spectrometry (XL-MS) and hydrogen-deuterium exchange mass spectrometry (HX-MS). However, while the structural proteomics community has effective tools for primary data analysis, there is a need for structure modeling pipelines that are accessible to the proteomics specialist. Integrative structural biology requires the aggregation of multiple distinct types of data to generate models that satisfy all inputs. Here, we describe IMProv, an app in the Mass Spec Studio that combines XL-MS data with other structural data, such as cryo-EM densities and crystallographic structures, for integrative structure modeling on high-performance computing platforms. The resource provides an easily deployed bundle that includes the open-source Integrative Modeling Platform program (IMP) and its dependencies. IMProv also provides functionality to adjust cross-link distance restraints according to the underlying dynamics of cross-linked sites, as characterized by HX-MS. A dynamics-driven conditioning of restraint values can improve structure modeling precision, as illustrated by an integrative structure of the five-membered Polycomb Repressive Complex 2. IMProv is extensible to additional types of data.
MeSH term(s)	Mass Spectrometry ; Models, Molecular ; Polycomb Repressive Complex 2/chemistry ; Protein Conformation ; Proteomics/methods ; Software
Chemical Substances	Polycomb Repressive Complex 2 (EC 2.1.1.43)
Language	English
Publishing date	2021-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2021.100139
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Article ; Online: Modeling Biological Complexes Using Integrative Modeling Platform.

Saltzberg, Daniel / Greenberg, Charles H / Viswanath, Shruthi / Chemmama, Ilan / Webb, Ben / Pellarin, Riccardo / Echeverria, Ignacia / Sali, Andrej

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2022, Page(s) 353–377

Abstract: Integrative structure modeling provides 3D models of macromolecular systems that are based on information from multiple types of experiments, physical principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic ... ...

Abstract	Integrative structure modeling provides 3D models of macromolecular systems that are based on information from multiple types of experiments, physical principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic example of integrative structure modeling of the quaternary structure of the actin, tropomyosin, and gelsolin protein assembly based on electron microscopy, solution X-ray scattering, and chemical crosslinking data for the complex as well as excluded volume, sequence connectivity, and rigid atomic X-ray structures of the individual subunits. We follow the general four-stage process for integrative modeling, including gathering the input information, converting the input information into a representation of the system and a scoring function, sampling alternative model configurations guided by the scoring function, and analyzing the results. The computational aspects of this approach are implemented in our open-source Integrative Modeling Platform (IMP), a comprehensive and extensible software package for integrative modeling ( https://integrativemodeling.org ). In particular, we rely on the Python Modeling Interface (PMI) module of IMP that provides facile mixing and matching of macromolecular representations, restraints based on different types of information, sampling algorithms, and analysis including validations of the input data and output models. Finally, we also outline how to deposit an integrative structure and corresponding experimental data into PDB-Dev, the nascent worldwide Protein Data Bank (wwPDB) resource for archiving and disseminating integrative structures ( https://pdb-dev.wwpdb.org ). The example application provides a starting point for a user interested in using IMP for integrative modeling of other biomolecular systems.
MeSH term(s)	Computational Biology/methods ; Databases, Protein ; Macromolecular Substances/chemistry ; Models, Molecular ; Protein Conformation ; Software
Chemical Substances	Macromolecular Substances
Language	English
Publishing date	2019-08-07
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9608-7_15
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Article ; Online: Enzyme Substrate Specificity Conferred by Distinct Conformational Pathways.

Rago, Florencia / Saltzberg, Daniel / Allen, Karen N / Tolan, Dean R

Journal of the American Chemical Society

2015 Volume 137, Issue 43, Page(s) 13876–13886

Abstract: Substrate recognition is one of the hallmarks of enzyme catalysis. Enzyme conformational changes have been linked to selectivity between substrates with little direct evidence. Aldolase, a glycolytic enzyme, must distinguish between two physiologically ... ...

Abstract	Substrate recognition is one of the hallmarks of enzyme catalysis. Enzyme conformational changes have been linked to selectivity between substrates with little direct evidence. Aldolase, a glycolytic enzyme, must distinguish between two physiologically important substrates, fructose 1-phosphate and fructose 1,6-bisphosphate, and provides an excellent model system for the study of this question. Previous work has shown that isozyme specific residues (ISRs) distant from the active site are responsible for kinetic distinction between these substrates. Notably, most of the ISRs reside in a cluster of five surface α-helices, and the carboxyl-terminal region (CTR), and cooperative interactions among these helices have been demonstrated. To test the hypothesis that conformational changes are at the root of these changes, single surface-cysteine variants were created with the cysteine located on helices of the cluster and CTR. This allowed for site-specific labeling with an environmentally sensitive fluorophore, and subsequent monitoring of conformational changes by fluorescence emission spectrophotometry. These labeled variants revealed different spectra in the presence of saturating amounts of each substrate, which suggested the occurrence of different conformations. Emission spectra collected at various substrate concentrations showed a concentration dependence of the fluorescence spectra, consistent with binding events. Lastly, stopped-flow fluorescence spectrophotometry showed that the rate of these fluorescence changes was on the same time-scale as catalysis, thus suggesting a link between the different fluorescence changes and events during catalysis. On the basis of these results, we propose that different conformational changes may be a common mechanism for dictating substrate specificity in other enzymes with multiple substrates.
MeSH term(s)	Fructose-Bisphosphate Aldolase/chemistry ; Fructose-Bisphosphate Aldolase/metabolism ; Fructosediphosphates/chemistry ; Fructosediphosphates/metabolism ; Fructosephosphates/chemistry ; Fructosephosphates/metabolism ; Kinetics ; Models, Molecular ; Protein Conformation ; Spectrometry, Fluorescence ; Substrate Specificity
Chemical Substances	Fructosediphosphates ; Fructosephosphates ; Fructose-Bisphosphate Aldolase (EC 4.1.2.13) ; fructose-1,6-diphosphate (M7522JYX1H)
Language	English
Publishing date	2015-11-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3155-0
ISSN	1520-5126 ; 0002-7863
ISSN (online)	1520-5126
ISSN	0002-7863
DOI	10.1021/jacs.5b08149
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Article ; Online: Integrative structure modeling with the Integrative Modeling Platform.

Webb, Benjamin / Viswanath, Shruthi / Bonomi, Massimiliano / Pellarin, Riccardo / Greenberg, Charles H / Saltzberg, Daniel / Sali, Andrej

Protein science : a publication of the Protein Society

2017 Volume 27, Issue 1, Page(s) 245–258

Abstract: Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological ... ...

Abstract	Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use.
MeSH term(s)	Computational Biology ; Computer Simulation ; Models, Molecular ; Software
Language	English
Publishing date	2017-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3311
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Article: A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen–Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein–Ligand Interactions

Saltzberg, DanielJ / Broughton, Howard B / Pellarin, Riccardo / Chalmers, Michael J / Espada, Alfonso / Dodge, Jeffrey A / Pascal, Bruce D / Griffin, Patrick R / Humblet, Christine / Sali, Andrej

Journal of physical chemistry. 2017 Apr. 20, v. 121, no. 15

2017

Abstract: Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of ... ...

Abstract	Characterization of interactions between proteins and other molecules is crucial for understanding the mechanisms of action of biological systems and, thus, drug discovery. An increasingly useful approach to mapping these interactions is measurement of hydrogen/deuterium exchange (HDX) using mass spectrometry (HDX-MS), which measures the time-resolved deuterium incorporation of peptides obtained by enzymatic digestion of the protein. Comparison of exchange rates between apo- and ligand-bound conditions results in a mapping of the differential HDX (ΔHDX) of the ligand. Residue-level analysis of these data, however, must account for experimental error, sparseness, and ambiguity due to overlapping peptides. Here, we propose a Bayesian method consisting of a forward model, noise model, prior probabilities, and a Monte Carlo sampling scheme. This method exploits a residue-resolved exponential rate model of HDX-MS data obtained from all peptides simultaneously, and explicitly models experimental error. The result is the best possible estimate of ΔHDX magnitude and significance for each residue given the data. We demonstrate the method by revealing richer structural interpretation of ΔHDX data on two nuclear receptors: vitamin D-receptor (VDR) and retinoic acid receptor gamma (RORγ). The method is implemented in HDX Workbench and as a standalone module of the open source Integrative Modeling Platform.
Keywords	Bayesian theory ; deuterium ; drugs ; ligands ; mass spectrometry ; mechanism of action ; models ; peptides ; physical chemistry ; retinoic acid receptors
Language	English
Dates of publication	2017-0420
Size	p. 3493-3501.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-6106
DOI	10.1021/acs.jpcb.6b09358
Database	NAL-Catalogue (AGRICOLA)

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Article: Reinforcement of self-directed learning and the development of professional attitudes through peer- and self-assessment.

Asch, E / Saltzberg, D / Kaiser, S

Academic medicine : journal of the Association of American Medical Colleges

1998 Volume 73, Issue 5, Page(s) 575

MeSH term(s)	Attitude of Health Personnel ; Clinical Clerkship ; Humans ; Learning ; New York ; Peer Group ; Professional Competence ; Self-Evaluation Programs ; Students, Medical
Language	English
Publishing date	1998-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	96192-9
ISSN	1938-808X ; 1040-2446
ISSN (online)	1938-808X
ISSN	1040-2446
DOI	10.1097/00001888-199805000-00034
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Article: Observation of light transmission through randomly rough glass surfaces beyond the critical angle.

Griswold, Martin / Harrison, Mark / Saltzberg, David

Journal of the Optical Society of America. A, Optics, image science, and vision

2007 Volume 24, Issue 10, Page(s) 3207–3210

Abstract: In this series of experiments we study the transmission of laser light through a randomly rough interface between air and ground-glass diffusers. We verify the refractive index suppression predicted by Dogariu and Boreman [Opt. Lett.21, 701 (1996)]. We ... ...

Abstract	In this series of experiments we study the transmission of laser light through a randomly rough interface between air and ground-glass diffusers. We verify the refractive index suppression predicted by Dogariu and Boreman [Opt. Lett.21, 701 (1996)]. We also observe and quantify transmission beyond the critical angle for total internal reflection defined by Snell's law. In particular, these results may be applied to the ANITA experiment, which detects astrophysical neutrino interactions via radio waves produced under the ice. These radio waves must pass through the rough surfaces of the Antarctic ice sheets and shelves.
Language	English
Publishing date	2007-09-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	283633-6
ISSN	1520-8532 ; 1084-7529 ; 0740-3232
ISSN (online)	1520-8532
ISSN	1084-7529 ; 0740-3232
DOI	10.1364/josaa.24.003207
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Article: Experimental limit on the cosmic diffuse ultrahigh energy neutrino flux.

Gorham, P W / Hebert, C L / Liewer, K M / Naudet, C J / Saltzberg, D / Williams, D

Physical review letters

2004 Volume 93, Issue 4, Page(s) 41101

Abstract: We report results from 120 h of live time with the Goldstone lunar ultrahigh energy neutrino experiment (GLUE). The experiment searches for < or = 10 ns microwave pulses from the lunar regolith, appearing in coincidence at two large radio telescopes ... ...

Abstract	We report results from 120 h of live time with the Goldstone lunar ultrahigh energy neutrino experiment (GLUE). The experiment searches for < or = 10 ns microwave pulses from the lunar regolith, appearing in coincidence at two large radio telescopes separated by 22 km and linked by optical fiber. Such pulses would arise from subsurface electromagnetic cascades induced by interactions of > or = 100 EeV (1 EeV = 10(18) eV neutrinos in the lunar regolith. No candidates are yet seen, and the implied limits constrain several current models for ultrahigh energy neutrino fluxes.
Language	English
Publishing date	2004-07-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	208853-8
ISSN	1079-7114 ; 0031-9007
ISSN (online)	1079-7114
ISSN	0031-9007
DOI	10.1103/PhysRevLett.93.041101
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Article: A young mother with weight loss and persistent lymphadenopathy.

Saltzberg, D S

Hospital practice (Office ed.)

1985 Volume 20, Issue 11, Page(s) 18, 23, 25

MeSH term(s)	Acquired Immunodeficiency Syndrome/immunology ; Acquired Immunodeficiency Syndrome/physiopathology ; Acquired Immunodeficiency Syndrome/transmission ; Adolescent ; Body Weight ; Diagnosis, Differential ; Female ; Homosexuality ; Humans ; Lymphatic Diseases/etiology ; Lymphatic Diseases/immunology ; Lymphatic Diseases/physiopathology ; Pregnancy ; Sexual Behavior ; Time Factors
Language	English
Publishing date	1985-11-15
Publishing country	United States
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2570453-9
ISSN	2377-1003 ; 8750-2836 ; 2154-8331
ISSN (online)	2377-1003
ISSN	8750-2836 ; 2154-8331
DOI	10.1080/21548331.1985.11703181
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Article ; Online: Nuclear Import Receptor Inhibits Phase Separation of FUS through Binding to Multiple Sites.

Yoshizawa, Takuya / Ali, Rustam / Jiou, Jenny / Fung, Ho Yee Joyce / Burke, Kathleen A / Kim, Seung Joong / Lin, Yuan / Peeples, William B / Saltzberg, Daniel / Soniat, Michael / Baumhardt, Jordan M / Oldenbourg, Rudolf / Sali, Andrej / Fawzi, Nicolas L / Rosen, Michael K / Chook, Yuh Min

Cell

2018 Volume 173, Issue 3, Page(s) 693–705.e22

Abstract: Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution ... ...

Abstract	Liquid-liquid phase separation (LLPS) is believed to underlie formation of biomolecular condensates, cellular compartments that concentrate macromolecules without surrounding membranes. Physical mechanisms that control condensate formation/dissolution are poorly understood. The RNA-binding protein fused in sarcoma (FUS) undergoes LLPS in vitro and associates with condensates in cells. We show that the importin karyopherin-β2/transportin-1 inhibits LLPS of FUS. This activity depends on tight binding of karyopherin-β2 to the C-terminal proline-tyrosine nuclear localization signal (PY-NLS) of FUS. Nuclear magnetic resonance (NMR) analyses reveal weak interactions of karyopherin-β2 with sequence elements and structural domains distributed throughout the entirety of FUS. Biochemical analyses demonstrate that most of these same regions also contribute to LLPS of FUS. The data lead to a model where high-affinity binding of karyopherin-β2 to the FUS PY-NLS tethers the proteins together, allowing multiple, distributed weak intermolecular contacts to disrupt FUS self-association, blocking LLPS. Karyopherin-β2 may act analogously to control condensates in diverse cellular contexts.
MeSH term(s)	Active Transport, Cell Nucleus ; Binding Sites ; Frontotemporal Lobar Degeneration/metabolism ; Humans ; Karyopherins/metabolism ; Light ; Liquid-Liquid Extraction ; Macromolecular Substances ; Magnetic Resonance Spectroscopy ; Mutation ; Nephelometry and Turbidimetry ; Nuclear Localization Signals ; Protein Binding ; Protein Domains ; RNA/chemistry ; RNA-Binding Protein FUS/chemistry ; Scattering, Radiation ; Temperature ; beta Karyopherins/chemistry
Chemical Substances	FUS protein, human ; Karyopherins ; Macromolecular Substances ; Nuclear Localization Signals ; RNA-Binding Protein FUS ; TNPO1 protein, human ; beta Karyopherins ; RNA (63231-63-0)
Language	English
Publishing date	2018-06-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2018.03.003
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