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Article ; Online: No hype in hyperspace.

Goldman, Yale E

2021 Volume 120, Issue 8, Page(s) 1306–1308

MeSH term(s)	Biophysical Phenomena ; Single Molecule Imaging
Language	English
Publishing date	2021-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Comment
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.02.026
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Article ; Online: Enhancing Nanoparticle Detection in Interferometric Scattering (iSCAT) Microscopy Using a Mask R-CNN.

Boyle, Michael J / Goldman, Yale E / Composto, Russell J

The journal of physical chemistry. B

2023 Volume 127, Issue 16, Page(s) 3737–3745

Abstract: Interferometric scattering microscopy (iSCAT) is a label-free optical microscopy technique that enables imaging of individual nano-objects such as nanoparticles, viruses, and proteins. Essential to this technique is the suppression of background ... ...

Abstract	Interferometric scattering microscopy (iSCAT) is a label-free optical microscopy technique that enables imaging of individual nano-objects such as nanoparticles, viruses, and proteins. Essential to this technique is the suppression of background scattering and identification of signals from nano-objects. In the presence of substrates with high roughness, scattering heterogeneities in the background, when coupled with tiny stage movements, cause features in the background to be manifested in background-suppressed iSCAT images. Traditional computer vision algorithms detect these background features as particles, limiting the accuracy of object detection in iSCAT experiments. Here, we present a pathway to improve particle detection in such situations using supervised machine learning via a mask region-based convolutional neural network (mask R-CNN). Using a model iSCAT experiment of 19.2 nm gold nanoparticles adsorbing to a rough layer-by-layer polyelectrolyte film, we develop a method to generate labeled datasets using experimental background images and simulated particle signals and train the mask R-CNN using limited computational resources via transfer learning. We then compare the performance of the mask R-CNN trained with and without inclusion of experimental backgrounds in the dataset against that of a traditional computer vision object detection algorithm, Haar-like feature detection, by analyzing data from the model experiment. Results demonstrate that including representative backgrounds in training datasets improved the mask R-CNN in differentiating between background and particle signals and elevated performance by markedly reducing false positives. The methodology for creating a labeled dataset with representative experimental backgrounds and simulated signals facilitates the application of machine learning in iSCAT experiments with strong background scattering and thus provides a useful workflow for future researchers to improve their image processing capabilities.
Language	English
Publishing date	2023-04-19
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.3c00097
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Article: DDX3X and DDX3Y constitutively form nano-sized RNA-protein clusters that foster enzymatic activity.

Yanas, Amber / Shweta, Him / Owens, Michael C / Liu, Kathy Fange / Goldman, Yale E

bioRxiv : the preprint server for biology

2023

Abstract: DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous ... ...

Abstract	DEAD-box helicases, which are crucial for many aspects of RNA metabolism, often contain intrinsically disordered regions (IDRs), whose functions remain unclear. Using multiparameter confocal microscopy, we reveal that sex chromosome-encoded homologous RNA helicases, DDX3X and DDX3Y, form nano-sized RNA-protein clusters (RPCs) that foster their catalytic activities
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.29.569239
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Article ; Online: High-Speed Optical Traps Address Dynamics of Processive and Non-Processive Molecular Motors.

Gardini, Lucia / Woody, Michael S / Kashchuk, Anatolii V / Goldman, Yale E / Ostap, E Michael / Capitanio, Marco

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

2022 Volume 2478, Page(s) 513–557

Abstract: Interactions between biological molecules occur on very different time scales, from the minutes of strong protein-protein bonds, down to below the millisecond duration of rapid biomolecular interactions. Conformational changes occurring on sub-ms time ... ...

Abstract	Interactions between biological molecules occur on very different time scales, from the minutes of strong protein-protein bonds, down to below the millisecond duration of rapid biomolecular interactions. Conformational changes occurring on sub-ms time scales and their mechanical force dependence underlie the functioning of enzymes (e.g., motor proteins) that are fundamental for life. However, such rapid interactions are beyond the temporal resolution of most single-molecule methods. We developed ultrafast force-clamp spectroscopy (UFFCS), a single-molecule technique based on laser tweezers that allows us to investigate early and very fast dynamics of a variety of enzymes and their regulation by mechanical load. The technique was developed to investigate the rapid interactions between skeletal muscle myosin and actin, and then applied to the study of different biological systems, from cardiac myosin to processive myosin V, microtubule-binding proteins, transcription factors, and mechanotransducer proteins. Here, we describe two different implementations of UFFCS instrumentation and protocols using either acousto- or electro-optic laser beam deflectors, and their application to the study of processive and non-processive motor proteins.
MeSH term(s)	Actins/metabolism ; Myosins/metabolism ; Optical Tweezers ; Optics and Photonics ; Protein Binding
Chemical Substances	Actins ; Myosins (EC 3.6.4.1)
Language	English
Publishing date	2022-09-05
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2229-2_19
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Article ; Online: Measuring Molecular Forces Using Calibrated Optical Tweezers in Living Cells.

Hendricks, Adam G / Goldman, Yale E

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

2017 Volume 1486, Page(s) 537–552

Abstract: Optical tweezers have been instrumental in uncovering the mechanisms motor proteins use to generate and react to force. While optical traps have primarily been applied to purified, in vitro systems, emerging methods enable measurements in living cells ... ...

Abstract	Optical tweezers have been instrumental in uncovering the mechanisms motor proteins use to generate and react to force. While optical traps have primarily been applied to purified, in vitro systems, emerging methods enable measurements in living cells where the actively fluctuating, viscoelastic environment and varying refractive index complicate calibration of the instrument. Here, we describe techniques to calibrate optical traps in living cells using the forced response to sinusoidal oscillations and spontaneous fluctuations, and to measure the forces exerted by endogenous ensembles of kinesin and dynein motor proteins as they transport cargoes in the cell.
Language	English
Publishing date	2017
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-6421-5_21
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Article ; Online: Processivity and Velocity for Motors Stepping on Periodic Tracks.

Mugnai, Mauro L / Caporizzo, Matthew A / Goldman, Yale E / Thirumalai, D

Biophysical journal

2020 Volume 118, Issue 7, Page(s) 1537–1551

Abstract: Processive molecular motors enable cargo transportation by assembling into dimers capable of taking several consecutive steps along a cytoskeletal filament. In the well-accepted hand-over-hand stepping mechanism, the trailing motor detaches from the ... ...

Abstract	Processive molecular motors enable cargo transportation by assembling into dimers capable of taking several consecutive steps along a cytoskeletal filament. In the well-accepted hand-over-hand stepping mechanism, the trailing motor detaches from the track and binds the filament again in the leading position. This requires fuel consumption in the form of ATP hydrolysis and coordination of the catalytic cycles between the leading and the trailing heads. Alternate stepping pathways also exist, including inchworm-like movements, backward steps, and foot stomps. Whether all the pathways are coupled to ATP hydrolysis remains to be determined. Here, to establish the principles governing the dynamics of processive movement, we present a theoretical framework that includes all of the alternative stepping mechanisms. Our theory bridges the gap between the elemental rates describing the biochemical and structural transitions in each head and the experimentally measurable quantities such as velocity, processivity, and probability of backward stepping. Our results, obtained under the assumption that the track is periodic and infinite, provide expressions that hold regardless of the topology of the network connecting the intermediate states, and are therefore capable of describing the function of any molecular motor. We apply the theory to myosin VI, a motor that takes frequent backward steps and moves forward with a combination of hand-over-hand and inchworm-like steps. Our model quantitatively reproduces various observables of myosin VI motility reported by four experimental groups. The theory is used to predict the gating mechanism, the pathway for backward stepping, and the energy consumption as a function of ATP concentration.
MeSH term(s)	Adenosine Triphosphate ; Probability
Chemical Substances	Adenosine Triphosphate (8L70Q75FXE)
Language	English
Publishing date	2020-02-25
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	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2020.01.047
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Article ; Online: Ataluren and aminoglycosides stimulate read-through of nonsense codons by orthogonal mechanisms.

Ng, Martin Y / Li, Hong / Ghelfi, Mikel D / Goldman, Yale E / Cooperman, Barry S

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 2

Abstract: During protein synthesis, nonsense mutations, resulting in premature stop codons (PSCs), produce truncated, inactive protein products. Such defective gene products give rise to many diseases, including cystic fibrosis, Duchenne muscular dystrophy (DMD), ... ...

Abstract	During protein synthesis, nonsense mutations, resulting in premature stop codons (PSCs), produce truncated, inactive protein products. Such defective gene products give rise to many diseases, including cystic fibrosis, Duchenne muscular dystrophy (DMD), and some cancers. Small molecule nonsense suppressors, known as TRIDs (translational read-through-inducing drugs), stimulate stop codon read-through. The best characterized TRIDs are ataluren, which has been approved by the European Medicines Agency for the treatment of DMD, and G418, a structurally dissimilar aminoglycoside. Previously [1], we applied a highly purified in vitro eukaryotic translation system to demonstrate that both aminoglycosides like G418 and more hydrophobic molecules like ataluren stimulate read-through by direct interaction with the cell's protein synthesis machinery. Our results suggested that they might do so by different mechanisms. Here, we pursue this suggestion through a more-detailed investigation of ataluren and G418 effects on read-through. We find that ataluren stimulation of read-through derives exclusively from its ability to inhibit release factor activity. In contrast, G418 increases functional near-cognate tRNA mispairing with a PSC, resulting from binding to its tight site on the ribosome, with little if any effect on release factor activity. The low toxicity of ataluren suggests that development of new TRIDs exclusively directed toward inhibiting termination should be a priority in combatting PSC diseases. Our results also provide rate measurements of some of the elementary steps during the eukaryotic translation elongation cycle, allowing us to determine how these rates are modified when cognate tRNA is replaced by near-cognate tRNA ± TRIDs.
MeSH term(s)	Aminoglycosides/metabolism ; Aminoglycosides/pharmacology ; Animals ; Artemia/genetics ; Codon, Nonsense/drug effects ; Codon, Nonsense/metabolism ; Codon, Terminator/drug effects ; Codon, Terminator/metabolism ; Cystic Fibrosis/genetics ; Muscular Dystrophy, Duchenne/genetics ; Oxadiazoles/metabolism ; Oxadiazoles/pharmacology ; Peptide Chain Elongation, Translational/drug effects ; Protein Biosynthesis/drug effects ; Protein Synthesis Inhibitors ; RNA, Transfer/drug effects ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Ribosomes/drug effects ; Saccharomyces/genetics
Chemical Substances	Aminoglycosides ; Codon, Nonsense ; Codon, Terminator ; Oxadiazoles ; Protein Synthesis Inhibitors ; RNA, Transfer (9014-25-9) ; ataluren (K16AME9I3V)
Language	English
Publishing date	2021-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2020599118
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Article ; Online: Ataluren binds to multiple protein synthesis apparatus sites and competitively inhibits release factor-dependent termination.

Huang, Shijie / Bhattacharya, Arpan / Ghelfi, Mikel D / Li, Hong / Fritsch, Clark / Chenoweth, David M / Goldman, Yale E / Cooperman, Barry S

Nature communications

2022 Volume 13, Issue 1, Page(s) 2413

Abstract: Genetic diseases are often caused by nonsense mutations, but only one TRID (translation readthrough inducing drug), ataluren, has been approved for clinical use. Ataluren inhibits release factor complex (RFC) termination activity, while not affecting ... ...

Abstract	Genetic diseases are often caused by nonsense mutations, but only one TRID (translation readthrough inducing drug), ataluren, has been approved for clinical use. Ataluren inhibits release factor complex (RFC) termination activity, while not affecting productive binding of near-cognate ternary complex (TC, aa-tRNA.eEF1A.GTP). Here we use photoaffinity labeling to identify two sites of ataluren binding within rRNA, proximal to the decoding center (DC) and the peptidyl transfer center (PTC) of the ribosome, which are directly responsible for ataluren inhibition of termination activity. A third site, within the RFC, has as yet unclear functional consequences. Using single molecule and ensemble fluorescence assays we also demonstrate that termination proceeds via rapid RFC-dependent hydrolysis of peptidyl-tRNA followed by slow release of peptide and tRNA from the ribosome. Ataluren is an apparent competitive inhibitor of productive RFC binding, acting at or before the hydrolysis step. We propose that designing more potent TRIDs which retain ataluren's low toxicity should target areas of the RFC binding site proximal to the DC and PTC which do not overlap the TC binding site.
MeSH term(s)	Oxadiazoles/pharmacology ; Peptide Termination Factors/metabolism ; Protein Biosynthesis ; RNA, Transfer/metabolism ; Ribosomes/metabolism
Chemical Substances	Oxadiazoles ; Peptide Termination Factors ; RNA, Transfer (9014-25-9) ; ataluren (K16AME9I3V)
Language	English
Publishing date	2022-05-06
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-30080-6
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Article: Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation

Shen, Hui / Yanas, Amber / Owens, Michael C. / Zhang, Celia / Fritsch, Clark / Fare, Charlotte M. / Copley, Katie E. / Shorter, James / Goldman, Yale E. / Liu, Kathy Fange

Molecular cell. 2022 July 21, v. 82, no. 14

2022

Abstract: Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs ... ...

Abstract	Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. Herein, using ensemble and single-molecule techniques, we report that the sex chromosome-encoded RNA helicases DDX3X and DDX3Y are distinct in their propensities for liquid-liquid phase separation (LLPS), dissolution, and translation repression. We demonstrate that the N-terminal intrinsically disordered region of DDX3Y more strongly promotes LLPS than the corresponding region of DDX3X and that the weaker ATPase activity of DDX3Y, compared with DDX3X, contributes to the slower disassembly dynamics of DDX3Y-positive condensates. Interestingly, DDX3Y-dependent LLPS represses mRNA translation and enhances aggregation of FUS more strongly than DDX3X-dependent LLPS. Our study provides a platform for future comparisons of sex chromosome-encoded protein homologs, providing insights into sex differences in RNA metabolism and human disease.
Keywords	RNA helicases ; Y chromosome ; adenosinetriphosphatase ; human diseases ; human health ; metabolism ; separation ; sexual dimorphism
Language	English
Dates of publication	2022-0721
Size	p. 2588-2603.e9.
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.04.022
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Straightening Out the Elasticity of Myosin Cross-Bridges.

Linari, Marco / Piazzesi, Gabriella / Pertici, Irene / Dantzig, Jody A / Goldman, Yale E / Lombardi, Vincenzo

Biophysical journal

2020 Volume 118, Issue 5, Page(s) 994–1002

Abstract: In a contracting muscle, myosin cross-bridges extending from thick filaments pull the interdigitating thin (actin-containing) filaments during cyclical ATP-driven interactions toward the center of the sarcomere, the structural unit of striated muscle. ... ...

Abstract	In a contracting muscle, myosin cross-bridges extending from thick filaments pull the interdigitating thin (actin-containing) filaments during cyclical ATP-driven interactions toward the center of the sarcomere, the structural unit of striated muscle. Cross-bridge attachments in the sarcomere have been reported to exhibit a similar stiffness under both positive and negative forces. However, in vitro measurements on filaments with a sparse complement of heads detected a decrease of the cross-bridge stiffness at negative forces attributed to the buckling of the subfragment 2 tail portion. Here, we review some old and new data that confirm that cross-bridge stiffness is nearly linear in the muscle filament lattice. The implications of high myosin stiffness at positive and negative strains are considered in muscle fibers and in nonmuscle intracellular cargo transport.
MeSH term(s)	Actins ; Elasticity ; Muscle Contraction ; Myosins ; Sarcomeres
Chemical Substances	Actins ; Myosins (EC 3.6.4.1)
Language	English
Publishing date	2020-01-13
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. ; Review
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2020.01.002
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