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Article ; Online: prepareforleap: An automated tool for fast PDB-to-parameter generation.

Roe, Daniel R / Bergonzo, Christina

2022 Volume 43, Issue 13, Page(s) 930–935

Abstract: Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can be linked in a variety of ways. ...

Abstract	Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can be linked in a variety of ways. Here we present a stand-alone tool implemented in the widely-used software CPPTRAJ that can be used to automate building structures and generating a "ready to run" parameter and coordinate file pair. This tool automatically identifies carbohydrate anomer type, configuration, linkage, and functional groups, and performs topology modifications (e.g., renaming residue/atom names) required to build the final system using state of the art GLYCAM force field parameters. It will also generate the necessary commands for bonding carbohydrates and creating any disulfide bonds.
MeSH term(s)	Carbohydrates/chemistry ; Molecular Dynamics Simulation ; Software
Chemical Substances	Carbohydrates
Language	English
Publishing date	2022-03-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	1479181-X
ISSN	1096-987X ; 0192-8651
ISSN (online)	1096-987X
ISSN	0192-8651
DOI	10.1002/jcc.26847
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Article ; Online: Divalent ions as mediators of carbonylation in cardiac myosin binding protein C.

Bergonzo, Christina / Aryal, Baikuntha / Rao, V Ashutosh

Journal of molecular graphics & modelling

2023 Volume 124, Page(s) 108576

Abstract: The dosing and efficacy of chemotherapeutic drugs can be limited by toxicity caused by off-pathway reactions. One hypothesis for how such toxicity arises is via metal-catalyzed oxidative damage of cardiac myosin binding protein C (cMyBP-C) found in ... ...

Abstract	The dosing and efficacy of chemotherapeutic drugs can be limited by toxicity caused by off-pathway reactions. One hypothesis for how such toxicity arises is via metal-catalyzed oxidative damage of cardiac myosin binding protein C (cMyBP-C) found in cardiac tissue. Previous research indicates that metal ion mediated reactive oxygen species induce high levels of protein carbonylation, changing the structure and function of this protein. In this work, we use long timescale all-atom molecular dynamics simulations to investigate the ion environment surrounding the C0 and C1 subunits of cMyBP-C responsible for actin binding. We show that divalent cations are co-localized with protein carbonylation-prone amino acid residues and that carbonylation of these residues can lead to site-specific interruption to the actin-cMyBP-C binding.
MeSH term(s)	Actins/chemistry ; Carrier Proteins/chemistry ; Protein C/metabolism ; Protein Binding ; Metals/metabolism ; Cardiac Myosins/metabolism ; Phosphorylation
Chemical Substances	Actins ; Carrier Proteins ; Protein C ; Metals ; Cardiac Myosins (EC 3.6.1.-)
Language	English
Publishing date	2023-07-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	1396450-1
ISSN	1873-4243 ; 1093-3263
ISSN (online)	1873-4243
ISSN	1093-3263
DOI	10.1016/j.jmgm.2023.108576
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Article: Atomic Model Structure of the NIST Monoclonal Antibody (NISTmAb) Reference Material.

Bergonzo, Christina / Gallagher, D Travis

Journal of research of the National Institute of Standards and Technology

2021 Volume 126, Page(s) 126012

Language	English
Publishing date	2021-07-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	1473724-3
ISSN	1044-677X ; 0160-1741
ISSN	1044-677X ; 0160-1741
DOI	10.6028/jres.126.012
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Article ; Online: Effects of glycans and hinge on dynamics in the IgG1 Fc.

Bergonzo, Christina / Hoopes, J Todd / Kelman, Zvi / Gallagher, D Travis

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–9

Abstract: The crystallizable fragment (Fc) domain of immunoglobulin subclass IgG1 antibodies is engineered for a wide variety of pharmaceutical applications. Two important structural variables in Fc constructs are the hinge region connecting the Fc to the antigen ... ...

Abstract	The crystallizable fragment (Fc) domain of immunoglobulin subclass IgG1 antibodies is engineered for a wide variety of pharmaceutical applications. Two important structural variables in Fc constructs are the hinge region connecting the Fc to the antigen binding fragments (Fab) and the glycans present in various glycoforms. These components affect receptor binding interactions that mediate immune activation. To design new antibody drugs, a robust in silico method for linking stability to structural changes is necessary. In this work, all-atom simulations were used to compare the dynamic behavior of the four structural variants arising from presence or absence of the hinge and glycans. We expressed the simplest of these constructs, the 'minimal Fc' with no hinge and no glycans, in
Language	English
Publishing date	2023-10-28
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2270749
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Article ; Online: Conformational heterogeneity of UCAAUC RNA oligonucleotide from molecular dynamics simulations, SAXS, and NMR experiments.

Bergonzo, Christina / Grishaev, Alexander / Bottaro, Sandro

RNA (New York, N.Y.)

2022 Volume 28, Issue 7, Page(s) 937–946

Abstract: We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and ... ...

Abstract	We describe the conformational ensemble of the single-stranded r(UCAAUC) oligonucleotide obtained using extensive molecular dynamics (MD) simulations and Rosetta's FARFAR2 algorithm. The conformations observed in MD consist of A-form-like structures and variations thereof. These structures are not present in the pool generated using FARFAR2. By comparing with available nuclear magnetic resonance (NMR) measurements, we show that the presence of both A-form-like and other extended conformations is necessary to quantitatively explain experimental data. To further validate our results, we measure solution X-ray scattering (SAXS) data on the RNA hexamer and find that simulations result in more compact structures than observed from these experiments. The integration of simulations with NMR via a maximum entropy approach shows that small modifications to the MD ensemble lead to an improved description of the conformational ensemble. Nevertheless, we identify persisting discrepancies in matching experimental SAXS data.
MeSH term(s)	Magnetic Resonance Spectroscopy ; Molecular Dynamics Simulation ; Oligonucleotides ; Protein Conformation ; RNA ; Scattering, Small Angle ; X-Ray Diffraction
Chemical Substances	Oligonucleotides ; RNA (63231-63-0)
Language	English
Publishing date	2022-04-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.078888.121
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Zs.A 4777: Show issues

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Article ; Online: Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops.

Bergonzo, Christina / Szakal, Andrea L

International journal of molecular sciences

2020 Volume 21, Issue 17

Abstract: A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5' untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or ...

Abstract	A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5' untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or otherwise measured. To this end, we have combined molecular dynamics simulations with previous Nuclear Magnetic Resonance measurements for stem loop 2 of SARS-CoV-1 to refine 3D structure predictions of that stem loop. We find that relatively short sampling times allow for loop rearrangement from predicted structures determined in absence of water or ions, to structures better aligned with experimental data. We then use molecular dynamics to predict the refined structure of the transcription regulatory leader sequence (TRS-L) region which includes stem loop 3, and show that arrangement of the loop around exchangeable monovalent potassium can interpret the conformational equilibrium determined by in-cell dimethyl sulfate (DMS) data.
MeSH term(s)	5' Untranslated Regions/genetics ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus Infections/virology ; Humans ; Inverted Repeat Sequences/genetics ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Pandemics ; Pneumonia, Viral/virology ; RNA, Viral/genetics ; SARS-CoV-2
Chemical Substances	5' Untranslated Regions ; RNA, Viral
Keywords	covid19
Language	English
Publishing date	2020-08-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms21176188
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Article ; Online: Contributions from ClpS surface residues in modulating N-terminal peptide binding and their implications for NAAB development.

Callahan, Nicholas / Siegall, William B / Bergonzo, Christina / Marino, John P / Kelman, Zvi

Protein engineering, design & selection : PEDS

2023 Volume 36

Abstract: Numerous technologies are currently in development for use in next-generation protein sequencing platforms. A notable published approach employs fluorescently-tagged binding proteins to identity the N-terminus of immobilized peptides, in-between rounds ... ...

Abstract	Numerous technologies are currently in development for use in next-generation protein sequencing platforms. A notable published approach employs fluorescently-tagged binding proteins to identity the N-terminus of immobilized peptides, in-between rounds of digestion. This approach makes use of N-terminal amino acid binder (NAAB) proteins, which would identify amino acids by chemical and shape complementarity. One source of NAABs is the ClpS protein family, which serve to recruit proteins to bacterial proteosomes based on the identity of the N-terminal amino acid. In this study, a Thermosynechococcus vestitus (also known as Thermosynechococcus elongatus) ClpS2 protein was used as the starting point for direct evolution of an NAAB with affinity and specificity for N-terminal leucine. Enriched variants were analyzed and shown to improve the interaction between the ClpS surface and the peptide chain, without increasing promiscuity. Interestingly, interactions were found that were unanticipated which favor different charged residues located at position 5 from the N-terminus of a target peptide.
MeSH term(s)	Peptides/chemistry ; Protein Binding ; Amino Acids ; Carrier Proteins/chemistry
Chemical Substances	Peptides ; Amino Acids ; Carrier Proteins
Language	English
Publishing date	2023-07-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1466729-0
ISSN	1741-0134 ; 1741-0126
ISSN (online)	1741-0134
ISSN	1741-0126
DOI	10.1093/protein/gzad007
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Article ; Online: Maximizing accuracy of RNA structure in refinement against residual dipolar couplings.

Bergonzo, Christina / Grishaev, Alexander

Journal of biomolecular NMR

2019 Volume 73, Issue 3-4, Page(s) 117–139

Abstract: Structural information about ribonucleic acid (RNA) is lagging behind that of proteins, in part due to its high charge and conformational variability. Molecular dynamics (MD) has played an important role in describing RNA structure, complementing ... ...

Abstract	Structural information about ribonucleic acid (RNA) is lagging behind that of proteins, in part due to its high charge and conformational variability. Molecular dynamics (MD) has played an important role in describing RNA structure, complementing information from both nuclear magnetic resonance (NMR), or X-ray crystallography. We examine the impact of the choice of the empirical force field for RNA structure refinement using cross-validation against residual dipolar couplings (RDCs) as structural accuracy reporter. Four force fields, representing both the state-of-the art in RNA simulation and the most popular selections in NMR structure determination, are compared for a prototypical A-RNA helix. RNA structural accuracy is also evaluated as a function of both density and nature of input NMR data including RDCs, anisotropic chemical shifts, and distance restraints. Our results show a complex interplay between the experimental restraints and the force fields indicating two best-performing choices: high-fidelity refinement in explicit solvent, and the conformational database-derived potentials. Accuracy of RNA models closely tracks the density of 1-bond C-H RDCs, with other data types having beneficial, but smaller effects. At lower RDC density, or when refining against NOEs only, the two selected force fields are capable of accurately describing RNA helices with little or no experimental RDC data, making them available for the higher order structure assembly or better quantification of the intramolecular dynamics. Unrestrained simulations of simple RNA motifs with state-of-the art MD force fields appear to capture the flexibility inherent in nucleic acids while also maintaining a good agreement with the experimental observables.
MeSH term(s)	Algorithms ; Crystallography, X-Ray ; Models, Molecular ; Molecular Dynamics Simulation ; Nuclear Magnetic Resonance, Biomolecular ; Nucleic Acid Conformation ; RNA/chemistry ; Reproducibility of Results
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2019-05-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1081696-3
ISSN	1573-5001 ; 0925-2738
ISSN (online)	1573-5001
ISSN	0925-2738
DOI	10.1007/s10858-019-00236-6
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Article ; Online: Accuracy of MD solvent models in RNA structure refinement assessed via liquid-crystal NMR and spin relaxation data.

Bergonzo, Christina / Grishaev, Alexander

Journal of structural biology

2019 Volume 207, Issue 3, Page(s) 250–259

Abstract: Molecular dynamics (MD) simulations play an important role in characterizing Ribonucleic Acid (RNA) structure, augmenting information from experimental techniques such as Nuclear Magnetic Resonance (NMR). In this work, we examine the accuracy of ... ...

Abstract	Molecular dynamics (MD) simulations play an important role in characterizing Ribonucleic Acid (RNA) structure, augmenting information from experimental techniques such as Nuclear Magnetic Resonance (NMR). In this work, we examine the accuracy of structural representation resulting from application of a number of explicit and implicit solvent models and refinement protocols against experimental data ranging from high density of residual dipolar coupling (RDC) restraints to completely unrestrained simulations. For a prototype A-form RNA helix, our results indicate that AMBER RNA force field with either implicit or explicit solvent can produce a realistic dynamic representation of RNA helical structure, accurately cross-validating with respect to a diverse array of NMR observables. In refinement against NMR distance restraints, modern MD force fields are found to be equally adequate, with high fidelity cross-validation to the residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs), while slightly over-estimating structural order as monitored via NMR relaxation data. With restraints trimmed to encode only for base pairing information, cross-validation quality significantly deteriorates, now exhibiting a pronounced dependence on the choice of the solvent model. This deterioration is found to be partially reversible by increasing planarity restraints on the nucleobase geometry. For completely unrestrained MD simulations, the choice of water model becomes very important, with the best-performing TIP4P-Ew accurately reproducing both the RDC and RCSA data, while closely matching the NMR-derived order parameters. The information provided here will serve as a foundation for MD-based refinement of solution state NMR structures of RNA.
MeSH term(s)	Algorithms ; Magnetic Resonance Spectroscopy ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; RNA/chemistry ; Solvents/chemistry
Chemical Substances	Solvents ; RNA (63231-63-0)
Language	English
Publishing date	2019-07-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1032718-6
ISSN	1095-8657 ; 1047-8477
ISSN (online)	1095-8657
ISSN	1047-8477
DOI	10.1016/j.jsb.2019.07.001
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Article ; Online: Using All-Atom Potentials to Refine RNA Structure Predictions of SARS-CoV-2 Stem Loops

Christina Bergonzo / Andrea L. Szakal

International Journal of Molecular Sciences, Vol 21, Iss 6188, p

2020 Volume 6188

Abstract: A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5′ untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or ...

Abstract	A considerable amount of rapid-paced research is underway to combat the SARS-CoV-2 pandemic. In this work, we assess the 3D structure of the 5′ untranslated region of its RNA, in the hopes that stable secondary structures can be targeted, interrupted, or otherwise measured. To this end, we have combined molecular dynamics simulations with previous Nuclear Magnetic Resonance measurements for stem loop 2 of SARS-CoV-1 to refine 3D structure predictions of that stem loop. We find that relatively short sampling times allow for loop rearrangement from predicted structures determined in absence of water or ions, to structures better aligned with experimental data. We then use molecular dynamics to predict the refined structure of the transcription regulatory leader sequence (TRS-L) region which includes stem loop 3, and show that arrangement of the loop around exchangeable monovalent potassium can interpret the conformational equilibrium determined by in-cell dimethyl sulfate (DMS) data.
Keywords	structure refinement ; molecular dynamics ; RNA stem loops ; discontinuous transcription ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999 ; covid19
Subject code	612
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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