Theresa A Ramelot

Theresa A Ramelot
Rensselaer Polytechnic Institute | RPI · Center for Biotechnology and Interdisciplinary Studies

PhD Cornell, Researcher in protein NMR at RPI

About

84
Publications
7,338
Reads
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1,707
Citations
Introduction
I study protein structures and dynamics by NMR and MS techniques in the lab of Dr. Gaetano Montelione at RPI.
Additional affiliations
January 2016 - June 2020
Miami University
Position
  • Manager
Description
  • I managed the NMR/MS Facility at Miami University including all training, calibrations, repairs, maintenance and billing.
August 2006 - December 2015
Miami University
Position
  • Senior Researcher
January 2001 - July 2006
Pacific Northwest National Laboratory
Position
  • PostDoc Position
Education
September 1993 - December 2000
Cornell University
Field of study
  • Biophysics and Biochemistry
September 1989 - May 1993
University of San Diego
Field of study
  • Chemistry and Biochemistry with Minor in Mathematics

Publications

Publications (84)
Article
IscU is a highly conserved protein that serves as the scaffold for IscS-mediated assembly of iron-sulfur ([Fe-S]) clusters. We report the NMR solution structure of monomeric Haemophilus influenzae IscU with zinc bound at the [Fe-S] cluster assembly site. The compact core of the globular structure has an alpha-beta sandwich architecture with a three...
Article
The structure of human protein HSPC034 has been determined by both solution nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography. Refinement of the NMR structure ensemble, using a Rosetta protocol in the absence of NMR restraints, resulted in significant improvements not only in structure quality, but also in molecular replacemen...
Article
While structural symmetry is a prevailing feature of homo-oligomeric proteins, asymmetry provides unique mechanistic opportunities. We present the crystal structure of full-length TRAP1, the mitochondrial Hsp90 molecular chaperone, in a catalytically active closed state. The TRAP1 homodimer adopts a distinct, asymmetric conformation, where one prot...
Article
Psilocybin, the prodrug of the psychoactive molecule psilocin, has demonstrated promising results in clinical trials for the treatment of addiction, depression, and post-traumatic stress disorder. The development of a psilocybin production platform in a highly engineerable microbe could lead to rapid advances towards the bioproduction of psilocybin...
Article
Full-text available
There has been considerable recent progress in protein structure prediction using deep neural networks to predict inter-residue distances from amino acid sequences1,2,3. Here we investigate whether the information captured by such networks is sufficiently rich to generate new folded proteins with sequences unrelated to those of the naturally occurr...
Article
NMR is a valuable experimental tool in the structural biologist’s toolkit to elucidate the structures, functions, and motions of biomolecules. The progress of machine learning, particularly in structural biology, reveals the critical importance of large, diverse, and reliable datasets in developing new methods and understanding in structural biolog...
Article
Full-text available
Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NM...
Preprint
Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracy rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR...
Preprint
NMR is a valuable experimental tool in the structural biologist’s toolkit to elucidate the structures, functions, and motions of biomolecules. The progress of machine learning, particularly in structural biology, reveals the critical importance of large, diverse, and reliable datasets in developing new methods and understanding in structural biolog...
Article
Full-text available
Effective control of COVID-19 requires antivirals directed against SARS-CoV-2. We assessed ten hepatitis C virus (HCV) protease-inhibitor drugs as potential SARS-CoV-2 antivirals. There is a striking structural similarity of the substrate binding clefts of SARS-CoV-2 main protease (Mpro) and HCV NS3/4A protease. Virtual docking experiments show tha...
Preprint
Effective control of COVID-19 requires antivirals directed against SARS-CoV-2 virus. Here we assess ten available HCV protease inhibitor drugs as potential SARS-CoV-2 antivirals. There is a striking structural similarity of the substrate binding clefts of SARS- CoV-2 M pro and HCV NS3/4A proteases, and virtual docking experiments show that all ten...
Article
Proanthocyanidins (condensed tannins) are important in food chemistry, agriculture, and health, driving demand for improvements in structure determination. We used ultrahigh resolution Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) methods to determine the exact composition of individual species in heterogeneous mixtures of...
Article
Full-text available
Rational design of protein-polymer bioconjugates is hindered by limited experimental data and mechanistic understanding on interactions between the two. In this communication, nuclear magnetic resonance (NMR) paramagnetic relaxation enhancement (PRE) reports on distances between paramagnetic spin labels and NMR active nuclei, informing on the confo...
Article
Full-text available
SP_0782 from Streptococcus pneumoniae is a dimeric protein that potentially binds with single-stranded DNA (ssDNA) in a manner similar to human PC4, the prototype of PC4-like proteins, which plays roles in transcription and maintenance of genome stability. In a previous NMR study, SP_0782 exhibited an ssDNA-binding property different from YdbC, a p...
Article
Protein CGL2373 from Corynebacterium glutamicum was previously proposed to be a member of the polyketide_cyc2 family, based on amino‐acid sequence and secondary structure features derived from NMR chemical shift assignments. We report here the solution NMR structure of CGL2373, which contains three α‐helices and one antiparallel β‐sheet and adopts...
Article
Growth arrest specific 7 (Gas7) protein is a cytoskeleton regulator playing a crucial role in neural cell development and function, and has been implicated in Alzheimer disease, schizophrenia and cancers. In human, three Gas7 isoforms can be expressed from a single Gas7 gene, while only the longest isoform, hGas7c, possesses an SH3 domain at the N-...
Article
Full-text available
The ever-increasing occurrence of antibiotic resistance presents a major threat to public health. Specifically, resistance conferred by β-lactamases places the efficacy of currently available antibiotics at risk. Klebsiella pneumoniae carbapenemase-2 (KPC-2) is a β-lactamase that enables carbapenem resistance and represents a clear and present dang...
Article
We report the solution NMR structure of CHU_1110 from Cytophaga hutchinsonii. CHU_1110 contains three α‐helices and one antiparallel β‐sheet, forming a large cavity in the center of the protein, which are consistent with the structural characteristics of AHSA1 protein family. This protein shows high structural similarities to the prokaryotic protei...
Article
SH2 domain-containing inositol 5-phosphatase 2 (SHIP2) binds with the Y1356-phosphorylated hepatocyte growth factor (HGF) receptor, c-MET, through its SH2 domain, which is essential for the role of SHIP2 in HGF-induced cell scattering and cell spreading. Previously, the experimental structure of the SH2 domain from SHIP2 (SHIP2-SH2) had not been re...
Article
Full-text available
The forkhead-associated (FHA) domain is known as a phosphopeptide recognition domain embedded in regulatory proteins from both eukaryotes and bacteria with various biological functions. In this study, the gene encoding a predicted FHA domain from Mb1858 (residues V24-D155 from the 162 amino acid protein Mb1858) in Mycobacterium bovis was cloned, an...
Article
Human protein TGIF1 is an essential regulator of cell fate with broad roles in different tissues, and has been implicated in holoprosencephaly (HPE) and many cancers. The function of TGIF1 in transcriptional regulation depends on its three-amino acid loop extension (TALE) type of homeodomain (HD). Two missense mutations that led to P192A and R219C...
Article
Full-text available
Protein CGL2373 from Corynebacterium glutamicum, which is 155 amino acids long and 17.7 kDa, is a member of the polyketide_cyc2 family. As a potential polyketide cyclase, it may play an important role in the biosynthesis of aromatic polyketides that are the source of many bioactive molecules. Here we report the complete (1)H, (13)C and (15)N chemic...
Article
Full-text available
Hsp90 is a homodimeric ATP-dependent molecular chaperone that remodels its substrate ‘client’ proteins, facilitating their folding and activating them for biological function. Despite decades of research, the mechanism connecting ATP hydrolysis and chaperone function remains elusive. Particularly puzzling has been the apparent lack of cooperativity...
Data
Data collection and refinement statistics for zebrafish TRAP1 crystals. Each dataset was collected from a single crystal. Values in parentheses are for highest-resolution shell. DOI: http://dx.doi.org/10.7554/eLife.25235.014
Article
Full-text available
A strategy for acquiring structural information from sparsely isotopically labeled large proteins is illustrated with an application to the E. coli heat-shock protein, HtpG (high temperature protein G), a 145 kDa dimer. It uses (13)C-alanine methyl labeling in a perdeuterated background to take advantage of the sensitivity and resolution of Methyl-...
Article
Aqueous initiators for continuous activator regeneration atom transfer radical polymerization (ICAR ATRP) was applied to graft well defined acrylamide, N,N-dimethylacrylamide and N-vinylimidazole homo and block copolymers from a model protein initiator (bovine serum albumin (BSA)) under bio-relevant conditions. Using N-vinylimidazole as a ligand ca...
Article
Full-text available
Genetic and functional studies showed that some components of the Acinetobacter baumannii ATCC 17978 A1S_0112-A1S_0119 gene cluster are critical for biofilm biogenesis and surface motility. Recently, our group has shown that the A1S_0114 gene was involved in biofilm formation, a process related with pathogenesis. Confirming our previous results, mi...
Data
Ac-505 MS/MS spectra. (A) MS data collected on the FT-ICR with ECD fragmentation in positive ion mode. (B) MS/MS collected on a MaXis QTOF in positive ion mode (LC-MS) and (C) negative ion mode (direct injection).
Data
Confirmation of the polycistronic nature of the A. baumannii ATCC 17978 A1S_0112-A1S_0119 operon. Total DNA (lanes 2–7), cDNA (lanes 8–13) and total RNA (lanes 14–19) samples were used as templates in PCR reactions using primers annealing to the A1S_0112-A1S 0113 (lanes 2, 8, and 14), A1S_0113-A1S_0115 (lanes 3, 9, and 15), A1S_0115-A1S_0116 (lanes...
Data
MS/MS—based fragmentation predictions (A,B) are two of the 40 total MSn spectra from MS(3) to MS(6) recorded on the OSU Bruker amaZon in positive ion mode using direct injection of a HPLC purified Ac-505. MS(2) for 488.3 and MS(4) for 235.2 m/z fragment ions are shown in (A,B), respectively. Neutral losses are shown in black. Panel (C) is a schemat...
Data
Predicted product ions of Ac-505 based on accurate mass and typical bond cleavage patterns under electrospray conditions in positive ion mode.
Data
Predicted product ions of Ac-505 based on accurate mass and typical bond cleavage patterns under electrospray conditions in negative ion mode.
Data
Oligonucleotides used in the present study.
Data
HRMS data of Ac-505 and MS2 fragments measured on a ESI MaXis QTOF (direct infusion) in negative ion mode.
Data
Growth of the 17978 parental and the Δ0114 isogenic deletion derivative strains. The OD600values of each strain grown in LB or SB at 37°C for 24 h with shaking were determined hourly. Error bars represent the standard error (SE) of the mean.
Data
HRMS data of Ac-505. Measured m/z-values are reported for MS fragment ions measured on ESI MaXis QTOF (LC-MS2) and 15T FT-ICR ECD (direct infusion) instruments in positive ion mode, respectively. The molecular formulas of the product ions are based on accurate mass and isotopic pattern matching of the ions as well as typical bond cleavage patterns...
Article
Full-text available
Hsp90 is a homodimeric ATP-dependent molecular chaperone that remodels its substrate " client " proteins, facilitating their folding and activating them for biological function. Despite decades of research, the mechanism connecting ATP hydrolysis and chaperone function remains elusive. Particularly puzzling has been the apparent lack of cooperativi...
Article
We report the solution NMR structure of RHE_CH02687 from Rhizobium etli. Its structure consists of two β-sheets that together with two short and one long α-helix form a hydrophobic cavity. This protein shows a high structural similarity to the prokaryotic protein YndB from Bacillus subtilis, and the eukaryotic protein Aha1. NMR titration experiment...
Article
Human INSM1 containing five C-terminal C2H2-type zinc fingers (ZFs), is a key regulator of neuroendocrine development. Previous research reported that full-length INSM1 containing all five ZFs recognized a consensus DNA sequence. Structure elucidation of human INSM1 ZFs is currently insufficient to understand the DNA binding mechanism. Herein, we p...
Article
Full-text available
The protein SP_0782 from Streptococcus pneumonia is a small homodimeric protein that belongs to a protein family containing representative members with single-stranded DNA (ssDNA) binding functions. The ssDNA binding of the homolog YdbC from Lactococcus lactis was previously characterized when bound to a 20-mer of pyridine-rich ssDNA, sharing an ov...
Article
Full-text available
Importance: In this study, we found that our P[19] strain and other P[II] RVs recognize mucin cores and the type 1 HBGA precursors as the minimal functional units and that additional saccharides adjacent to these units can alter binding outcomes and thereby possibly host ranges. These data may help to explain why some P[II] RVs, such as P[6] and P...
Article
Full-text available
We have developed an on-line NMR/X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for pr...
Article
The success of homodimer structure determination by conventional solution NMR spectroscopy relies greatly on interchain distance restraints (less than 6 Å) derived from nuclear Overhauser effects (NOEs) obtained from (13)C-edited, (12)C-filtered NOESY experiments. However, these experiments may fail when the mixed (13)C-/(12)C-homodimer is never si...
Article
Calicheamicin ɣ1I (1) is an enediyne antitumor compound produced by Micromonospora echinospora spp. calichensis and its biosynthetic gene cluster has been previously reported. Despite extensive analysis and biochemical study, several genes in the biosynthetic gene cluster of 1 remain functionally unassigned. Using a structural genomics approach and...
Article
We have determined the solution NMR structure of the intermembrane space domain (IMSD) of the human mitochondrial ATPase associated with various activities (AAA) protease known as AFG3-like protein 2 (AFG3L2). Our structural analysis and molecular dynamics results indicate that the IMSD is peripherally bound to the membrane surface. This is a modif...
Article
Full-text available
CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e(-07)) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the functio...
Article
Full-text available
Here, we report novel methods to measure rate constants for homodimer subunit exchange using double electron–electron resonance (DEER) electron paramagnetic resonance spectroscopy measurements and nuclear magnetic resonance spectroscopy based paramagnetic relaxation enhancement (PRE) measurements. The techniques were demonstrated using the homodime...
Article
The solution nuclear magnetic resonance (NMR) structures and backbone (15)N dynamics of the specialized acyl carrier protein (ACP), RpAcpXL, from Rhodopseudomonas palustris, in both the apo form and holo form modified by covalent attachment of 4'-phosphopantetheine at S37, are virtually identical, monomeric, and correspond to the closed conformatio...
Article
Full-text available
The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of...
Article
The protein domain family PF12095 (DUF3571) is a functionally uncharacterized family of small proteins conserved from cyanobacteria to plants that are typically 85 to 95 amino acids in length in cyanobacteria. In this report, we describe the solution NMR structure of the 86-residue protein Asl3597 from Nostoc sp. PCC7120. The structure of Asl3597,...
Article
Here we describe the solution NMR structure of the 120 amino acid fragment of BT_0084, without the N-terminal lipoprotein targeting sequence, encoded in a conjugative transposon (CTn) in the genome of Bacteroides thetaiotamicron. BT_0084 belongs to a conserved family of TraQ lipoproteins that are encoded at the end of the tra operon, which contains...
Article
Full-text available
After severe burn injury, proinflammatory cytokine levels are elevated in serum and skeletal muscle, which in turn increases protein breakdown and decreases protein synthesis. In this study, C2C12 mouse skeletal muscle cell line myotubes were exposed to proinflammatory cytokines tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ) as an in vitr...
Article
Full-text available
Protein domain family YabP (PF07873) is a family of small protein domains that are conserved in a wide range of bacteria and involved in spore coat assembly during the process of sporulation. The 62-residue fragment of Dsy0195 from Desulfitobacterium hafniense, which belongs to the YabP family, exists as a homodimer in solution under the conditions...
Article
GmACP3 from Geobacter metallireducens is a specialized acyl carrier protein (ACP) whose gene, gmet_2339, is located near genes encoding many proteins involved in lipopolysaccharide (LPS) biosynthesis, indicating a likely function for GmACP3 in LPS production. By overexpression in Escherichia coli, about 50% holo-GmACP3 and 50% apo-GmACP3 were obtai...
Article
Oxygenic photosynthesis is initiated by photosystem II (PSII) in the thylakoid membranes of plants, algae and cyanobacteria. PSII is a multi-subunit pigment-protein complex responsible for splitting water into oxygen gas, hydrogen ions and electrons transferred to electron acceptors during photosynthesis.1 Two homologous membrane-spanning proteins...
Article
One goal of the CASP community wide experiment on the critical assessment of techniques for protein structure prediction is to identify the current state of the art in protein structure prediction and modeling. A fundamental principle of CASP is blind prediction on a set of relevant protein targets, that is, the participating computational methods...
Article
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein c...
Article
Full-text available
Conventional protein structure determination from nuclear magnetic resonance data relies heavily on side-chain proton-to-proton distances. The necessary side-chain resonance assignment, however, is labor intensive and prone to error. Here we show that structures can be accurately determined without nuclear magnetic resonance (NMR) information on th...