Tom A. Rapoport

Bio: Tom A. Rapoport is an academic researcher from Howard Hughes Medical Institute. The author has contributed to research in topics: Endoplasmic reticulum & Sec61. The author has an hindex of 112, co-authored 279 publications receiving 41685 citations. Previous affiliations of Tom A. Rapoport include Humboldt University of Berlin & ETH Zurich.

A Linear Steady‐State Treatment of Enzymatic Chains

Abstract: A theoretical analysis of linear enzymatic chains is presented By linear approximation simple analytical solutions can be obtained for the metabolite concentrations and the flux through the chain for steady-state conditions The equations are greatly simplified if the common kinetic constants are expressed as functions of two parameters, ie the thermodynamic equilibrium constant and the “characteristic time” Three cardinal terms are proposed for the quantitative description of enzyme systems The first two are the control strength and the control matrix; these indicate the dependence of the flux and the metabolite concentrations, respectively, on the kinetic properties of a given enzyme The third is the effector strength, which defines the dependence of the velocity of an enzyme on the concentration of an effector; it expresses the importance of an effector By linear approximation simple analytical expressions were derived for the control strength, the control matrix and the mass-action ratios The effector strength was calculated for two cases: for a competitive inhibitor and for allosteric effectors according to the Monod (1965) model The influence of an effector on the concentrations of the metabolites was considered

X-ray structure of a protein-conducting channel

Abstract: A conserved heterotrimeric membrane protein complex, the Sec61 or SecY complex, forms a protein-conducting channel, allowing polypeptides to be transferred across or integrated into membranes. We report the crystal structure of the complex from Methanococcus jannaschii at a resolution of 3.2 A. The structure suggests that one copy of the heterotrimer serves as a functional translocation channel. The α-subunit has two linked halves, transmembrane segments 1–5 and 6–10, clamped together by the γ-subunit. A cytoplasmic funnel leading into the channel is plugged by a short helix. Plug displacement can open the channel into an ‘hourglass’ with a ring of hydrophobic residues at its constriction. This ring may form a seal around the translocating polypeptide, hindering the permeation of other molecules. The structure also suggests mechanisms for signal-sequence recognition and for the lateral exit of transmembrane segments of nascent membrane proteins into lipid, and indicates binding sites for partners that provide the driving force for translocation.

Sec61-mediated transfer of a membrane protein from the endoplasmic reticulum to the proteasome for destruction.

Abstract: The human cytomegalovirus genome encodes proteins that trigger destruction of newly synthesized major histocompatibility complex (MHC) class I molecules. The human cytomegalovirus gene US2 specifies a product capable of dislocating MHC class I molecules from the endoplasmic reticulum to the cytosol and delivering them to the proteasome. This process involves the Sec61 complex, in what appears to be a reversal of the reaction by which it translocates nascent chains into the endoplasmic reticulum.

partners transport proteins from the ER into the cytosol

Abstract: 6colony-forming units per 10 ml -1 in SFM supplemented with 0.3 mM calcium chloride, and inoculated onto the surface of the tissue. After inoculation, we incubated tissue samples at 37 8C with 5% CO2 and no supplemental humidity. Transwells containing the inoculated tissue samples were transferred to fresh blood agar every 2 h. The blood agar plates were then incubated overnight at 37 8C for enumeration of colony-forming units representing the number of organisms emerging from the basal surface of the tissue.

The Ubiquitin System

Abstract: The selective degradation of many short-lived proteins in eukaryotic cells is carried out by the ubiquitin system. In this pathway, proteins are targeted for degradation by covalent ligation to ubiquitin, a highly conserved small protein. Ubiquitin-mediated degradation of regulatory proteins plays important roles in the control of numerous processes, including cell-cycle progression, signal transduction, transcriptional regulation, receptor down-regulation, and endocytosis. The ubiquitin system has been implicated in the immune response, development, and programmed cell death. Abnormalities in ubiquitin-mediated processes have been shown to cause pathological conditions, including malignant transformation. In this review we discuss recent information on functions and mechanisms of the ubiquitin system. Since the selectivity of protein degradation is determined mainly at the stage of ligation to ubiquitin, special attention is focused on what we know, and would like to know, about the mode of action of ubiquitin-protein ligation systems and about signals in proteins recognized by these systems.

The Ubiquitin-Proteasome Proteolytic Pathway: Destruction for the Sake of Construction

Abstract: Between the 1960s and 1980s, most life scientists focused their attention on studies of nucleic acids and the translation of the coded information. Protein degradation was a neglected area, conside...

Metabolomics - the link between genotypes and phenotypes

Abstract: Metabolites are the end products of cellular regulatory processes, and their levels can be regarded as the ultimate response of biological systems to genetic or environmental changes. In parallel to the terms ‘transcriptome’ and ‘proteome’, the set of metabolites synthesized by a biological system constitute its ‘metabolome’. Yet, unlike other functional genomics approaches, the unbiased simultaneous identification and quantification of plant metabolomes has been largely neglected. Until recently, most analyses were restricted to profiling selected classes of compounds, or to fingerprinting metabolic changes without sufficient analytical resolution to determine metabolite levels and identities individually. As a prerequisite for metabolomic analysis, careful consideration of the methods employed for tissue extraction, sample preparation, data acquisition, and data mining must be taken. In this review, the differences among metabolite target analysis, metabolite profiling, and metabolic fingerprinting are clarified, and terms are defined. Current approaches are examined, and potential applications are summarized with a special emphasis on data mining and mathematical modelling of metabolism.

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing.

Abstract: A newly described coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which is the causative agent of coronavirus disease 2019 (COVID-19), has infected over 2.3 million people, led to the death of more than 160,000 individuals and caused worldwide social and economic disruption1,2. There are no antiviral drugs with proven clinical efficacy for the treatment of COVID-19, nor are there any vaccines that prevent infection with SARS-CoV-2, and efforts to develop drugs and vaccines are hampered by the limited knowledge of the molecular details of how SARS-CoV-2 infects cells. Here we cloned, tagged and expressed 26 of the 29 SARS-CoV-2 proteins in human cells and identified the human proteins that physically associated with each of the SARS-CoV-2 proteins using affinity-purification mass spectrometry, identifying 332 high-confidence protein–protein interactions between SARS-CoV-2 and human proteins. Among these, we identify 66 druggable human proteins or host factors targeted by 69 compounds (of which, 29 drugs are approved by the US Food and Drug Administration, 12 are in clinical trials and 28 are preclinical compounds). We screened a subset of these in multiple viral assays and found two sets of pharmacological agents that displayed antiviral activity: inhibitors of mRNA translation and predicted regulators of the sigma-1 and sigma-2 receptors. Further studies of these host-factor-targeting agents, including their combination with drugs that directly target viral enzymes, could lead to a therapeutic regimen to treat COVID-19. A human–SARS-CoV-2 protein interaction map highlights cellular processes that are hijacked by the virus and that can be targeted by existing drugs, including inhibitors of mRNA translation and predicted regulators of the sigma receptors.