David Cowburn

David Cowburn
Albert Einstein College of Medicine | AECOM · Departments of Biochemistry and Physiology & Biophysics

PhD DSc

About

300
Publications
16,864
Reads
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13,435
Citations
Introduction
David Cowburn currently works at the Departments of Biochemistry and Physiology & Biophysics, Albert Einstein College of Medicine.
Additional affiliations
September 2010 - present
Albert Einstein College of Medicine
Position
  • Professor (Full)
September 2010 - January 2017
Albert Einstein College of Medicine
Position
  • Professor
September 2000 - September 2010
New York Structural Biology Center
Position
  • President and CEO
Description
  • Start up and operation of NYSBC, covering NMR, EM, XRC.

Publications

Publications (300)
Article
Full-text available
The human immunodeficiency virus type 1 (HIV-1) capsid protein plays a critical role in virus core particle assembly and is an important target for novel therapeutic strategies. In a previous study, we characterized the binding affinity of a hydrocarbon stapled helical peptide, NYAD-1, for the capsid protein (K(d) approximately 1 mum) and demonstra...
Article
Full-text available
Powassan virus (POWV) is an emerging tick borne flavivirus (TBFV) that causes severe neuroinvasive disease. Currently, there are no approved treatments or vaccines to combat POWV infection. Here, we generated and characterized a nanoparticle immunogen displaying domain III (EDIII) of the POWV E glycoprotein. Immunization with POWV EDIII presented o...
Article
Full-text available
Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. This paper introduces LIAN (LInear prog...
Article
Nuclear pore complexes (NPCs) mediate nucleocytoplasmic exchange controlling the flow of molecules into and out of the nucleus. The selective filter properties of NPCs enable translocation of specific molecules known as nuclear transport factors (NTRs) and their cargo. Central to this selectivity barrier is a group of largely intrinsically disorder...
Article
Full-text available
Zika virus (ZIKV) is a flavivirus that can cause severe disease, but there are no approved treatments or vaccines. A complication for flavivirus vaccine development is the potential of immunogens to enhance infection via antibody-dependent enhancement (ADE), a process mediated by poorly neutralizing and cross-reactive antibodies. Thus, there is a g...
Article
Full-text available
INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses...
Preprint
Nuclear Magnetic Resonance (NMR) Spectroscopy is the second most used technique (after X-ray crystallography) for structural determination of proteins. A computational challenge in this technique involves solving a discrete optimization problem that assigns the resonance frequency to each atom in the protein. We present a novel linear programming f...
Chapter
Nuclear magnetic resonance (NMR) titration and isothermal titration calorimetry can be combined to provide an assessment of how multivalent intrinsically disordered protein (IDP) interactions can involve enthalpy–entropy balance. Here, we describe the underlying technical details and additional methods, such as dynamic light scattering analysis, ne...
Article
Phase separation of multivalent protein and RNA molecules enables cells the formation of reversible nonstoichiometric, membraneless assemblies. These assemblies, referred to as biomolecular condensates, help with the spatial organization and compartmentalization of cellular matter. Each biomolecular condensate is defined by a distinct macromolecula...
Article
Split inteins associate to trigger protein splicing in trans, a post-translational modification in which protein sequences fused to the intein pair are ligated together in a traceless manner. Recently, a family of naturally split inteins has been identified that is split at a non-canonical location in the primary sequence. These atypically split in...
Article
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism that enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interactin...
Article
Full-text available
Intrinsically disordered proteins (IDPs) play important roles in many biological systems. Given the vast conformational space that IDPs can explore, the thermodynamics of the interactions with their partners is closely linked to their biological functions. Intrinsically disordered regions of Phe-Gly nucleoporins (FG Nups) that contain multiple phen...
Article
Full-text available
Nucleoplasmin (Npm) is a highly conserved histone chaperone responsible for the maternal storage and zygotic release of histones H2A/H2B. Npm contains a pentameric N-terminal core domain and an intrinsically disordered C-terminal tail domain. Though intrinsically disordered regions are common among histone chaperones, their roles in histone binding...
Article
Full-text available
The largely intrinsically disordered phenylalanine-glycine-rich nucleoporins (FG Nups) underline a selectivity mechanism, which enables the rapid translocation of transport factors (TFs) through the nuclear pore complexes (NPCs). Conflicting models of NPC transport have assumed that FG Nups undergo different conformational transitions upon interact...
Chapter
Segmental isotopic labeling of samples for NMR studies is attractive for large complex biomacromolecular systems, especially for studies of function-related protein-ligand interactions and protein dynamics (Goto and Kay, Curr Opin Struct Biol 10:585-592, 2000; Rosa et al., Molecules (Basel, Switzerland) 18:440, 2013; Hiroaki, Expert Opin Drug Disco...
Article
Full-text available
The protein trans-splicing (PTS) activity of naturally split inteins has found widespread use in chemical biology and biotechnology. However, currently used naturally split inteins suffer from an "extein dependence," whereby residues surrounding the splice junction strongly affect splicing efficiency, limiting the general applicability of many PTS-...
Article
Full-text available
We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints a...
Article
We revisit the problem of protein structure determination from geometrical restraints from NMR, using convex optimization. It is well-known that the NPhard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a convex semidefinite program (SDP). However, often the NOE distance restraints ar...
Article
Full-text available
Author summary Receptor tyrosine kinases are proteins integral to relaying signals from outside the cell to activators inside the cell that stimulate cell growth and development. Therefore, when these proteins show intrinsic activity independent of extracellular signaling, they can frequently cause developmental abnormalities, if the unchecked acti...
Data
“Monophosphorylated” conformations. Representative structures from 12 clusters of metadynamics trajectory structures in which pTyr656 is pointed inward, and not pTyr657. (EPS)
Data
Conformational heterogeneity from metadynamics. Superimposed representative structures of 56 clusters of metadynamics trajectory structures. (EPS)
Data
Convergence of the string method. Root-mean-square displacement of string in CV space from its original position in CV space. (PNG)
Data
Convergence of the string method (alternate CVs). Root-mean-square displacement of string in CV space from its original position in CV space, for the set of CVs discussed in S1 Text. (TIF)
Data
String method algorithm using alternate CVs. Discussion of string method algorithm using an alternate set of CVs to confirm results discussed in main text. (DOCX)
Data
Atom groups used for CVs in alternate string method algorithm. (DOCX)
Data
Simulation of the precatalytic structure with Arg664. Simulation of the FGFR2 kinase precatalytic complex with Arg664 in the active site. (MPG)
Data
Simulation of the precatalytic structure without Arg664. Simulation of the FGFR2 kinase precatalytic complex with Arg664 constrained to remain outside of the active site. (MPG)
Data
Motion of pTyr657 and Arg664 in string method algorithm using alternate CVs. Distances between key atoms over the course of the string method pathway using alternate CVs discussed in S1 Text. (TIF)
Article
The membrane ring that equatorially circumscribes the nuclear pore complex (NPC) in the perinuclear lumen of the nuclear envelope is composed largely of Pom152 in yeast and its ortholog Nup210 (or Gp210) in vertebrates. Here, we have used a combination of negative-stain electron microscopy, nuclear magnetic resonance, and small-angle X-ray scatteri...
Poster
Macromolecular traffic through the nuclear pore complex (NPC) occurs by either passive or facilitated diffusion. While passive diffusion rates are believed to decrease dramatically beyond the approximately 30-60 kDa size threshold, facilitated diffusion, which is mediated by soluble nuclear transport receptors (NTRs), proceeds rapidly even for larg...
Article
Full-text available
Proteins with large molecular weight exhibit increased number of NMR signals, and the resulting spectral overlap typically imposes limitations. Segmental isotope labeling of individual domains of multidomain protein facilitates spectral interpretation by reducing the number of signals and thus provides a solution to spectral overlap (Liu et al., 20...
Article
Full-text available
The Src Homology 2 (SH2) domain is a structurally conserved protein domain that typically binds to a phosphorylated tyrosine in a peptide motif from the target protein. The SH2 domain of C-terminal Src kinase (Csk) contains a single disulfide bond, which is unusual for most SH2 domains. Although the global motion of SH2 domain regulates Csk functio...
Article
Full-text available
Estimation of the Saupe tensor is central to the determination of molecular structures from residual dipolar couplings (RDC) or chemical shift anisotropies. Assuming a given template structure, the singular value decomposition (SVD) method proposed in Losonczi et al. 1999 has been used traditionally to estimate the Saupe tensor. Despite its simplic...
Article
Full-text available
Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In...
Article
Full-text available
We investigate the classical problem of protein structure determination in NMR spectroscopy from geometrical restraints using convex optimization. It is well-known that the NP-hard distance geometry problem of determining atomic positions from pairwise distance restraints can be relaxed into a semidefinite program (SDP). However, in practice there...
Article
Protein trans-splicing (PTS) by split inteins has found widespread use in chemical biology and biotechnology. Herein, we describe the use of a consensus design approach to engineer a split intein with enhanced stability and activity that make it more robust than any known PTS system. Using batch mutagenesis, we first conduct a detailed analysis of...
Poster
Unregulated activity of tyrosine kinases (TKs) is responsible for numerous developmental, oncologic and musculoskeletal diseases, yet the regulatory mechanisms of TKs are still in need of elucidation. Fibroblast growth factor receptor (FGFR) kinases are a TK family whose catalytic activity appears to be regulated by phosphorylation of two adjacent...
Article
Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. However, the...
Article
Anti-DNA antibodies are the serological hallmark of systemic lupus erythematosus, and participate in the pathogenesis of lupus nephritis by cross-reacting with multiple renal antigens. Previously, using a panel of murine anti-DNA IgGs that share identical variable regions but that differ in the constant regions, we demonstrated that the cross-react...
Article
Full-text available
The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a pepti...
Article
Full-text available
Anti-DNA antibodies play a pivotal role in the pathogenesis of lupus nephritis by cross reacting with renal antigens. Previously, we demonstrated that the binding affinity of anti-DNA antibodies to self-antigens is isotype dependent. Furthermore, significant variability in renal pathogenicity was seen among a panel of anti-DNA isotypes (derived fro...
Article
Full-text available
Abstract Nuclear pore complexes (NPCs) form a selective filter that allows the rapid passage of transport factors (TFs) and their cargoes across the nuclear envelope, while blocking the passage of other macromolecules. Intrinsically disordered proteins (IDPs) containing phenylalanyl-glycyl (FG)-rich repeats line the pore and interact with TFs. Howe...
Article
Lipid-based micelles provide an attractive option for therapeutic and diagnostic applications due to their small size (< 20 nm) and ability to self-assemble and improve the solubility of both hydrophobic drugs and dyes. Their use, however, has been challenged by the fact that these particles are inherently unstable in serum due to interactions with...
Poster
Unregulated activity of tyrosine kinases (TKS) is responsible for numerous developmental musculoskeletal diseases and cancers. The regulatory mechanisms of tks and how they are affected by point mutations are still in need of elucidation. Fibroblast growth factor receptor (FGFR) kinase is a TK whose regulatory element, the “molecular brake,” is tho...
Article
Full-text available
There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We...
Article
Full-text available
Protein splicing is a posttranslational modification where intervening proteins (inteins) cleave themselves from larger precursor proteins and ligate their flanking polypeptides (exteins) through a multistep chemical reaction. First thought to be an anomaly found in only a few organisms, protein splicing by inteins has since been observed in microo...
Article
Split inteins are a class of naturally occurring proteins that carry out protein splicing in trans. The chemical mechanism of protein trans-splicing is well-understood and has been exploited to develop several powerful protein engineering technologies. Split intein chemistry is preceded by efficient molecular recognition between two protomers that...
Article
Full-text available
The basal (ligand-independent) kinase activity of receptor tyrosine kinases (RTKs) promotes trans-phosphorylation on activation loop tyrosines upon ligand-induced receptor dimerization, thus upregulating intrinsic kinase activity and triggering intracellular signaling. To understand the molecular determinants of intrinsic kinase activity, we used X...
Article
The multi-domain scaffolding protein NHERF1 modulates the assembly and intracellular trafficking of various transmembrane receptors and ion-transport proteins. The two PDZ domains of NHERF1 possess very different ligand-binding capabilities: PDZ1 recognizes a variety of membrane proteins with high affinity, while PDZ2 only binds limited number of t...
Article
Split inteins play an important role in modern protein semisynthesis techniques. These naturally occurring protein splicing domains can be used for in vitro and in vivo protein modification, peptide and protein cyclization, segmental isotopic labeling, and the construction of biosensors. The most well-characterized family of split inteins, the cyan...
Article
The Nuclear Pore Complex (NPC) mediates all transport between the nucleus and cytoplasm. The channel of the NPC is lined with “FG Nups”, a family of intrinsically disordered proteins characterized by phenylalanine-glycine repeat motifs. FG nups form the exquisitely selective filter of the NPC; non-binding proteins are excluded while the binding of...
Article
Full-text available
The graph realization problem has received a great deal of attention in recent years, due to its importance in applications such as wireless sensor networks and structural biology. In this paper, we extend the previous work and propose the 3D-As-Synchronized-As-Possible (3D-ASAP) algorithm, for the graph realization problem in ℝ(3), given a sparse...
Article
Full-text available
The finding that the antibody (Ab) constant (C) region can influence fine specificity suggests that isotype switching contributes to the generation of Ab diversity and idiotype restriction. Despite the centrality of this observation for diverse immunological effects such as vaccine responses, isotype-restricted antibody responses, and the origin of...
Article
Full-text available
A great portion of tyrosine kinases are involved in cell development and their structural alteration is intimately involved in associated pathologies of development and oncology. These kinases are one of the major groups of targets under investigation for molecular therapeutics. To carry out biochemical and structural biological studies on these ki...
Article
Hydrocarbon stapling of peptides is a powerful technique to transform linear peptides into cell-permeable helical structures that can bind to specific biological targets. In this study, we have used high resolution solution NMR techniques complemented by dynamic light scattering to characterize extensively a family of hydrocarbon stapled peptides w...
Chapter
Structural biology in general, including NMR, is highly reductionist – simplifying complex systems to their component parts, and extrapolating to the native interactions that occur in cells and tissues. The strengths of NMR analysis – high-resolution structure determination, intermolecular interface identification, dynamic molecular descriptions, s...