Crystal and solution structures of fragments of the human leucocyte common antigen-related protein

Abstract

PDB references: human leucocyte common antigen-related protein, FNIII domains 3 and 4, 6tpt; 6tpu; FNIII domains 1 and 2, 6tpv; FNIII domains 1-4, 6tpwSupporting information: this article has supporting information at journals.iucr.org/d Crystal and solution structures of fragments of the human leucocyte common antigen-related protein Leucocyte common antigen-related protein (LAR) is a post-synaptic type I transmembrane receptor protein that is important for neuronal functionality and is genetically coupled to neuronal disorders such as attention deficit hyperactivity disorder (ADHD). To understand the molecular function of LAR, structural and biochemical studies of protein fragments derived from the ectodomain of human LAR have been performed. The crystal structure of a fragment encompassing the first four FNIII domains (LAR FN1-4 ) showed a characteristic L shape. SAXS data suggested limited flexibility within LAR FN1-4 , while rigid-body refinement of the SAXS data using the X-ray-derived atomic model showed a smaller angle between the domains defining the L shape compared with the crystal structure. The capabilities of the individual LAR fragments to interact with heparin was examined using microscale thermophoresis and heparin-affinity chromatography. The results showed that the three N-terminal immunoglobulin domains (LAR Ig1-3 ) and the four C-terminal FNIII domains (LAR FN5-8 ) both bound heparin, while LAR FN1-4 did not. The lowmolecular-weight heparin drug Innohep induced a shift in hydrodynamic volume as assessed by size-exclusion chromatography of LAR Ig1-3 and LAR FN5-8 , while the chemically defined pentameric heparin drug Arixtra did not. Together, the presented results suggest the presence of an additional heparin-binding site in human LAR.

Molecular Inversion Probe-Based Sequencing of USH2A Exons and Splice Sites as a Cost-Effective Screening Tool in USH2 and arRP Cases

“…Several models were created and combined into a single best-fit hybrid model, predominantly informed by PDB file 4U3H [49]. Small parts of models created with PDB files 4YFE, 6TPW and 4M4P were also used [50][51][52]. The final hybrid model was subjected to one more energy minimization round and used for further analysis.…”

Structural insights into the substrate-binding proteins Mce1A and Mce4A from Mycobacterium tuberculosis

“…For MtMce1A 36-148 , the entire compact and elongated models were generated with Robetta using the MtMce4A 39-140 compact and elongated crystal structures as the template. The models were evaluated against the experimental data using an in-house-written program (Steiner et al, 2018;Vilstrup et al, 2020 and MtMce4A 36-400 were generated using I-TASSER. Summaries of the data-collection and analysis parameters are provided in Supplementary Tables S4, S5 and S6.…”

“…The scattering of the buffer was subtracted from the protein scattering using ScÅ tter. The data were rebinned using in-house-developed software (Vilstrup et al, 2020) to be approximately equidistantly spaced on a logarithmic q scale. The radius of gyration (R g ), forward scattering I(0) and maximum particle distance (D max ) were calculated using PRIMUS.…”

“…For MtMce1A 36-148 , the entire compact and elongated models were generated with Robetta using the MtMce4A 39-140 compact and elongated crystal structures as the template. The models were evaluated against the experimental data using an in-house-written program (Steiner et al, 2018;Vilstrup et al, 2020 MtMce1A 38-454 , MtMce4A 39-320 , MtMce4A 121-400 and MtMce4A 36-400 . The SAXS data for research papers the complexes of DDM with the various constructs were also analyzed using in-house-developed software.…”

“…The SAXS data for research papers the complexes of DDM with the various constructs were also analyzed using in-house-developed software. The program is based on the methods described previously (Kaspersen et al, 2014;Steiner et al, 2018;Vilstrup et al, 2020;Calcutta et al, 2012). The DDM micellar structure is represented by Monte Carlo points in a triaxial core-shell structure with superellipsoidal shape with shape parameter t = 3 (Maric et al, 2017), and the protein is represented by the atoms in the PDB structures.…”