Biology subjects

Latham, M. P.

Publications and source records attributed to Latham, M. P..

5 recordsLinked to original sources

bioRxiv2026

SPINDLE: Unlocking protein dynamics from single-field NMR relaxation data using a deep learning ensemble.

A proteins function is derived from its three-dimensional structure and the motions of the atoms about that structure. The detailed characterization of both macromolecular structure and dynamics provides an opportunity for understanding enzyme catalysis, ligand binding, and allostery, along with providing insights into how the function changes upon mutation or post-translational modification. Among the various methods for characterizing biomolecular motions, nuclear magnetic resonance (NMR) spin relaxation methods are a standard for determining nanosecond global tumbling times along with the amplitude and timescale of faster local motions. Within the model-free formalism, various mathematical models are used to extract dynamic parameters. Unfortunately, as the number of fitted parameters increases within these models, they become mathematically underdetermined for standard NMR relaxation data collected at a single magnetic field, necessitating multi-field datasets. Here, we present SPINDLE, an ensemble of deep neural networks trained on a large synthetic set of NMR relaxation data. Unlike traditional least-squares fitting, SPINDLE predicts both fast and slow timescale dynamics parameters from a single set (i.e., collected at a single magnetic field) of three relaxation datasets using the ensemble for error estimation. We demonstrate a strong correlation to ground truth dynamics parameters on synthetic benchmarks, with more precision than traditional fitting techniques, and precisely reproduce experimental dynamics parameters for [~]50 proteins with relaxation data in the Biological Magnetic Resonance Data Bank. We also leverage the architecture of the deep neural network to show how the model emphasizes rigid residues for the prediction of global correlation times. This strategy may be useful in the future for elucidating correlated networks of dynamic residues from multiple relaxation datasets.

biophysics↗

bioRxiv2025

DNA modulates structural transitions and oligomerization kinetics of the functional amyloid CRES

Functional amyloids play critical roles in diverse physiological processes; however, the molecular mechanisms regulating their assembly remain unknown. The mouse epididymal lumen contains a functional amyloid- and nucleic acid-rich extracellular matrix with roles in host defense and sperm maturation. Cystatin-related epididymal spermatogenic (CRES), a reproductive cystatin and key component of the mammalian epididymal amyloid matrix, assembles into structurally heterogeneous amyloid forms to support the various roles of this extracellular matrix. Here, we show that CRES binds double-stranded DNA with sub-micromolar affinity in a sequence independent manner and that DNA binding accelerates amyloid formation by increasing local protein concentration and promoting specific oligomerization pathways. Using NMR spectroscopy, site-directed mutagenesis, and biophysical analyses, we find that DNA interacts primarily with the CRES loop region, thereby occluding one assembly mechanism and redirecting oligomerization through a pathway involving the L1 loop. These DNA-mediated changes in assembly kinetics and pathway selection suggest a regulatory mechanism for achieving structural and functional diversity in non-pathological amyloid systems. Our findings provide a molecular framework for understanding nucleic acid-guided amyloidogenesis and highlight how functional amyloids may exploit multiple assembly routes to fulfill their physiological roles.

biophysics↗

bioRxiv2023

How a highly acidic SH3 domain folds in the absence of its charged peptide target

Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years. Statement for broader audienceSome protein domains are highly charged because they are adapted to bind oppositely charged proteins and nucleic acids. However, it is unknown how these highly charged domains fold as during folding there will be significant repulsion between like-charges. We investigate how one of these highly charged domains folds in the presence of salt, which can screen the charge repulsion and make folding easier, allowing us to understand how folding occurs despite the proteins high charge. Supplementary materialO_LISupplementary material document containing additional details on protein expression methods, thermodynamics and kinetics equations, and the effect of urea on electrostatic interactions, as well as 4 supplemental figures and 4 supplemental data tables. (Supplementary_Material.docx), 15 pages C_LIO_LISupplemental excel file containing covariation data across AbpSH3 orthologs (FileS1.xlsx) C_LI O_FIG O_LINKSMALLFIG WIDTH=104 HEIGHT=200 SRC="FIGDIR/small/532811v1_fig4.gif" ALT="Figure 4"> View larger version (21K): org.highwire.dtl.DTLVardef@185b8eeorg.highwire.dtl.DTLVardef@303c18org.highwire.dtl.DTLVardef@b98532org.highwire.dtl.DTLVardef@1d7ce68_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Analysis of domain backbone dynamics. A. 1H-15N heteronuclear NOE of AbpSH3 domain at 0 and 800 mM NaCl. B. Backbone 15N order parameters calculated from Modelfree. Error bars come from the fit. C. Atomic fluctuations of the AbpSH3 domain in no salt, 300 mM NaCl, 800 mM NaCl, and 800 mM KCl simulations. Average standard deviations in the atomic fluctuations (0.2 [A], 0.2 [A], 0.3 [A], and 0.1 [A] respectively) are larger than the difference between the lines. C_FIG

biophysics↗

bioRxiv2022

Structural features of Dnase1L3 responsible for serum antigen clearance

Autoimmunity develops when extracellular DNA released from dying cells is not cleared from serum. While serum DNA is primarily digested by Dnase1 and Dnase1L3, Dnase1 does not rescue autoimmunity arising from Dnase1L3 deficiencies. Dnase1L3 uniquely degrades antigenic forms of cell-free DNA, including DNA complexed with lipids and proteins. The distinct activity of Dnase1L3 relies on its unique C-terminal Domain (CTD), but the mechanism is unknown. We used multiple biophysical techniques and functional assays to study the interplay between the core catalytic domain and the CTD. While the core domain resembles Dnase1, there are several key differences between the two enzymes. Dnase1L3 is not inhibited by actin due to multiple differences in the actin recognition site. The CTD augments the ability of the core to bind DNA, thereby facilitating the degradation of complexed DNA to prevent autoimmune pathology. Together, these structural insights will inform the development of Dnase1L3-based therapies for autoimmunity.

biochemistry↗

bioRxiv2020

A Point Mutation in the RNA Recognition Motif of CSTF2 Associated with Intellectual Disability in Humans Causes Defects in 3' End Processing

CSTF2 encodes an RNA-binding protein that is essential for mRNA cleavage and polyadenylation (C/P). No disease-associated mutations have been described for this gene. Here, we report a mutation in the RNA recognition motif (RRM) of CSTF2 that changes an aspartic acid at position 50 to alanine (p.D50A), resulting in intellectual disability in male patients. In mice, this mutation was sufficient to alter polyadenylation sites in over 1,000 genes critical for brain development. Using a reporter gene assay, we demonstrated that C/P efficiency of CSTF2D50A was lower than wild type. To account for this, we determined that p.D50A changed locations of amino acid side chains altering RNA binding sites in the RRM. The changes modified the electrostatic potential of the RRM leading to a greater affinity for RNA. These results highlight the importance of 3' end mRNA processing in correct expression of genes important for brain plasticity and neuronal development.

molecular biology↗