Side-chain Coordinates Research Articles

FlowPacker: Protein side-chain packing with torsional flow matching.

Accurate prediction of protein side-chain conformations is necessary to understand protein folding, protein-protein interactions and facilitate de novo protein design. Here we apply torsional flow matching and equivariant graph attention to develop FlowPacker, a fast and performant model to predict protein side-chain conformations conditioned on the protein sequence and backbone. We show that FlowPacker outperforms previous state-of-the-art baselines across most metrics with improved runtime. We further show that FlowPacker can be used to inpaint missing side-chain coordinates and also for multimeric targets, and exhibits strong performance on a test set of antibody-antigen complexes. Code is available at https://gitlab.com/mjslee0921/flowpacker. Supplementary data are available at Bioinformatics online.

Invariant point message passing for protein side chain packing.

Protein side chain packing (PSCP) is a fundamental problem in the field of protein engineering, as high-confidence and low-energy conformations of amino acid side chains are crucial for understanding (and designing) protein folding, protein-protein interactions, and protein-ligand interactions. Traditional PSCP methods (such as the Rosetta Packer) often rely on a library of discrete side chain conformations, or rotamers, and a forcefield to guide the structure to low-energy conformations. Recently, deep learning (DL) based methods (such as DLPacker, AttnPacker, and DiffPack) have demonstrated state-of-the-art predictions and speed in the PSCP task. Building off the success of geometric graph neural networks for protein modeling, we present the Protein Invariant Point Packer (PIPPack) which effectively processes local structural and sequence information to produce realistic, idealized side chain coordinates using -angle distribution predictions and geometry-aware invariant point message passing (IPMP). On a test set of ∼1400 high-quality protein chains, PIPPack is highly competitive with other state-of-the-art PSCP methods in rotamer recovery and per-residue RMSD but is significantly faster.

An end-to-end deep learning method for protein side-chain packing and inverse folding

Protein side-chain packing (PSCP), the task of determining amino acid side-chain conformations given only backbone atom positions, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to tackle this problem, but their speed or accuracy is still unsatisfactory. To address this, we present AttnPacker, a deep learning (DL) method for directly predicting protein side-chain coordinates. Unlike existing methods, AttnPacker directly incorporates backbone 3D geometry to simultaneously compute all side-chain coordinates without delegating to a discrete rotamer library or performing expensive conformational search and sampling steps. This enables a significant increase in computational efficiency, decreasing inference time by over 100× compared to the DL-based method DLPacker and physics-based RosettaPacker. Tested on the CASP13 and CASP14 native and nonnative protein backbones, AttnPacker computes physically realistic side-chain conformations, reducing steric clashes and improving both rmsd and dihedral accuracy compared to state-of-the-art methods SCWRL4, FASPR, RosettaPacker, and DLPacker. Different from traditional PSCP approaches, AttnPacker can also codesign sequences and side chains, producing designs with subnative Rosetta energy and high in silico consistency.

Crystal structure and reaction mechanism of a bacterial Mg-dechelatase homolog from the Chloroflexi Anaerolineae.

Chlorophyll degradation plays a myriad of physiological roles in photosynthetic organisms, including acclimation to light environment and nutrient remobilization during senescence. Mg extraction from chlorophyll a is the first and committed step of the chlorophyll degradation pathway. This reaction is catalyzed by the Mg-dechelatase enzyme encoded by Stay-Green (SGR). The reaction mechanism of SGR protein remains elusive since metal ion extraction from organic molecules is not a common enzymatic reaction. Additionally, experimentally derived structural information about SGR or its homologs has not yet been reported. In this study, the crystal structure of the SGR homolog from Anaerolineae bacterium was determined using the molecular replacement method at 1.85 Å resolution. Our previous study showed that three residues-H32, D34, and D62 are essential for the catalytic activity of the enzyme. Biochemical analysis involving mutants of D34 residue further strengthened its importance in the functioning of the dechelatase. Docking simulation also revealed the interaction between the D34 side chain and central Mg ion of chlorophyll a. Structural analysis showed the arrangement of D34/H32/D62 in the form of a catalytic triad that is generally found in hydrolases. The probable reaction mechanism suggests that deprotonated D34 side chain coordinates and destabilizes Mg, resulting in Mg extraction. Besides, H32 possibly acts as a general base catalyst and D62 facilitates H32 to be a better proton acceptor. Taken together, the reaction mechanism of SGR partially mirrors the one observed in hydrolases.

Solid-State-NMR-Structure-Based Inhibitor Design to Achieve Selective Inhibition of the Parallel-in-Register β-Sheet versus Antiparallel Iowa Mutant β-Amyloid Fibrils.

Solid-state nuclear magnetic resonance (ssNMR) spectroscopy has been widely applied to characterize the high-resolution structures of β-amyloid (Aβ) fibrils. While these structures provide crucial molecular insights on the deposition of amyloid plaques in Alzheimer's diseases (AD), ssNMR structures have been rarely used so far as the basis for designing inhibitors. It remains a challenge because the ssNMR-based Aβ fibril structures were usually obtained with sparsely isotope-labeled peptides with limited experimental constraints, where the structural models, especially the side-chain coordinates, showed restricted precision. However, these structural models often possess a higher accuracy within the hydrophobic core regions with more well-defined experimental data, which provide potential targets for the molecular design. This work presents an ssNMR-based molecular design to achieve selective inhibition of a particular type of Aβ fibrillar structure, which was formed with the Iowa mutant of Aβ with parallel-in-register β-sheet hydrophobic core. The results show that short peptides that mimic the C-terminal β-strands of the fibril may have a preference in binding to the parallel Aβ fibrils rather than the antiparallel fibrils, mainly due to the differences in the high-resolution structures in the fibril elongation interfaces. The Iowa mutant Aβ fibrils are utilized in this work mainly as a model to demonstrate the feasibility of the strategy because it is relatively straightforward to distinguish the parallel and antiparallel fibril structures using ssNMR. Our results suggest that it is potentially feasible to design structure-selective inhibitors and/or diagnostic agents to Aβ fibrils using ssNMR-based structural models.

BCL::SAXS: GPU accelerated Debye method for computation of small angle X-ray scattering profiles.

Small angle X-ray scattering (SAXS) is an experimental technique used for structural characterization of macromolecules in solution. Here, we introduce BCL::SAXS--an algorithm designed to replicate SAXS profiles from rigid protein models at different levels of detail. We first show our derivation of BCL::SAXS and compare our results with the experimental scattering profile of hen egg white lysozyme. Using this protein we show how to generate SAXS profiles representing: (1) complete models, (2) models with approximated side chain coordinates, and (3) models with approximated side chain and loop region coordinates. We evaluated the ability of SAXS profiles to identify a correct protein topology from a non-redundant benchmark set of proteins. We find that complete SAXS profiles can be used to identify the correct protein by receiver operating characteristic (ROC) analysis with an area under the curve (AUC) > 99%. We show how our approximation of loop coordinates between secondary structure elements improves protein recognition by SAχS for protein models without loop regions and side chains. Agreement with SAXS data is a necessary but not sufficient condition for structure determination. We conclude that experimental SAXS data can be used as a filter to exclude protein models with large structural differences from the native.

Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.

Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be turned on to create mixed-resolution models. For example, an AA region of interest such as a binding site can be coupled to a CG model for the rest of the protein. We have additionally developed a hybrid implementation of the generalized Born/surface area (GBSA) implicit solvent model suitable for mixed-resolution models, which in turn was ported to a graphics processing unit (GPU) for faster calculation. The new software was applied to study two systems: (i) the behavior of spin labels on the B1 domain of protein G (GB1) and (ii) docking of randomly initialized estradiol configurations to the ligand binding domain of the estrogen receptor (ERα). The performance of the GPU version of the code was also benchmarked in a number of additional systems.

Interaction of Actin with Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1) Receptor in Liposomes Is Ca2+- and Phospholipid-dependent

The regulation of binding of G-actin to cytoplasmic domains of cell surface receptors is a common mechanism to control diverse biological processes. To model the regulation of G-actin binding to a cell surface receptor we used the cell-cell adhesion molecule carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1-S) in which G-actin binds to its short cytoplasmic domain (12 amino acids; Chen, C. J., Kirshner, J., Sherman, M. A., Hu, W., Nguyen, T., and Shively, J. E. (2007) J. Biol. Chem. 282, 5749-5760). A liposome model system demonstrates that G-actin binds to the cytosolic domain peptide of CEACAM1-S in the presence of negatively charged palmitoyl-oleoyl phosphatidylserine (POPS) liposomes and Ca(2+). In contrast, no binding of G-actin was observed in palmitoyl-oleoyl phosphatidylcholine (POPC) liposomes or when a key residue in the peptide, Phe-454, is replaced with Ala. Molecular Dynamics simulations on CEACAM1-S in an asymmetric phospholipid bilayer show migration of Ca(2+) ions to the lipid leaflet containing POPS and reveal two conformations for Phe-454 explaining the reversible availability of this residue for G-actin binding. NMR transverse relaxation optimized spectroscopic analysis of (13)C-labeled Phe-454 CEACAM1-S peptide in liposomes plus actin further confirmed the existence of two peptide conformers and the Ca(2+) dependence of actin binding. These findings explain how a receptor with a short cytoplasmic domain can recruit a cytosolic protein in a phospholipid and Ca(2+)-specific manner. In addition, this model system provides a powerful approach that can be applied to study other membrane protein interactions with their cytosolic targets.

Structure of the Protein BPTI Derived with NOESY in Supercooled Water: Validation and Refinement of Solution Structures

Fidelity without frostbite: Refinement of an NMR solution structure of 6-kDa protein BPTI determined at 36 °C (see picture, red) with NOE distance constraints measured in supercooled water at −15 °C increased precision of backbone and core side-chain coordinates about twofold (blue). In contrast to cryogenic X-ray crystallography (−150 °C), supercooling to about −15 °C hardly affects the conformation of flexibly disordered surface side chains.

Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway

E2 conjugating proteins that transfer ubiquitin and ubiquitin-like modifiers to substrate lysine residues must first activate the lysine nucleophile for conjugation. Genetic complementation revealed three side chains of the E2 Ubc9 that were crucial for normal growth. Kinetic analysis revealed modest binding defects but substantially lowered catalytic rates for these mutant alleles with respect to wild-type Ubc9. X-ray structures for wild-type and mutant human Ubc9-RanGAP1 complexes showed partial loss of contacts to the substrate lysine in mutant complexes. Computational analysis predicted pK perturbations for the substrate lysine, and Ubc9 mutations weakened pK suppression through improper side chain coordination. Biochemical studies with p53, RanGAP1 and the Nup358/RanBP2 E3 were used to determine rate constants and pK values, confirming both structural and computational predictions. It seems that Ubc9 uses an indirect mechanism to activate lysine for conjugation that may be conserved among E2 family members.

Side-chain coordination polymers containing redox-active pendants: complexation of ferrocene-based bidentate ligands with M(hfac)2(hfac = 1,1,1,5,5,5-hexafluoroacetylacetonate, M = Mn, Ni, Cu, Zn) and CuX (X = I, Br)

Coordination polymers with redox active pendants, {5-ferrocenylpyrimidine·M(hfac)2}n [M = Mn (1a), Ni (1b), Cu (1c), Zn (1d)] and {5-ferrocenylpyrimidine·CuX}n [X = I (2a), Br (2b)], have been prepared and characterized. In complex 1c, the Cu(II) ions are linked by the bridging ligands to form one-dimensional chains. This complex was shown to exhibit an antiferromagnetic intra-chain interaction, which was analyzed by the Bonner–Fisher model (2J/kB = −6.3 K). Complex 2a shows a two-dimensional sheet-like structure, in which one-dimensional chains, consisting of the Cu(I) ions and the ligands, are further bridged by iodide anions. These compounds show quasi-reversible redox processes of the ferrocenyl groups in the solid state.

Coordination modes of aminoacids to zinc

Two new binary zinc–aminoacid complexes were crystallized: Zn(Ile) 2(H 2O) 2 is octahedral with two O,N-chelating aminoacid ligands; Zn(Phe) 2 is a one-dimensional coordination polymer with η 2-carboxylate bridges. The pyrazolylborate zinc complex Tp Ph,MeZnOH reacted with simple aminoacids to form the complexes Tp Ph,MeZn-AA (AA=Gly, Val, Leu, Met, Phe, Trp) in which AA is a O,N-chelate ligand. In a similar fashion aminoacid-nitroanilides were deprotonated at the N atom yielding the Tp Ph,MeZn complexes with the N,N-chelating ligands Gly-Nit, Ala-Nit and Leu-Nit. When terminal amino functions were missing, pure carboxylate coordination resulted, as in Tp Ph,MeZn-GlyPheBoc and Tp Ph,MeZn-AspPheOMe. Exclusive side-chain coordination was enforced in Bz-Tyr-OEt resulting in the Tp Ph,MeZn complex with the phenolate-bound aminoacid. Combinations of the binding types (O,N-chelate+carboxylate, O,N-chelate+phenolate, O,N-chelate+thiolate) were realized in the binuclear complexes Tp Ph,MeZn-AA-ZnTp Ph,Me for AA=Asp, Glu, Tyr and Cys.

Lithium and Sodium Ion Binding Energies of N-Acetyl and N-Glycyl Amino Acids

Using a quadrupole ion-trap mass spectrometer with an electrospray ionization source, the Cooks kinetic method has been used to measure the lithium and sodium ion binding energies of the N-acetyl and N-glycyl derivatives of a series of 14 amino acids. For comparison, the gas-phase basicities of the amino acid derivatives were also determined by the kinetic method. The lithium binding free energies range from 47.2 to 56.4 kcal/mol, and the sodium affinities from 30.8 to 41.2 kcal/mol. Comparisons between basicities and metal ion binding energies indicate that the presence of a coordinating group (e.g., −OH, −CO2H, etc.) in the amino acid side chain can significantly increase the lithium and sodium binding energies. Dynamics calculations (CHARMm) confirm that side-chain coordination is a common stabilizing effect in the metalated systems. A good correlation, with a slope near unity, is found between the metal ion binding energies of the N-acetyl and N-glycyl derivatives. This indicates that the two groups o...

Optimizing the metal binding parameters of an EF-hand-like calcium chelation loop: coordinating side chains play a more important tuning role than chelation loop flexibility.

In calcium signaling pathways regulated by the EF-hand Ca2+ binding motif, proper regulation requires that the equilibrium and kinetics of Ca2+ binding to the EF-hand chelation loop be precisely optimized for each physiological application. Studies of small-molecule organic chelators have shown that metal binding parameters can be tuned both by the nature of the coordinating ligands and by the structural framework to which these ligands are attached. By analogy, the present study tests the relative importance of (i) coordinating side chains and (ii) backbone torsion angle constraints to the tuning of an EF-hand-like Ca2+ chelation loop. A series of engineered chelation loops are generated by modifying Ca2+ binding site of the Escherichia coli galactose binding protein. The resulting loops, each containing an altered coordinating side chain or a Gly substitution, are compared with respect to their metal binding affinities, specificities, and dissociation kinetics. The Gly variants examined include substitutions which eliminate or introduce a Gly at each of the nine chelation loop positions. The results reveal that Gly is not tolerated at loop positions 1, 3, 5, or 8 or at the external coordinating position, where the removal of a key coordinating or hydrophobic side chain destabilizes the protein. In contrast, Gly residues at loop positions 2, 4, 6, and 7, none of which is required for side chain coordination, have little effect on Ca2+ affinity and the ability to discriminate between cations of different size and charge. Kinetic measurements show that some of these Gly residues measurably alter the rates of metal ion association and dissociation, but in each case the two rates are changed by approximately the same factor so that the effects on equilibrium are minor. Overall, Gly residues yield surprisingly small effects at loop positions 2, 4, 6, and 7, especially when compared to the larger equilibrium and kinetic effects observed for coordinating side chain substitutions. It follows that the conserved Gly at position 6 is not required for Ca2+ binding and that constraints on the backbone torsion angles at the non-coordinating side chain positions 2, 4, 6, and 7 play a relatively minor role in tuning metal binding parameters. Instead, specific coordinating side chains optimize the metal binding parameters of the GBP chelation loop for its protein context and biological application.

Hydrating peptides using a sprouting technique

AbstractA scheme for generating water coordinates, whose proton orientations are random, and simultaneously generating side chain coordinates of peptides, preparatory to studying solvation of peptides using molecular dynamics schemes is presented in an X‐PLOR context. Examples from the Integrin and Tropomyosin systems are used to illustrate the procedure. © 1994 by John Wiley & Sons, Inc.

Database algorithm to generate protein backbone and side-chain coordinates from a C α, trace

Database algorithm to generate protein backbone and side-chain coordinates from a C α, trace

Metal complexes of sulphur-containinng ligands. V. Interactions of cobalt(II) ion with L-cysteine and its derivatives

Potentiometry and spectrophotometry were used to study the cobalt(II) complexes of L-cysteine, D-penicillamine, DL-mercaptosuccinic acid, N-acetyl-L-cysteine, N-acetyl-D-penicillamine, α-mercaptopropionylglycine and glutathione. It was found that L-cysteine and D-penicillamine form octahedral bis complexes of composition CoA 2 with the cobalt(II) ion. At intermediate pH values polynuclear complexes too are formed; this is the case primarily for L-cysteine. Pentacoordinated complexes CoA 2 are produced with mercaptosuccinic acid, and the concentration of the polynuclear species is negligible. N-acetyl-D-penicillamine forms a distorted tetrahedral bis complex by (S,O) coordination. Besides an analogous species, polynuclear and mixed hydroxo complexes too may be present in the cobalt(II)N-acetyl-L-cysteine system. In a weakly basic medium the cobalt(II) ion does not induce deprotonation of the peptide NH group for either mercaptopropionylglycine or glutathione. In the case of mercaptopropionylglycine the formation of the parent complexes is accompanied by their hydrolysis, while for glutathione there is the possibility of both cysteine-type and glutamic acid side-chain coordination.

Magnetic and natural circular dichroism of metalloporphyrin complexes of human and rabbit hemopexin.

Magnetic circular dichroism (MCD) spectra of several metalloporphyrin complexes of rabbit and human serum hemopexins in the spectral region of 300 to 650 nm and natural circular dichroism (CD) in the 300 to 450 nm region are reported. The MCD spectra of the heme (iron-protoporphyrin IX) complexes of both proteins were essentially identical suggesting similar iron coordination. The Soret region MCD spectrum of ferriheme . hemopexin has a shape and amplitude typical of other completely low spin (S = /sup 1///sub 2/) ferric hemeproteins, and the temperature dependence of the MCD intensity indicates that it is composed predominantly of Faraday C-type, terms. The visible region MCD spectrum of this complex closely resembles those characteristic of cytochrome b/sub 5/ and other bisimidazole-coordinated heme derivatives. Under aerobic conditions, heme . hemopexin is in the fully oxidized state. The ferroheme . hemopexins also exhibit MCD spectra similar to that of ferrocytochrome b/sub 5/, consistent with a low spin state and histidyl side-chain coordination of the heme iorn in the reduced as well as in the oxidized state. The deuteroheme derivatives of rabbit hemopexin exhibit MCD spectra similar to those of the heme complex except for the expected slight differences in wavelength extrema, indicatingmore » that the vinyl side chains of protoporphyrin have little influence on the coordination. In contrast, the natural CD spectra of the heme complexes of rabbit and human hemopexin do not resemble the CD of cytochrome b/sub 5/, reflecting differences in the crevice regions of the different hemeproteins. Furthermore, the CD spectra of the ferroheme complexes of rabbit and human hemopexin point to differences in the local environments of the heme chromophores.« less