Structural analysis of a new carotenoid-binding protein: the C-terminal domain homolog of the OCP

N-Terminal domain homologs of the orange carotenoid protein increase quenching of cyanobacterial phycobilisomes

Stress exerted by excess captured light energy in cyanobacteria is prevented by the photoprotective activity of the orange carotenoid protein (OCP). Under high light, the OCP converts from an orange, inactive form (OCPO) into the red form (OCPR) that binds to and quenches the phycobilisome (PBS). Structurally, the OCP consists of 2 domains: the N-terminal effector domain and a C-terminal regulatory domain. Structural analysis of the OCP-PBS complex showed that the N-terminal domains of an OCP dimer interact with the PBS core. These N-terminal OCP domains have single-domain protein paralogs known as helical carotenoid proteins (HCPs). Using PBS quenching assays, we show that the HCP4 and HCP5 homologs efficiently quench PBS fluorescence in vitro, surpassing the quenching ability of the OCP. This is consistent with computational quantum mechanics/molecular mechanics results. Interestingly, when using a maximum quenching concentration of OCP with PBSs, HCP5 addition further increases PBS quenching. Our results provide mechanistic insight into the quenching capacity and roles of HCP4 and HCP5 in cyanobacteria, suggesting that they are more than simply functionally redundant to the OCP.

Mutational interference with oligomerization properties of OCP-related apo- and holoproteins studied by analytical ultracentrifugation

In this study, the oligomerization pattern of apo- and holoforms of the Orange Carotenoid Protein (OCP) was examined under different conditions such as photoactivation state, concentration, and carotenoid embedment using analytical ultracentrifugation. Furthermore, studies were conducted on OCP constructs carrying point mutations of amino acid residues affecting OCP oligomerization. Our findings reveal that the concentration-dependent dimerization of dark-adapted OCP holoprotein from Synechocystis sp. PCC 6803 can be effectively prevented by the R27L mutation in the OCP-NTD. By introducing the E258R mutation (also in conjunction with R27L) into the OCP-CTD, monomeric OCP apoprotein can be obtained. Additionally, the holoprotein of the dark-adapted OCP-R27L/E258R variant was monomeric, and, supported by size-exclusion chromatography experiments, the photoactivated form of the OCP-R27L/E258R variant was monomeric as well. This variant, which does not oligomerize in either photocycle state, returns from the photoactivated to the dark-adapted state at a significantly faster rate than the OCP wild-type and the R27L mutant thereof. These observations also highlight the crucial interdependence between OCP dimerization in both photocycle states, the lifetime of the photoactive state of OCP, and the kinetics of the OCP photocycle.

Enabling simultaneous photoluminescence spectroscopy and X-ray footprinting mass spectrometry to study protein conformation and interactions

X-ray footprinting mass spectrometry (XFMS) is a structural biology method that uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation in solution. However, while XFMS alone provides important structural information on biomolecules, as we move into the era of the interactome, hybrid methods are becoming increasingly necessary to gain a comprehensive understanding of protein complexes and interactions. Toward this end, we report the development of the first synergetic application of inline and real-time fluorescent spectroscopy at the Advanced Light Source's XFMS facility to study local protein interactions and global conformational changes simultaneously. To facilitate general use, we designed a flexible and optimum system for producing high-quality spectroscopy-XFMS hybrid data, with rapid interchangeable liquid jet or capillary sample delivery for multimodal inline spectroscopy, and several choices for optofluidic environments. To validate the hybrid system, we used the covalently interacting SpyCatcher-SpyTag split protein system. We show that our hybrid system can be used to detect the interaction of SpyTag and SpyCatcher via fluorescence resonance energy transfer (FRET), while elucidating key structural features throughout the complex at the residue level via XFMS. Our results highlight the usefulness of hybrid method in providing binding and structural details to precisely engineer protein interactions.

Multiplex Trifluoromethyl and Hydroxyl Radical Chemistry Enables High-Resolution Protein Footprinting

Hydroxyl radical-based protein footprinting (HRPF) coupled with mass spectrometry is a valuable medium-resolution technique in structural biology, facilitating the assessment of protein structure and molecular-level interactions in solution conditions. In HRPF with X-rays (XFP), hydroxyl radicals generated by water radiolysis covalently label multiple amino acid (AA) side chains. However, HRPF technologies face challenges in achieving their full potential due to the broad (>103) dynamic range of AA reactivity with •OH and difficulty in detecting slightly modified residues, most notably in peptides with highly reactive residues like methionine, or where all residues have low •OH reactivities. To overcome this limitation, we developed a multiplex labeling chemistry that utilizes both CF3 radicals (•CF3) produced from a trifluoromethylation (TFM) reagent and OH radicals (•OH), under controlled and optimized radiolysis doses generated by X-rays. We optimized the dual •CF3/•OH chemistry using model peptides and proteins, thereby extending the existing •OH labeling platform to incorporate simultaneous •CF3 labeling. We labeled >50% of the protein sequence and >80% of protein solvent-accessible AAs via multiplex TFM labeling resulting in high-resolution footprinting, primarily by enhancing the labeling of AAs with low •OH reactivity via the •CF3 channel, while labeling moderate and highly •OH-reactive AAs in both •CF3 and •OH channels. Moreover, the low reactivity of methionine with •CF3 enabled the detection and quantification of additional AAs labeled by •CF3 within methionine-containing peptides. Finally, we found that the solvent accessibility of protein AAs directly correlated with •CF3 labeling, demonstrating that multiplex TFM labeling enables a high-resolution assessment of molecular interactions for enhanced HRPF.

Light sensitive orange carotenoid proteins (OCPs) in cyanobacterial photoprotection: evolutionary insights, structural-functional dynamics and biotechnological prospects

Among all photosynthetic life forms, cyanobacteria exclusively possess a water-soluble, light-sensitive carotenoprotein complex known as orange carotenoid proteins (OCPs), crucial for their photoprotective mechanisms. These protein complexes exhibit both structural and functional modularity, with distinct C-terminal (CTD) and N-terminal domains (NTD) serving as light-responsive sensor and effector regions, respectively. The majority of cyanobacterial genomes contain genes for OCP homologs and related proteins, highlighting their essential role in survival of the organism over time. Cyanobacterial photoprotection primarily involves the translocation of carotenoid entity into the NTD, leading to remarkable conformational changes in both domains and formation of metastable OCPR. Subsequently, OCPR interacts with phycobiliprotein, inducing the quenching of excitation energy and a significant reduction in PS II fluorescence yield. In dark conditions, OCPR detaches from phycobilisomes and reverts to OCPO in the presence of fluorescent recovery proteins (FRP), sustaining a continuous cycle. Research suggests that the modular structure of the OCPs, coupled with its unique light-driven dissociation and re-association capability, opens avenues for exploiting its potential as light-controlled switches, offering various biotechnological applications.

Orange carotenoid proteins: structural understanding of evolution and function

Cyanobacteria uniquely contain a primitive water-soluble carotenoprotein, the orange carotenoid protein (OCP). Nearly all extant cyanobacterial genomes contain genes for the OCP or its homologs, implying an evolutionary constraint for cyanobacteria to conserve its function. Genes encoding the OCP and its two constituent structural domains, the N-terminal domain, helical carotenoid proteins (HCPs), and its C-terminal domain, are found in the most basal lineages of extant cyanobacteria. These three carotenoproteins exemplify the importance of the protein for carotenoid properties, including protein dynamics, in response to environmental changes in facilitating a photoresponse and energy quenching. Here, we review new structural insights for these carotenoproteins and situate the role of the protein in what is currently understood about their functions.

Elements of the C-terminal tail of a C-terminal domain homolog of the Orange Carotenoid Protein determining xanthophyll uptake from liposomes

Carotenoids perform multifaceted roles in life ranging from coloration over light harvesting to photoprotection. The Orange Carotenoid Protein (OCP), a light-driven photoswitch involved in cyanobacterial photoprotection, accommodates a ketocarotenoid vital for its function. OCP extracts its ketocarotenoid directly from membranes, or accepts it from homologs of its C-terminal domain (CTDH). The CTDH from Anabaena (AnaCTDH) was shown to be important for carotenoid transfer and delivery from/to membranes. The C-terminal tail of AnaCTDH is a critical structural element likely serving as a gatekeeper and facilitator of carotenoid uptake from membranes. We investigated the impact of amino acid substitutions within the AnaCTDH-CTT on echinenone and canthaxanthin uptake from DOPC and DMPG liposomes. The transfer rate was uniformly reduced for substitutions of Arg-137 and Arg-138 to Gln or Ala, and depended on the lipid type, indicating a weaker interaction particularly with the lipid head group. Our results further suggest that Glu-132 has a membrane-anchoring effect on the PC lipids, specifically at the choline motif as inferred from the strongly different effects of the CTT variants on the extraction from the two liposome types. The substitution of Pro-130 by Gly suggests that the CTT is perpendicular to both the membrane and the main AnaCTDH protein during carotenoid extraction. Finally, the simultaneous mutation of Leu-133, Leu-134 and Leu-136 for alanines showed that the hydrophobicity of the CTT is crucial for carotenoid uptake. Since some substitutions accelerated carotenoid transfer into AnaCTDH while others slowed it down, carotenoprotein properties can be engineered toward the requirements of applications.

Molecular design of microalgae as sustainable cell factories

Microalgae are regarded as sustainable and potent chassis for biotechnology. Their capacity for efficient photosynthesis fuels dynamic growth independent from organic carbon sources and converts atmospheric CO2 directly into various valuable hydrocarbon-based metabolites. However, approaches to gene expression and metabolic regulation have been inferior to those in more established heterotrophs (e.g., prokaryotes or yeast) since the genetic tools and insights in expression regulation have been distinctly less advanced. In recent years, however, these tools and their efficiency have dramatically improved. Various examples have demonstrated new trends in microalgal biotechnology and the potential of microalgae for the transition towards a sustainable bioeconomy.

Lipid composition and properties affect protein-mediated carotenoid uptake efficiency from membranes

Carotenoids are pigments of diverse functions ranging from coloration over light-harvesting to photoprotection. Yet, the number of carotenoid-binding proteins, which mobilize these pigments in physiological media, is limited, and the mechanisms of carotenoid mobilization are still not well understood. The same applies for the determinants of carotenoid uptake from membranes into carotenoproteins, especially regarding the dependence on the chemical properties of membrane lipids. Here, we investigate xanthophyll uptake capacity and kinetics of a paradigmatic carotenoid-binding protein, the homolog of the Orange Carotenoid Protein's C-terminal domain from Anabaena sp. PCC 7120 (AnaCTDH), using liposomes formed from defined lipid species and loaded with canthaxanthin (CAN) and echinenone (ECN), respectively. Phospholipids with different chain length and degree of saturation were investigated. The composition of carotenoid-loaded liposomes directly affected the incorporation yield and storage ratio of CAN and ECN as well as the rate of carotenoid uptake by AnaCTDH. Generally, saturated PC lipids were identified as unsuitable, and a high phase transition temperature of the lipids negatively affected the carotenoid incorporation and storage yield. For efficient carotenoid transfer, the velocity increases with increasing chain length or membrane thickness. An average transfer yield of 93 % and 43 % were obtained for the formation of AnaCTDH(CAN) and AnaCTDH(ECN) holoproteins, respectively. In summary, the most suitable lipids for the formation of AnaCTDH(CAN/ECN) holoproteins by carotenoid transfer from artificial liposomes are phosphatidylcholine (18:1) and phosphatidylglycerol (14:0). Thus, these two lipids provide the best conditions for further investigation of lipid-protein interaction and the carotenoid uptake process.

Recent Progress in Solution Structure Studies of Photosynthetic Proteins Using Small-Angle Scattering Methods

Utilized for gaining structural insights, small-angle neutron and X-ray scattering techniques (SANS and SAXS, respectively) enable an examination of biomolecules, including photosynthetic pigment-protein complexes, in solution at physiological temperatures. These methods can be seen as instrumental bridges between the high-resolution structural information achieved by crystallography or cryo-electron microscopy and functional explorations conducted in a solution state. The review starts with a comprehensive overview about the fundamental principles and applications of SANS and SAXS, with a particular focus on the recent advancements permitting to enhance the efficiency of these techniques in photosynthesis research. Among the recent developments discussed are: (i) the advent of novel modeling tools whereby a direct connection between SANS and SAXS data and high-resolution structures is created; (ii) the employment of selective deuteration, which is utilized to enhance spatial selectivity and contrast matching; (iii) the potential symbioses with molecular dynamics simulations; and (iv) the amalgamations with functional studies that are conducted to unearth structure-function relationships. Finally, reference is made to time-resolved SANS/SAXS experiments, which enable the monitoring of large-scale structural transformations of proteins in a real-time framework.

Structural basis for the ligand promiscuity of the neofunctionalized, carotenoid-binding fasciclin domain protein AstaP

Fasciclins (FAS1) are ancient adhesion protein domains with no common small ligand binding reported. A unique microalgal FAS1-containing astaxanthin (AXT)-binding protein (AstaP) binds a broad repertoire of carotenoids by a largely unknown mechanism. Here, we explain the ligand promiscuity of AstaP-orange1 (AstaPo1) by determining its NMR structure in complex with AXT and validating this structure by SAXS, calorimetry, optical spectroscopy and mutagenesis. α1-α2 helices of the AstaPo1 FAS1 domain embrace the carotenoid polyene like a jaw, forming a hydrophobic tunnel, too short to cap the AXT β-ionone rings and dictate specificity. AXT-contacting AstaPo1 residues exhibit different conservation in AstaPs with the tentative carotenoid-binding function and in FAS1 proteins generally, which supports the idea of AstaP neofunctionalization within green algae. Intriguingly, a cyanobacterial homolog with a similar domain structure cannot bind carotenoids under identical conditions. These structure-activity relationships provide the first step towards the sequence-based prediction of the carotenoid-binding FAS1 members.

Stages of OCP-FRP Interactions in the Regulation of Photoprotection in Cyanobacteria, Part 2: Small-Angle Neutron Scattering with Partial Deuteration

We used small-angle neutron scattering partially coupled with size-exclusion chromatography to unravel the solution structures of two variants of the Orange Carotenoid Protein (OCP) lacking the N-terminal extension (OCP-ΔNTE) and its complex formation with the Fluorescence Recovery Protein (FRP). The dark-adapted, orange form OCP-ΔNTE^O is fully photoswitchable and preferentially binds the pigment echinenone. Its complex with FRP consists of a monomeric OCP component, which closely resembles the compact structure expected for the OCP ground state, OCP^O. In contrast, the pink form OCP-ΔNTE^P, preferentially binding the pigment canthaxanthin, is mostly nonswitchable. The pink OCP form appears to occur as a dimer and is characterized by a separation of the N- and C-terminal domains, with the canthaxanthin embedded only into the N-terminal domain. Therefore, OCP-ΔNTE^P can be viewed as a prototypical model system for the active, spectrally red-shifted state of OCP, OCP^R. The dimeric structure of OCP-ΔNTE^P is retained in its complex with FRP. Small-angle neutron scattering using partially deuterated OCP-FRP complexes reveals that FRP undergoes significant structural changes upon complex formation with OCP. The observed structures are assigned to individual intermediates of the OCP photocycle in the presence of FRP.

A primordial Orange Carotenoid Protein: Structure, photoswitching activity and evolutionary aspects

Cyanobacteria are photosynthesizing prokaryotes responsible for the Great Oxygenation Event on Earth ~2.5 Ga years ago. They use a specific photoprotective mechanism based on the 35-kDa photoactive Orange Carotenoid Protein (OCP), a promising target for developing novel optogenetic tools and for biomass engineering. The two-domain OCP presumably stems from domain fusion, yet the primitive thylakoid-less cyanobacteria Gloeobacter encodes a complete OCP. Its photosynthesis regulation lacks the so-called Fluorescence Recovery Protein (FRP), which in Synechocystis inhibits OCP-mediated phycobilisome fluorescence quenching, and Gloeobacter OCP belongs to the recently defined, heterogeneous clade OCPX (GlOCPX), the least characterized compared to OCP2 and especially OCP1 clades. Here, we describe the first crystal structure of OCPX, which explains unique functional adaptations of Gloeobacter OCPX compared to OCP1 from Synechocystis. We show that monomeric GlOCPX exploits a remarkable intramolecular locking mechanism stabilizing its dark-adapted state and exhibits drastically accelerated, less temperature-dependent recovery after photoactivation. While GlOCPX quenches Synechocystis phycobilisomes similar to Synechocystis OCP1, it evades interaction with and regulation by FRP from other species and likely uses alternative mechanisms for fluorescence recovery. This analysis of a primordial OCPX sheds light on its evolution, rationalizing renaming and subdivision of the OCPX clade into subclades - OCP3a, OCP3b, OCP3c.

Environmental Tuning of Homologs of the Orange Carotenoid Protein-Encoding Gene in the Cyanobacterium Fremyella diplosiphon

The orange carotenoid protein (OCP) family of proteins are light-activated proteins that function in dissipating excess energy absorbed by accessory light-harvesting complexes, i.e., phycobilisomes (PBSs), in cyanobacteria. Some cyanobacteria contain multiple homologs of the OCP-encoding gene (ocp). Fremyella diplosiphon, a cyanobacterium studied for light-dependent regulation of PBSs during complementary chromatic acclimation (CCA), contains several OCP homologs – two full-length OCPs, three Helical Carotenoid Proteins (HCPs) with homology to the N-terminus of OCP, and one C-terminal domain-like carotenoid protein (CCP) with homology to the C-terminus of OCP. We examined whether these homologs are distinctly regulated in response to different environmental factors, which could indicate distinct functions. We observed distinct patterns of expression for some OCP, HCP, and CCP encoding genes, and have evidence that light-dependent aspects of ocp homolog expression are regulated by photoreceptor RcaE which controls CCA. RcaE-dependent transcriptional regulator RcaC is also involved in the photoregulation of some hcp genes. Apart from light, additional environmental factors associated with cellular redox regulation impact the mRNA levels of ocp homologs, including salt, cold, and disruption of electron transport. Analyses of conserved sequences in the promoters of ocp homologs were conducted to gain additional insight into regulation of these genes. Several conserved regulatory elements were found across multiple ocp homolog promoters that potentially control differential transcriptional regulation in response to a range of environmental cues. The impact of distinct environmental cues on differential accumulation of ocp homolog transcripts indicates potential functional diversification of this gene family in cyanobacteria. These genes likely enable dynamic cellular protection in response to diverse environmental stress conditions in F. diplosiphon.

Microalgal protein AstaP is a potent carotenoid solubilizer and delivery module with a broad carotenoid binding repertoire

Carotenoids are lipophilic substances with many biological functions, from coloration to photoprotection. Being potent antioxidants, carotenoids have multiple biomedical applications, including the treatment of neurodegenerative disorders and retina degeneration. Nevertheless, the delivery of carotenoids is substantially limited by their poor solubility in the aqueous phase. Natural water-soluble carotenoproteins can facilitate this task, necessitating studies on their ability to uptake and deliver carotenoids. One such promising carotenoprotein, AstaP (astaxanthin-binding protein), was recently identified in eukaryotic microalgae, but its structure and functional properties remained largely uncharacterized. By using a correctly folded recombinant protein, here we show that AstaP is an efficient carotenoid solubilizer that can stably bind not only astaxanthin but also zeaxanthin, canthaxanthin, and, to a lesser extent, β-carotene, that is, carotenoids especially valuable to human health. AstaP accepts carotenoids provided as acetone solutions or embedded in membranes, forming carotenoid-protein complexes with an apparent stoichiometry of 1:1. We successfully produced AstaP holoproteins in specific carotenoid-producing strains of Escherichia coli, proving it is amenable to cost-efficient biotechnology processes. Regardless of the carotenoid type, AstaP remains monomeric in both apo- and holoform, while its rather minimalistic mass (~ 20 kDa) makes it an especially attractive antioxidant delivery module. In vitro, AstaP transfers different carotenoids to liposomes and to unrelated proteins from cyanobacteria, which can modulate their photoactivity and/or oligomerization. These findings expand the toolkit of the characterized carotenoid binding proteins and outline the perspective of the use of AstaP as a unique monomeric antioxidant nanocarrier with an extensive carotenoid binding repertoire.

Integrated Structural Studies for Elucidating Carotenoid-Protein Interactions

Carotenoids are ancient pigment molecules that, when associated with proteins, have a tremendous range of functional properties. Unlike most protein prosthetic groups, there are no recognizable primary structure motifs that predict carotenoid binding, hence the structural details of their amino acid interactions in proteins must be worked out empirically. Here we describe our recent efforts to combine complementary biophysical methods to elucidate the precise details of protein-carotenoid interactions in the Orange Carotenoid Protein and its evolutionary antecedents, the Helical Carotenoid Proteins (HCPs), CTD-like carotenoid proteins (CCPs).

Heterologous expression of cyanobacterial Orange Carotenoid Protein (OCP2) as a soluble carrier of ketocarotenoids in Chlamydomonas reinhardtii

Photosynthetic organisms evolved different mechanisms to protect themselves from high irradiances and photodamage. In cyanobacteria, the photoactive Orange Carotenoid-binding Protein (OCP) acts both as a light sensor and quencher of excitation energy. It binds keto-carotenoids and, when photoactivated, interacts with phyco-bilisomes, thermally dissipating the excitation energy absorbed by the latter, and acting as efficient singlet oxygen quencher. Here, we report the heterologous expression of an OCP2 protein from the thermophilic cyanobacterium Fischerella thermalis (FtOCP2) in the model organism for green algae, Chlamydomonas reinhardtii. Robust expression of FtOCP2 was obtained through a synthetic redesigning strategy for optimized expression of the transgene. FtOCP2 expression was achieved both in UV-mediated mutant 4 strain, previously selected for efficient transgene expression, and in a background strain previously engineered for constitutive expression of an endogenous β-carotene ketolase, normally poorly expressed in this species, resulting into astaxanthin and other ketocarotenoids accumulation. Recombinant FtOCP2 was successfully localized into the chloroplast. Upon purification it was possible to demonstrate the formation of holoproteins with different xanthophylls and keto-carotenoids bound, including astaxanthin. Moreover, isolated ketocarotenoid-binding FtOCP2 holoproteins conserved their photoconversion properties. Carotenoids bound to FtOCP2 were thus maintained in solution even in absence of organic solvent. The synthetic biology approach herein reported could thus be considered as a novel tool for improving the solubility of ketocarotenoids produced in green algae, by binding to water-soluble carotenoids binding proteins.

Sub-lithic photosynthesis in hot desert habitats

In hyper-arid soil environments, photosynthetic microorganisms are largely restricted to hypolithic (sub-lithic) habitats: i.e., on the ventral surfaces of translucent pebbles in desert pavements. Here, we combined fluorometric, spectroscopic, biochemical and metagenomic approaches to investigate in situ the light transmission properties of quartz stones in the Namib Desert, and assess the photosynthetic activity of the underlying hypolithic cyanobacterial biofilms. Quartz pebbles greatly reduced the total photon flux to the ventral surface biofilms and filtered out primarily the short wavelength portion of the solar spectrum. Chlorophylls d and f were not detected in biofilm pigment extracts; however, hypolithic cyanobacterial communities showed some evidence of adaptation to sub-lithic conditions, including the prevalence of genes encoding Helical Carotenoid Proteins, which are associated with desiccation stress. Under water-saturated conditions, hypolithic communities showed no evidence of light stress, even when the quartz stones were exposed to full midday sunlight. This initial study creates a foundation for future in-situ and laboratory exploration of various adaptation mechanisms employed by photosynthetic organisms forming hypolithic microbial communities.

Excited-State Evolution of Keto-Carotenoids after Excess Energy Excitation in the UV Region

Carotenoids are molecules with rich photophysics that are in many biological systems involved in photoprotection. Yet, their response to excess energy excitation is only scarcely studied. Here we have explored excited state properties of three keto-carotenoids, echinenone, canthaxanthin and rhodoxanthin after excess energy excitation to a singlet state absorbing in UV. Though the basic spectral features and kinetics of S₂ , hot S₁ , relaxed S₁ states remain unchanged upon UV excitation, the clear increase of the S* signal is observed after excess energy excitation, associated with increased S* lifetime. A multiple origin of the S* signal, originating either from specific conformations in the S₁ state or from a non-equilibrated ground state, is confirmed in this work. We propose that the increased amount of energy stored in molecular vibrations, induced by the UV excitation, is the reason for the enhanced S* signal observed after UV excitation. Our data also suggest that a fraction of the UV excited state population may proceed through a non-sequential pathway, bypassing the S₂ state.

Comparison of angiopoietin-like protein 3 and 4 reveals structural and mechanistic similarities

Elevated plasma triglycerides are a risk factor for coronary artery disease, which is the leading cause of death worldwide. Lipoprotein lipase (LPL) reduces triglycerides in the blood by hydrolyzing them from triglyceride-rich lipoproteins to release free fatty acids. LPL activity is regulated in a nutritionally responsive manner by macromolecular inhibitors including angiopoietin-like proteins 3 and 4 (ANGPTL3 and ANGPTL4). However, the mechanism by which ANGPTL3 inhibits LPL is unclear, in part due to challenges in obtaining pure protein for study. We used a new purification protocol for the N-terminal domain of ANGPTL3, removing a DNA contaminant, and found DNA-free ANGPTL3 showed enhanced inhibition of LPL. Structural analysis showed that ANGPTL3 formed elongated, flexible trimers and hexamers that did not interconvert. ANGPTL4 formed only elongated flexible trimers. We compared the inhibition of ANGPTL3 and ANGPTL4 using human very-low-density lipoproteins as a substrate and found both were noncompetitive inhibitors. The inhibition constants for the trimeric ANGPTL3 (7.5 ± 0.7 nM) and ANGPTL4 (3.6 ± 1.0 nM) were only 2-fold different. Heparin has previously been reported to interfere with ANGPTL3 binding to LPL, so we questioned if the negatively charged heparin was acting in a similar fashion to the DNA contaminant. We found that ANGPTL3 inhibition is abolished by binding to low-molecular-weight heparin, whereas ANGPTL4 inhibition is not. Our data show new similarities and differences in how ANGPTL3 and ANGPTL4 regulate LPL and opens new avenues of investigating the effect of heparin on LPL inhibition by ANGPTL3.