scholarly journals The structural basis of odorant recognition in insect olfactory receptors

2021 ◽  
Author(s):  
Josefina del Mármol ◽  
Mackenzie Yedlin ◽  
Vanessa Ruta
Keyword(s):  
Olfactory Receptors ◽  
Binding Pocket ◽  
Structural Basis ◽  
Structural Determinants ◽  
Functional Studies ◽  
Chemical Recognition ◽  
Common Strategy ◽  
Olfactory Systems ◽  
Mechanistic Basis ◽  
Insight Into

AbstractOlfactory systems must detect and discriminate an enormous diversity of chemicals in the environment. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity is encoded through the combinatorial activation of large families of olfactory receptors (ORs), thus allowing a finite number of receptors to detect an almost infinite chemical world. Although most individual ORs are sensitive to a variety of odorants, the structural basis for such flexible chemical recognition remains unknown. Here, we combine cryo-electron microscopy with functional studies of receptor tuning to gain insight into the structural and mechanistic basis of promiscuous odorant recognition. We show that OR5 from the jumping bristletail, Machilis hrabei, assembles as a homo-tetrameric odorant-gated ion channel with broad chemical tuning. We elucidated the structure of OR5 in multiple gating states, alone and in complex with two of its agonists—the odorant eugenol and the insect repellent DEET. Both ligands bind to a common binding site located in the transmembrane region of each subunit, composed of a simple geometric arrangement of aromatic and hydrophobic residues. We reveal that binding is mediated by hydrophobic, non-directional interactions with residues distributed throughout the binding pocket, enabling the flexible recognition of structurally distinct odorants. Mutation of individual residues lining the binding pocket predictably altered OR5’s sensitivity to eugenol and DEET and broadly reconfigured the receptor’s tuning, supporting a model in which diverse odorants share the same structural determinants for binding. Together, these studies provide structural insight into odorant detection, shedding light onto the molecular recognition mechanisms that ultimately endow the olfactory system with its immense discriminatory capacity.

scholarly journals The structural basis of odorant recognition in insect olfactory receptors

Nature ◽  
2021 ◽  
Author(s):  
Josefina del Mármol ◽  
Mackenzie A. Yedlin ◽  
Vanessa Ruta
Keyword(s):  
Olfactory Receptor ◽  
Hydrophobic Interactions ◽  
Olfactory Receptors ◽  
Binding Pocket ◽  
Structural Basis ◽  
Structural Determinants ◽  
Cryo Electron Microscopy ◽  
Common Strategy ◽  
Olfactory Systems ◽  
Discriminatory Capacity

AbstractOlfactory systems must detect and discriminate amongst an enormous variety of odorants1. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity is encoded through the combinatorial activation of large families of olfactory receptors1–3, thus allowing a finite number of receptors to detect a vast chemical world. Here we offer structural and mechanistic insight into how an individual olfactory receptor can flexibly recognize diverse odorants. We show that the olfactory receptor MhOR5 from the jumping bristletail4Machilis hrabei assembles as a homotetrameric odorant-gated ion channel with broad chemical tuning. Using cryo-electron microscopy, we elucidated the structure of MhOR5 in multiple gating states, alone and in complex with two of its agonists—the odorant eugenol and the insect repellent DEET. Both ligands are recognized through distributed hydrophobic interactions within the same geometrically simple binding pocket located in the transmembrane region of each subunit, suggesting a structural logic for the promiscuous chemical sensitivity of this receptor. Mutation of individual residues lining the binding pocket predictably altered the sensitivity of MhOR5 to eugenol and DEET and broadly reconfigured the receptor’s tuning. Together, our data support a model in which diverse odorants share the same structural determinants for binding, shedding light on the molecular recognition mechanisms that ultimately endow the olfactory system with its immense discriminatory capacity.

scholarly journals The X-Ray Structure of the Haloalcohol Dehalogenase HheA from Arthrobacter sp. Strain AD2: Insight into Enantioselectivity and Halide Binding in the Haloalcohol Dehalogenase Family

2006 ◽  
Vol 188 (11) ◽  
pp. 4051-4056 ◽  
Author(s):  
René M. de Jong ◽  
Kor H. Kalk ◽  
Lixia Tang ◽  
Dick B. Janssen ◽  
Bauke W. Dijkstra
Keyword(s):  
Tertiary Structure ◽  
Halogen Bond ◽  
Environmental Pollutants ◽  
Binding Pocket ◽  
Catalytic Triad ◽  
Side Chain ◽  
Structural Determinants ◽  
Substrate Binding Pocket ◽  
X Ray ◽  
Insight Into

ABSTRACT Haloalcohol dehalogenases are bacterial enzymes that cleave the carbon-halogen bond in short aliphatic vicinal haloalcohols, like 1-chloro-2,3-propanediol, some of which are recalcitrant environmental pollutants. They use a conserved Ser-Tyr-Arg catalytic triad to deprotonate the haloalcohol oxygen, which attacks the halogen-bearing carbon atom, producing an epoxide and a halide ion. Here, we present the X-ray structure of the haloalcohol dehalogenase HheAAD2 from Arthrobacter sp. strain AD2 at 2.0-Å resolution. Comparison with the previously reported structure of the 34% identical enantioselective haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 shows that HheAAD2 has a similar quaternary and tertiary structure but a much more open substrate-binding pocket. Docking experiments reveal that HheAAD2 can bind both enantiomers of the haloalcohol substrate 1-p-nitrophenyl-2-chloroethanol in a productive way, which explains the low enantiopreference of HheAAD2. Other differences are found in the halide-binding site, where the side chain amino group of Asn182 is in a position to stabilize the halogen atom or halide ion in HheAAD2, in contrast to HheC, where a water molecule has taken over this role. These results broaden the insight into the structural determinants that govern reactivity and selectivity in the haloalcohol dehalogenase family.

scholarly journals Crystal Structures of Two Coronavirus ADP-Ribose-1″-Monophosphatases and Their Complexes with ADP-Ribose: a Systematic Structural Analysis of the Viral ADRP Domain

2008 ◽  
Vol 83 (2) ◽  
pp. 1083-1092 ◽  
Author(s):  
Yuanyuan Xu ◽  
Le Cong ◽  
Cheng Chen ◽  
Lei Wei ◽  
Qi Zhao ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Crystal Structures ◽  
Structural Information ◽  
Large Family ◽  
Binding Pocket ◽  
Structural Basis ◽  
Active Site Residues ◽  
Replication Process ◽  
Functional Studies ◽  
Group I

ABSTRACT The coronaviruses are a large family of plus-strand RNA viruses that cause a wide variety of diseases both in humans and in other organisms. The coronaviruses are composed of three main lineages and have a complex organization of nonstructural proteins (nsp's). In the coronavirus, nsp3 resides a domain with the macroH2A-like fold and ADP-ribose-1"-monophosphatase (ADRP) activity, which is proposed to play a regulatory role in the replication process. However, the significance of this domain for the coronaviruses is still poorly understood due to the lack of structural information from different lineages. We have determined the crystal structures of two viral ADRP domains, from the group I human coronavirus 229E and the group III avian infectious bronchitis virus, as well as their respective complexes with ADP-ribose. The structures were individually solved to elucidate the structural similarities and differences of the ADRP domains among various coronavirus species. The active-site residues responsible for mediating ADRP activity were found to be highly conserved in terms of both sequence alignment and structural superposition, whereas the substrate binding pocket exhibited variations in structure but not in sequence. Together with data from a previous analysis of the ADRP domain from the group II severe acute respiratory syndrome coronavirus and from other related functional studies of ADRP domains, a systematic structural analysis of the coronavirus ADRP domains was realized for the first time to provide a structural basis for the function of this domain in the coronavirus replication process.

scholarly journals Structural Basis for PPARs Activation by the Dual PPARα/γ Agonist Sanguinarine: A Unique Mode of Ligand Recognition

Molecules ◽  
2021 ◽  
Vol 26 (19) ◽  
pp. 6012
Author(s):  
Siyu Tian ◽  
Rui Wang ◽  
Shuming Chen ◽  
Jialing He ◽  
Weili Zheng ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Target Genes ◽  
Binding Pocket ◽  
Binding Mode ◽  
Structural Basis ◽  
Peroxisome Proliferator ◽  
Functional Studies ◽  
Glucose And Lipid Metabolism ◽  
Peroxisome Proliferator Activated Receptors ◽  
Dual Agonist

Peroxisome proliferator-activated receptors (PPARs) play crucial roles in glucose and lipid metabolism and inflammation. Sanguinarine is a natural product that is isolated from Sanguinaria Canadensis, a potential therapeutic agent for intervention in chronic diseases. In this study, biochemical and cell-based promoter-reporter gene assays revealed that sanguinarine activated both PPARα and PPARγ, and enhanced their transcriptional activity; thus, sanguinarine was identified as a dual agonist of PPARα/γ. Similar to fenofibrate, sanguinarine upregulates the expression of PPARα-target genes in hepatocytes. Sanguinarine also modulates the expression of key PPARγ-target genes and promotes adipocyte differentiation, but with a lower adipogenic activity compared with rosiglitazone. We report the crystal structure of sanguinarine bound to PPARα, which reveals a unique ligand-binding mode of sanguinarine, dissimilar to the classic Y-shaped binding pocket, which may represent a new pharmacophore that can be optimized for selectively targeting PPARα. Further structural and functional studies uncover the molecular basis for the selectivity of sanguinarine toward PPARα/γ among all three PPARs. In summary, our study identifies a PPARα/γ dual agonist with a unique ligand-binding mode, and provides a promising and viable novel template for the design of dual-targeting PPARs ligands.

scholarly journals Structural Basis of the Enhanced Pollutant-Degrading Capabilities of an Engineered Biphenyl Dioxygenase

2016 ◽  
Vol 198 (10) ◽  
pp. 1499-1512 ◽  
Author(s):  
Sonali Dhindwal ◽  
Leticia Gomez-Gil ◽  
David B. Neau ◽  
Thi Thanh My Pham ◽  
Michel Sylvestre ◽  
...  
Keyword(s):  
Polychlorinated Biphenyl ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Degradation Pathway ◽  
Dimensional Structure ◽  
Structural Basis ◽  
Biphenyl Dioxygenase ◽  
Pcb Congeners ◽  
Biphenyl Degradation ◽  
Insight Into

ABSTRACTBiphenyl dioxygenase, the first enzyme of the biphenyl catabolic pathway, is a major determinant of which polychlorinated biphenyl (PCB) congeners are metabolized by a given bacterial strain. Ongoing efforts aim to engineer BphAE, the oxygenase component of the enzyme, to efficiently transform a wider range of congeners. BphAEII9, a variant of BphAELB400in which a seven-residue segment,335TFNNIRI341, has been replaced by the corresponding segment of BphAEB356,333GINTIRT339, transforms a broader range of PCB congeners than does either BphAELB400or BphAEB356, including 2,6-dichlorobiphenyl, 3,3′-dichlorobiphenyl, 4,4′-dichlorobiphenyl, and 2,3,4′-trichlorobiphenyl. To understand the structural basis of the enhanced activity of BphAEII9, we have determined the three-dimensional structure of this variant in substrate-free and biphenyl-bound forms. Structural comparison with BphAELB400reveals a flexible active-site mouth and a relaxed substrate binding pocket in BphAEII9that allow it to bind different congeners and which could be responsible for the enzyme's altered specificity. Biochemical experiments revealed that BphAEII9transformed 2,3,4′-trichlorobiphenyl and 2,2′,5,5′-tetrachlorobiphenyl more efficiently than did BphAELB400and BphAEB356. BphAEII9also transformed the insecticide dichlorodiphenyltrichloroethane (DDT) more efficiently than did either parental enzyme (apparentkcat/Kmof 2.2 ± 0.5 mM−1s−1, versus 0.9 ± 0.5 mM−1s−1for BphAEB356). Studies of docking of the enzymes with these three substrates provide insight into the structural basis of the different substrate selectivities and regiospecificities of the enzymes.IMPORTANCEBiphenyl dioxygenase is the first enzyme of the biphenyl degradation pathway that is involved in the degradation of polychlorinated biphenyls. Attempts have been made to identify the residues that influence the enzyme activity for the range of substrates among various species. In this study, we have done a structural study of one variant of this enzyme that was produced by family shuffling of genes from two different species. Comparison of the structure of this variant with those of the parent enzymes provided an important insight into the molecular basis for the broader substrate preference of this enzyme. The structural and functional details gained in this study can be utilized to further engineer desired enzymatic activity, producing more potent enzymes.

scholarly journals Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Katherine E Huffer ◽  
Antoniya A Aleksandrova ◽  
Andrés Jara-Oseguera ◽  
Lucy R Forrest ◽  
Kenton J Swartz
Keyword(s):  
Transmembrane Domain ◽  
Ion Selectivity ◽  
Structural Data ◽  
Trp Channel ◽  
Structural Basis ◽  
Global Alignment ◽  
Functional Studies ◽  
Domain Structures ◽  
Mechanistic Basis ◽  
Channel Structures

The recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters toward the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.

scholarly journals Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms

2020 ◽  
Author(s):  
Katherine E. Huffer ◽  
Antoniya A. Aleksandrova ◽  
Andrés Jara-Oseguera ◽  
Lucy R. Forrest ◽  
Kenton J. Swartz
Keyword(s):  
Transmembrane Domain ◽  
Ion Selectivity ◽  
Structural Data ◽  
Trp Channel ◽  
Structural Basis ◽  
Global Alignment ◽  
Functional Studies ◽  
Domain Structures ◽  
Mechanistic Basis ◽  
Channel Structures

AbstractThe recent proliferation of published TRP channel structures provides a foundation for understanding the diverse functional properties of this important family of ion channel proteins. To facilitate mechanistic investigations, we constructed a structure-based alignment of the transmembrane domains of 120 TRP channel structures. Comparison of structures determined in the absence or presence of activating stimuli reveals similar constrictions in the central ion permeation pathway near the intracellular end of the S6 helices, pointing to a conserved cytoplasmic gate and suggesting that most available structures represent non-conducting states. Comparison of the ion selectivity filters towards the extracellular end of the pore supports existing hypotheses for mechanisms of ion selectivity. Also conserved to varying extents are hot spots for interactions with hydrophobic ligands, lipids and ions, as well as discrete alterations in helix conformations. This analysis therefore provides a framework for investigating the structural basis of TRP channel gating mechanisms and pharmacology, and, despite the large number of structures included, reveals the need for additional structural data and for more functional studies to establish the mechanistic basis of TRP channel function.

scholarly journals The structural basis of huntingtin (Htt) fibril polymorphism, revealed by cryo-EM of exon 1 Htt fibrils

2021 ◽  
Author(s):  
Sergey Nazarov ◽  
Anass Chiki ◽  
Driss Boudeffa ◽  
Hilal Lashuel
Keyword(s):  
Structural Heterogeneity ◽  
Structural Basis ◽  
Particle Analysis ◽  
Structural Determinants ◽  
Huntingtin Protein ◽  
Fibril Structure ◽  
Exon 1 ◽  
High Degree ◽  
Insight Into

The lack of detailed insight into the structure of aggregates formed by the huntingtin protein has hampered efforts to develop therapeutics and diagnostics targeting pathology formation in the brain of patients with Huntington's disease. To address this knowledge gap, we investigated the structural properties of in vitro generated fibrils from exon1 of the huntingtin protein by electron cryo-microscopy and single- particle analysis. We show that wildtype and mutant exon1 of the huntingtin protein form non-helical fibrils with a polygultamine amyloid core composed of β-hairpins with unique characteristics that have not been previously observed with other amyloid filaments. The stacks of β-hairpins form long planar β- sheets (protofilaments) with variable stacking angle and occasional out-of-register state of individual β-hairpins. These features and the propensity of protofilament to undergo lateral association results in a high degree of fibril polymorphism, including fibrils composed of varying numbers of protofilaments. Our results also represent the first direct observation of how the flanking domains are organized around the polyglutamine core of the fibril and provide insight into how they might affect huntingtin fibril structure, polymorphism, and stacking of β-hairpins within its core structure. Removal of the first 17 amino acids at the N-terminus resulted in surprising intra-fibril structural heterogeneity and reduced fibril's propensity to lateral associations. Overall, this work provides valuable insights that could guide future mechanistic studies to elucidate the sequence and structural determinants of huntingtin aggregation, as well as cryo- EM and structural studies of fibrils derived from huntingtin proteins and other disease-associated polyglutamine-containing proteins.

scholarly journals High-affinity nanobodies as tools for structural and functional studies on mammalian Arc

2021 ◽  
Author(s):  
Sigurbjorn Markusson ◽  
Erik I Hallin ◽  
Helene J Bustad ◽  
Arne Raasakka ◽  
Ju Xu ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Binding Pocket ◽  
Vital Role ◽  
Structural Basis ◽  
Intercellular Signaling ◽  
Saxs Data ◽  
Functional Studies ◽  
High Affinity

Activity-regulated cytoskeleton-associated protein (Arc) is a multidomain protein of retroviral origin with a vital role in the regulation of synaptic plasticity and memory formation in mammals. However, the mechanistic and structural basis of Arc function is little understood. Arc has an NTD involved in membrane binding and a CTD which binds postsynaptic protein ligands. In addition, the NTD and CTD both function in Arc oligomerization, including assembly of retrovirus-like capsid involved in intercellular signaling. We produced and characterised six ultra-high-affinity anti-Arc nanobodies (Nb). The CTD of both rat and human Arc could be crystallised in ternary complexes with two Nbs simultaneously bound (H11 and C11). H11 binding deep into the stargazing-binding pocket of Arc CTD suggested competitive binding with Arc ligand peptides, which was confirmed in vitro. This indicates that the H11 Nb could serve as a genetically-encoded tool for inhibition of endogenous Arc N-lobe interactions in study of neuronal function and plasticity. The crystallisation of the human Arc CTD in two different conformations, accompanied by SAXS data and molecular dynamics simulations, paints a dynamic picture of the mammalian Arc CTD. Dynamics were affected by mutations known to inhibit capsid formation, implying a role for Arc CTD dynamics in oligomerisation. Dimerisation of the NTD, together with structural dynamics of the CTD, suggest a mechanism, by which structural dynamics of the CTD may promote capsomer formation, and dimerisation of the NTD links capsomers, facilitating the formation of capsids. The described recombinant ultrahigh-affinity anti-Arc Nbs are versatile tools that can be further developed for studying mammalian Arc structure and function in vitro and in vivo.

scholarly journals Structural basis for active-site probes targeting Staphylococcus aureus serine hydrolase virulence factors

2020 ◽  
Author(s):  
Matthias Fellner ◽  
Christian S. Lentz ◽  
Sam A. Jamieson ◽  
Jodi L. Brewster ◽  
Linhai Chen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Active Site ◽  
Binding Pocket ◽  
Structural Basis ◽  
Serine Hydrolase ◽  
Serine Hydrolases ◽  
Substrate Binding Pocket ◽  
Hydrophobic Substrate ◽  
Substrate Analog ◽  
Insight Into

SummaryStaphylococcus aureus is a major cause of infection in the community and in hospitals. Serine hydrolases play key roles in bacterial homeostasis, in particular biofilms. Activity-based profiling has previously identified a family of serine hydrolases, designated fluorophosphonate-binding hydrolases (Fphs), which contribute to virulence of S. aureus in the biofilm niche. Here we report structures of the putative tributyrin esterase FphF, alone and covalently bound by a substrate analog, and small molecule inhibitors that occupy the hydrophobic substrate-binding pocket. We show that FphF has promiscuous esterase activity. Building from this, we extended our analysis to the wider Fph protein family using homology modeling and docking tools. We predict that other Fph enzymes, including FphB which was linked directly to virulence, may be more specific than FphF. This study provides insight into Fph function and a template for designing new imaging agents, diagnostic probes, and inhibitors to treat S. aureus infections.

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