RESUMEN
Protein SUMOylation is a prevalent stress-response posttranslational modification crucial for maintaining cellular homeostasis. Herein, we report that protein SUMOylation modulates cellular signaling mediated by cAMP, an ancient and universal stress-response second messenger. We identify K561 as a primary SUMOylation site in exchange protein directly activated by cAMP (EPAC1) via site-specific mapping of SUMOylation using mass spectrometry. Sequence and site-directed mutagenesis analyses reveal that a functional SUMO-interacting motif in EPAC1 is required for the binding of SUMO-conjugating enzyme UBC9, formation of EPAC1 nuclear condensate, and EPAC1 cellular SUMOylation. Heat shock-induced SUMO modification of EPAC1 promotes Rap1/2 activation in a cAMP-independent manner. Structural modeling and molecular dynamics simulation studies demonstrate that SUMO substituent on K561 of EPAC1 promotes Rap1 interaction by increasing the buried surface area between the SUMOylated receptor and its effector. Our studies identify a functional SUMOylation site in EPAC1 and unveil a novel mechanism in which SUMOylation of EPAC1 leads to its autonomous activation. The findings of SUMOylation-mediated activation of EPAC1 not only provide new insights into our understanding of cellular regulation of EPAC1 but also will open up a new field of experimentation concerning the cross-talk between cAMP/EPAC1 signaling and protein SUMOylation, two major cellular stress response pathways, during cellular homeostasis.
Asunto(s)
AMP Cíclico , Factores de Intercambio de Guanina Nucleótido , Sumoilación , Enzimas Ubiquitina-Conjugadoras , Proteínas de Unión al GTP rap1 , Factores de Intercambio de Guanina Nucleótido/metabolismo , Factores de Intercambio de Guanina Nucleótido/genética , Factores de Intercambio de Guanina Nucleótido/química , Humanos , AMP Cíclico/metabolismo , Enzimas Ubiquitina-Conjugadoras/metabolismo , Enzimas Ubiquitina-Conjugadoras/genética , Proteínas de Unión al GTP rap1/metabolismo , Proteínas de Unión al GTP rap1/genética , Células HEK293 , Simulación de Dinámica Molecular , Complejo Shelterina/metabolismo , Transducción de Señal , Proteínas de Unión a Telómeros/metabolismo , Proteínas de Unión al GTP rap/metabolismo , Proteínas de Unión al GTP rap/genética , Respuesta al Choque Térmico , Secuencia de Aminoácidos , Unión ProteicaRESUMEN
Exchange protein directly activated by cAMP (EPAC1) mediates the intracellular functions of a critical stress-response second messenger, cAMP. Herein, we report that EPAC1 is a cellular substrate of protein SUMOylation, a prevalent stress-response posttranslational modification. Site-specific mapping of SUMOylation by mass spectrometer leads to identifying K561 as a primary SUMOylation site in EPAC1. Sequence and site-directed mutagenesis analyses reveal a functional SUMO-interacting motif required for cellular SUMOylation of EPAC1. SUMO modification of EPAC1 mediates its heat shock-induced Rap1/2 activation in a cAMP-independent manner. Structural modeling and molecular dynamics simulation studies demonstrate that SUMO substituent on K561 of EPAC1 promotes Rap1 interaction by increasing the buried surface area between the SUMOylated receptor and its effector. Our studies identify a functional SUMOylation site in EPAC1 and unveil a novel mechanism in which SUMOylation of EPAC1 leads to its autonomous activation. The findings of SUMOylation-mediated activation of EPAC1 not only provide new insights into our understanding of cellular regulation of EPAC1 but also will open up a new field of experimentation concerning the cross-talk between cAMP/EPAC1 signaling and protein SUMOylation, two major cellular stress response pathways, during cellular homeostasis.
RESUMEN
The large dsDNA viruses replicate their DNA as concatemers consisting of multiple covalently linked genomes. Genome packaging is catalyzed by a terminase enzyme that excises individual genomes from concatemers and packages them into preassembled procapsids. These disparate tasks are catalyzed by terminase alternating between two distinct states-a stable nuclease that excises individual genomes and a dynamic motor that translocates DNA into the procapsid. It was proposed that bacteriophage λ terminase assembles as an anti-parallel dimer-of-dimers nuclease complex at the packaging initiation site. In contrast, all characterized packaging motors are composed of five terminase subunits bound to the procapsid in a parallel orientation. Here, we describe biophysical and structural characterization of the λ holoenzyme complex assembled in solution. Analytical ultracentrifugation, small angle X-ray scattering, and native mass spectrometry indicate that 5 subunits assemble a cone-shaped terminase complex. Classification of cryoEM images reveals starfish-like rings with skewed pentameric symmetry and one special subunit. We propose a model wherein nuclease domains of two subunits alternate between a dimeric head-to-head arrangement for genome maturation and a fully parallel arrangement during genome packaging. Given that genome packaging is strongly conserved in both prokaryotic and eukaryotic viruses, the results have broad biological implications.
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Empaquetamiento del Genoma Viral , Ensamble de Virus , Ensamble de Virus/genética , Bacteriófago lambda/genética , Endodesoxirribonucleasas/metabolismo , ADN , ADN Viral/metabolismo , Empaquetamiento del ADNRESUMEN
BACKGROUND: Enhanced Recovery After Surgery (ERAS) is a well-established, protocol-driven, evidence-based approach to peri-operative care. ERAS protocols have been used to improve patient morbidity and mortality outcomes in various surgical specialties. More recently, it has been introduced to neurosurgery. Our aim was to establish an Enhanced Recovery After Cranial Surgery (ERACraS) protocol for patients as part of a quality improvement project (QIP) with the intention of reducing hospital length of stay (HLOS). METHODS: This QIP was carried out in the Department of Neurosciences (DCN), Edinburgh, over two four-month periods. A total of 40 patients over 18 years of age undergoing elective craniotomy surgery under a sole neurosurgeon were invited to take part in this QIP. Subsequently, data was retrospectively collected through our institution's online documentation system. RESULTS: 19 patients received conventional perioperative care (pre-ERACraS group) during December 2021-March 2022, and 21 received care according to the novel ERACraS (ERACraS group) during June-September 2022. Regarding supra-tentorial surgery, there was a reduction of 73% in HLOS in the ERACraS group. No change was observed in infra-tentorial surgery. Overall, the ERACraS protocol reduced HLOS by 50% in cranial surgery. CONCLUSION: The QIP data from ERACraS in our unit has shown that implementing ERAS protocols is feasible. A reduction in HLOS has implications for patient morbidity, mortality, and quality of care. We endeavour to collect long-term data by collaborating with neurosurgical units across the UK and Ireland to validate its feasibility and sustainability as part of a major QIP in neurosurgical practice. This can be potentially adopted by neurosurgical centres across the globe in a safe and sustained manner.
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Recuperación Mejorada Después de la Cirugía , Mejoramiento de la Calidad , Humanos , Adolescente , Adulto , Estudios Retrospectivos , Complicaciones Posoperatorias/epidemiología , Atención Perioperativa/métodos , Tiempo de InternaciónRESUMEN
The genomes of positive-strand RNA viruses serve as a template for both protein translation and genome replication. In enteroviruses, a cloverleaf RNA structure at the 5' end of the genome functions as a switch to transition from viral translation to replication by interacting with host poly(C)-binding protein 2 (PCBP2) and the viral 3CDpro protein. We determined the structures of cloverleaf RNA from coxsackievirus and poliovirus. Cloverleaf RNA folds into an H-type four-way junction and is stabilized by a unique adenosine-cytidine-uridine (Aâ¢C-U) base triple involving the conserved pyrimidine mismatch region. The two PCBP2 binding sites are spatially proximal and are located on the opposite end from the 3CDpro binding site on cloverleaf. We determined that the Aâ¢C-U base triple restricts the flexibility of the cloverleaf stem-loops resulting in partial occlusion of the PCBP2 binding site, and elimination of the Aâ¢C-U base triple increases the binding affinity of PCBP2 to the cloverleaf RNA. Based on the cloverleaf structures and biophysical assays, we propose a new mechanistic model by which enteroviruses use the cloverleaf structure as a molecular switch to transition from viral protein translation to genome replication.
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Enterovirus , Genoma Viral , Poliovirus , ARN Viral , Humanos , Enterovirus/genética , Enterovirus/fisiología , Células HeLa , Conformación de Ácido Nucleico , Poliovirus/genética , Poliovirus/fisiología , Biosíntesis de Proteínas , ARN Viral/metabolismo , Proteínas de Unión al ARN/metabolismo , Proteínas Virales/genética , Proteínas Virales/metabolismo , Replicación Viral/genéticaRESUMEN
OBJECTIVES: Cognitive processing therapy (CPT) is an evidence-based psychotherapy for posttraumatic stress disorder (PTSD); however, little is known about how interrelationships between PTSD symptoms change over the course of treatment. The current study examined baseline, midtreatment, and posttreatment PTSD symptom networks during CPT for PTSD. METHOD: Adults with PTSD (n = 107) received 12 sessions of CPT as part of a randomized trial. Self-reported PTSD symptoms were assessed at pretreatment, midtreatment, and posttreatment, and network analysis was used to examine the interrelationships between symptoms at these three timepoints. Linear regression was conducted to examine whether any baseline symptoms or midpoint symptoms predicted overall treatment change. RESULTS: In the baseline PTSD network, feelings of detachment and feeling upset at reminders of the trauma were central to the symptom network. These symptoms were no longer central at midtreatment, possibly suggesting that CPT quickly reduces the importance of these symptoms. These findings were consistent with regression results that, after accounting for multiple comparisons, high baseline scores of feeling upset at trauma reminders predicted later treatment change. At the conclusion of treatment, strong negative emotions were the most central symptom and may be most important in maintaining or lowering other PTSD symptoms at the conclusion of treatment. CONCLUSIONS: Though replication is necessary, these findings offer insights into identifying which symptoms may be most predictive of treatment outcomes and the course by which CPT reduces PTSD symptoms. (PsycInfo Database Record (c) 2023 APA, all rights reserved).
RESUMEN
Cannabis use has been indicated as a risk factor for suicide in veterans. This study of Gulf War veterans tested the relationship between self-report past year cannabis use and (a) past year suicidal ideation and (b) risk for suicidal behavior. Data were from a national sample (N = 1126) of Gulf War veterans. Logistic regression models indicated cannabis use was associated with past year suicidal ideation and elevated risk for suicidal behavior, independent of key covariates. In corroboration with research on other military populations, this study indicates a potentially concerning association between cannabis use and suicide risk in Gulf War veterans.
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Cannabis , Trastornos por Estrés Postraumático , Suicidio , Veteranos , Humanos , Cannabis/efectos adversos , Guerra del Golfo , Ideación Suicida , Factores de RiesgoRESUMEN
Protein SUMOylation plays an essential role in maintaining cellular homeostasis when cells are under stress. However, precisely how SUMOylation is regulated, and a molecular mechanism linking cellular stress to SUMOylation, remains elusive. Here, we report that cAMP, a major stress-response second messenger, acts through Epac1 as a regulator of cellular SUMOylation. The Epac1-associated proteome is highly enriched with components of the SUMOylation pathway. Activation of Epac1 by intracellular cAMP triggers phase separation and the formation of nuclear condensates containing Epac1 and general components of the SUMOylation machinery to promote cellular SUMOylation. Furthermore, genetic knockout of Epac1 obliterates oxidized low-density lipoprotein-induced cellular SUMOylation in macrophages, leading to suppression of foam cell formation. These results provide a direct nexus connecting two major cellular stress responses to define a molecular mechanism in which cAMP regulates the dynamics of cellular condensates to modulate protein SUMOylation.
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AMP Cíclico , Factores de Intercambio de Guanina Nucleótido , Condensados Biomoleculares , AMP Cíclico/metabolismo , Células Espumosas/metabolismo , Factores de Intercambio de Guanina Nucleótido/genética , Factores de Intercambio de Guanina Nucleótido/metabolismo , SumoilaciónRESUMEN
During the life cycle of enteric bacterium Escherichia coli, it encounters a wide spectrum of pH changes. The asymmetric dimer of the cAMP receptor protein, CRP, plays a key role in regulating the expressions of genes and the survival of E. coli. To elucidate the pH effects on the mechanism of signal transmission, we present a combination of results derived from ITC, crystallography, and computation. CRP responds to a pH change by inducing a differential effect on the affinity for the binding events to the two cAMP molecules, ensuing in a reversible conversion between positive and negative cooperativity at high and low pH, respectively. The structures of four crystals at pH ranging from 7.8 to 6.5 show that CRP responds by inducing a differential effect on the structures of the two subunits, particularly in the DNA binding domain. Employing the COREX/BEST algorithm, computational analysis shows the change in the stability of residues at each pH. The change in residue stability alters the connectivity between residues including those in cAMP and DNA binding sites. Consequently, the differential impact on the topology of the connectivity surface among residues in adjacent subunits is the main reason for differential change in affinity; that is, the pH-induced differential change in residue stability is the biothermodynamic basis for the change in allosteric behavior. Furthermore, the structural asymmetry of this homodimer amplifies the differential impact of any perturbations. Hence, these results demonstrate that the combination of these approaches can provide insights into the underlying mechanism of an apparent complex allostery signal and transmission in CRP.
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Proteínas de Unión al ADN/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/química , Receptores de AMP Cíclico/metabolismo , Algoritmos , Regulación Alostérica , Sitios de Unión , AMP Cíclico/metabolismo , Proteínas de Unión al ADN/química , Proteínas de Escherichia coli/química , Concentración de Iones de Hidrógeno , Modelos Químicos , Unión Proteica , Conformación Proteica , Dominios Proteicos , Receptores de AMP Cíclico/química , TermodinámicaRESUMEN
Molecular segregation and biopolymer manipulation require the action of molecular motors to do work by applying directional forces to macromolecules. The additional strand conserved E (ASCE) ring motors are an ancient family of molecular motors responsible for diverse biological polymer manipulation tasks. Viruses use ASCE segregation motors to package their genomes into their protein capsids and provide accessible experimental systems due to their relative simplicity. We show by cryo-EM-focused image reconstruction that ASCE ATPases in viral double-stranded DNA (dsDNA) packaging motors adopt helical symmetry complementary to their dsDNA substrates. Together with previous data, our results suggest that these motors cycle between helical and planar configurations, providing a possible mechanism for directional translocation of DNA. Similar changes in quaternary structure have been observed for proteasome and helicase motors, suggesting an ancient and common mechanism of force generation that has been adapted for specific tasks over the course of evolution.
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Empaquetamiento del ADN , Empaquetamiento del Genoma Viral , ADN Viral/química , Genoma Viral , Proteínas Virales/química , Ensamble de VirusRESUMEN
Double-stranded DNA viruses package their genomes into pre-assembled capsids using virally-encoded ASCE ATPase ring motors. We present the first atomic-resolution crystal structure of a multimeric ring form of a viral dsDNA packaging motor, the ATPase of the asccφ28 phage, and characterize its atomic-level dynamics via long timescale molecular dynamics simulations. Based on these results, and previous single-molecule data and cryo-EM reconstruction of the homologous φ29 motor, we propose an overall packaging model that is driven by helical-to-planar transitions of the ring motor. These transitions are coordinated by inter-subunit interactions that regulate catalytic and force-generating events. Stepwise ATP binding to individual subunits increase their affinity for the helical DNA phosphate backbone, resulting in distortion away from the planar ring towards a helical configuration, inducing mechanical strain. Subsequent sequential hydrolysis events alleviate the accumulated mechanical strain, allowing a stepwise return of the motor to the planar conformation, translocating DNA in the process. This type of helical-to-planar mechanism could serve as a general framework for ring ATPases.
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Adenosina Trifosfatasas/química , Empaquetamiento del Genoma Viral , Proteínas Virales/química , Adenosina/química , Adenosina Difosfato/metabolismo , Adenosina Trifosfatasas/metabolismo , Arginina/química , Fagos de Bacillus/enzimología , Dominio Catalítico , Cristalografía por Rayos X , Simulación de Dinámica Molecular , Fosfatos/química , Estructura Cuaternaria de Proteína , Estructura Terciaria de Proteína , Subunidades de Proteína/química , Proteínas Virales/metabolismoRESUMEN
Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis.
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Bacteriófagos/aislamiento & purificación , Bacteriófagos/fisiología , Fenómenos Químicos , Empaquetamiento del ADN , ADN Viral , Lactococcus lactis/virología , Adenosina Trifosfatasas , Bacteriófagos/ultraestructura , Clonación Molecular , Expresión Génica , Modelos Moleculares , Proteínas Recombinantes , Análisis Espectral , Relación Estructura-Actividad , Estruvita , Proteínas Virales/química , Proteínas Virales/genética , Proteínas Virales/metabolismo , Virión/ultraestructura , Ensamble de VirusRESUMEN
UNC-45B is a multidomain molecular chaperone that is essential for the proper folding and assembly of myosin into muscle thick filaments in vivo. It has previously been demonstrated that the UCS domain is responsible for the chaperone-like properties of the UNC-45B. To better understand the chaperoning function of the UCS domain of the UNC-45B chaperone, we engineered mutations designed to 1) disrupt chaperone-client interactions by removing and altering the structure of a putative client-interacting loop and 2) disrupt chaperone-client interactions by changing highly conserved residues in a putative client-binding groove. We tested the effect of these mutations by using a, to our knowledge, novel combination of complementary biophysical assays (circular dichroism, chaperone activity, and small-angle x-ray scattering) and in vivo tools (Caenorhabditis elegans sarcomere structure). Removing the putative client-binding loop altered the secondary structure of the UCS domain (by decreasing the α-helix content), leading to a significant change in its solution conformation and a reduced chaperoning function. Additionally, we found that mutating several conserved residues in the putative client-binding groove did not alter the UCS domain secondary structure or structural stability but reduced its chaperoning activity. In vivo, these groove mutations were found to significantly alter the structure and organization of C. elegans sarcomeres. Furthermore, we tested the effect of R805W, a mutation distant from the putative client-binding region, which in humans, has been known to cause congenital and infantile cataracts. Our in vivo data show that, to our surprise, the R805W mutation appeared to have the most drastic detrimental effect on the structure and organization of the worm sarcomeres, indicating a crucial role of R805 in UCS-client interactions. Hence, our experimental approach combining biophysical and biological tools facilitates the study of myosin-chaperone interactions in mechanistic detail.
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Proteínas de Caenorhabditis elegans , Caenorhabditis elegans , Animales , Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/genética , Humanos , Chaperonas Moleculares/genética , Miosinas/genética , SarcómerosRESUMEN
Dengue virus (DENV) was designated as a top 10 public health threat by the World Health Organization in 2019. No clinically approved anti-DENV drug is currently available. Here we report the high-resolution cocrystal structure (1.5 Å) of the DENV-2 capsid protein in complex with an inhibitor that potently suppresses DENV-2 but not other DENV serotypes. The inhibitor induces a "kissing" interaction between two capsid dimers. The inhibitor-bound capsid tetramers are assembled inside virions, resulting in defective uncoating of nucleocapsid when infecting new cells. Resistant DENV-2 emerges through one mutation that abolishes hydrogen bonds in the capsid structure, leading to a loss of compound binding. Structure-based analysis has defined the amino acids responsible for the inhibitor's inefficacy against other DENV serotypes. The results have uncovered an antiviral mechanism through inhibitor-induced tetramerization of the viral capsid and provided essential structural and functional knowledge for rational design of panserotype DENV capsid inhibitors.
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Antivirales/química , Proteínas de la Cápside/química , Virus del Dengue , Modelos Moleculares , Conformación Proteica , Secuencia de Aminoácidos , Antivirales/farmacología , Sitios de Unión , Proteínas de la Cápside/genética , Virus del Dengue/efectos de los fármacos , Mutación , Nucleocápside/química , Nucleocápside/metabolismo , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Relación Estructura-ActividadRESUMEN
The transcription factor ΔFosB accumulates in response to chronic insults such as drugs of abuse, L-3,4-dihydroxyphenylalanine (l-DOPA) or stress in specific regions of the brain, triggering long lasting neural and behavioral changes that underlie aspects of drug addiction, dyskinesia, and depression. Thus, small molecule chemical probes are urgently needed to investigate biological functions of ΔFosB. Herein we describe the identification of a novel phenanthridine analogue ZL0220 (27) as an active and promising ΔFosB chemical probe with micromolar inhibitory activities against ΔFosB homodimers and ΔFosB/JunD heterodimers.
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ADN/efectos de los fármacos , Descubrimiento de Drogas , Fenantridinas/farmacología , Proteínas Proto-Oncogénicas c-fos/antagonistas & inhibidores , Proteínas Proto-Oncogénicas c-jun/antagonistas & inhibidores , Sitios de Unión/efectos de los fármacos , ADN/química , Relación Dosis-Respuesta a Droga , Humanos , Simulación del Acoplamiento Molecular , Estructura Molecular , Fenantridinas/química , Proteínas Proto-Oncogénicas c-fos/química , Proteínas Proto-Oncogénicas c-jun/química , Relación Estructura-ActividadRESUMEN
Patterned substitution of d-amino acids into the primary sequences of self-assembling peptides influences molecular-level packing and supramolecular morphology. We report that block heterochiral analogs of the model amphipathic peptide KFE8 (Ac-FKFEFKFE-NH2), composed of two FKFE repeat motifs with opposite chirality, assemble into helical tapes with dimensions greatly exceeding those of their fibrillar homochiral counterparts. At sufficient concentrations, these tapes form hydrogels with reduced storage moduli but retain the shear-thinning behavior and consistent mechanical recovery of the homochiral analogs. Varying the identity of charged residues (FRFEFRFE and FRFDFRFD) produced similarly sized nonhelical tapes, while a peptide with nonenantiomeric l- and d-blocks (FKFEFRFD) formed helical tapes closely resembling those of the heterochiral KFE8 analogs. A proposed energy-minimized model suggests that a kink at the interface between l- and d-blocks leads to the assembly of flat monolayers with nonidentical surfaces that display alternating stacks of hydrophobic and charged groups.
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Péptidos/química , Secuencia de Aminoácidos , Dicroismo Circular , Hidrogeles/química , Péptidos/metabolismo , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Reología , Dispersión del Ángulo Pequeño , Estereoisomerismo , Difracción de Rayos XRESUMEN
Boreal forests are experiencing dramatic climate change, having warmed 1.0°-1.9°C over the last century. Yet forest regeneration practices are often still dictated by a fixed seed zone framework, in which seeds are both harvested from and planted into predefined areas. Our goal was to determine whether seedlings sourced from southern seed zones in Minnesota USA are already better adapted to northerly seed zones because of climate change. Bur oak (Quercus macrocarpa) and northern red oak (Quercus rubra) seedlings from two seed zones (i.e., tree ecotypes) were planted into 16 sites in two northern seed zones and measured for 3 yr. Our hypotheses were threefold: (1) tree species with more southern geographic distributions would thrive in northern forests where climate has already warmed substantially, (2) southern ecotypes of these species would have higher survival and growth than the northern ecotype in northern environments, and (3) natural selection would favor seedlings that expressed phenotypic and phenological traits characteristic of trees sourced from the more southern seed zone. For both species, survival was high (>93%), and southern ecotypes expressed traits consistent with our climate adaptation hypotheses. Ecotypic differences were especially evident for red oak; the southern ecotype had had higher survival, lower specific leaf area (SLA), faster height and diameter growth, and extended leaf phenology relative to the northern ecotype. Bur oak results were weaker, but the southern ecotype also had earlier budburst and lower SLA than the northern ecotype. Models based on the fixed seed zones failed to explain seedling performance as well as those with continuous predictors (e.g., climate and geographical position), suggesting that plant adaptations within current seed zone delineations do align with changing climate conditions. Adding support for this conclusion, natural selection favored traits expressed by the more southern tree ecotypes. Collectively, these results suggest that state seed sourcing guidelines should be reexamined to permit plantings across seed zones, a form of assisted migration. More extensive experiments (i.e., provenance trails) are necessary to make species-specific seed transfer guidelines that account for climate trends while also considering the precise geographic origin of seed sources.
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Quercus , Árboles , Minnesota , Plantones , Semillas , Estados UnidosRESUMEN
Hemoglobin functions as a tetrameric oxygen transport protein, with each subunit containing a heme cofactor. Its denaturation, either in vivo or in vitro, involves autoxidation to methemoglobin, followed by cofactor loss and globin unfolding. We have proposed a global disassembly scheme for human methemoglobin, linking hemin (ferric protoporphyrin IX) disassociation and apoprotein unfolding pathways. The model is based on the evaluation of circular dichroism and visible absorbance measurements of guanidine-hydrochloride-induced disassembly of methemoglobin and previous measurements of apohemoglobin unfolding. The populations of holointermediates and equilibrium disassembly parameters were estimated quantitatively for adult and fetal hemoglobins. The key stages are characterized by hexacoordinated hemichrome intermediates, which are important for preventing hemin disassociation from partially unfolded, molten globular species during early disassembly and late-stage assembly events. Both unfolding experiments and independent small angle x-ray scattering measurements demonstrate that heme disassociation leads to the loss of tetrameric structural integrity. Our model predicts that after autoxidation, dimeric and monomeric hemichrome intermediates occur along the disassembly pathway inside red cells, where the hemoglobin concentration is very high. This prediction suggests why misassembled hemoglobins often get trapped as hemichromes that accumulate into insoluble Heinz bodies in the red cells of patients with unstable hemoglobinopathies. These Heinz bodies become deposited on the cell membranes and can lead to hemolysis. Alternatively, when acellular hemoglobin is diluted into blood plasma after red cell lysis, the disassembly pathway appears to be dominated by early hemin disassociation events, which leads to the generation of higher fractions of unfolded apo subunits and free hemin, which are known to damage the integrity of blood vessel walls. Thus, our model provides explanations of the pathophysiology of hemoglobinopathies and other disease states associated with unstable globins and red cell lysis and also insights into the factors governing hemoglobin assembly during erythropoiesis.
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Hemo , Hemoglobinas , Eritrocitos , Hemólisis , Humanos , MetahemoglobinaRESUMEN
The theory for allostery has evolved to a modern energy landscape ensemble theory, the major feature of which is the existence of multiple microstates in equilibrium. The properties of microstates are not well defined due to their transient nature. Characterization of apo protein microstates is important because the specific complex of the ligand-bound microstate defines the biological function. The information needed to link biological function and structure is a quantitative correlation of the energy landscapes between the apo and holo protein states. We employed the Escherichia coli cAMP receptor protein (CRP) system to test the features embedded in the ensemble theory because multiple crystalline apo and holo structures are available. Small angle X-ray scattering data eliminated one of the three apo states but not the other two. We defined the underlying energy landscape differences among the apo microstates by employing the computation algorithm COREX/BEST. The same connectivity patterns among residues in apo CRP are retained upon binding of cAMP. The microstates of apo CRP differ from one another by minor structural perturbations, resulting in changes in the energy landscapes of the various domains of CRP. Using the differences in energy landscapes among these apo states, we computed the cAMP binding energetics that were compared with solution biophysical results. Only one of the three apo microstates yielded data consistent with the solution data. The relative magnitude of changes in energy landscapes embedded in various apo microstates apparently defines the ultimate outcome of the cooperativity of binding.
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Regulación Alostérica/fisiología , Proteína Receptora de AMP Cíclico/química , Biología Computacional/métodos , AMP Cíclico/metabolismo , Proteína Receptora de AMP Cíclico/metabolismo , Escherichia coli/química , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Modelos Moleculares , Conformación Proteica , TermodinámicaRESUMEN
The Escherichia coli cAMP receptor protein, CRP, is a homodimeric global transcription activator that employs multiple mechanisms to modulate the expression of hundreds of genes. These mechanisms require different interfacial interactions among CRP, RNA, and DNA of varying sequences. The involvement of such a multiplicity of interfaces requires a tight control to ensure the desired phenotype. CRP-dependent promoters can be grouped into three classes. For decades scientists in the field have been puzzled over the differences in mechanisms between class I and II promoters. Using a new crystal structure, IR spectroscopy, and computational analysis, we defined the energy landscapes of WT and 14 mutated CRPs to determine how a homodimeric protein can distinguish nonpalindromic DNA sequences and facilitate communication between residues located in three different activation regions (AR) in CRP that are â¼30 Å apart. We showed that each mutation imparts differential effects on stability among the subunits and domains in CRP. Consequently, the energetic landscapes of subunits and domains are different, and CRP is asymmetric. Hence, the same mutation can exert different effects on ARs in class I or II promoters. The effect of a mutation is transmitted through a network by long-distance communication not necessarily relying on physical contacts between adjacent residues. The mechanism is simply the sum of the consequences of modulating the synchrony of dynamic motions of residues at a distance, leading to differential effects on ARs in different subunits. The computational analysis is applicable to any system and potentially with predictive capability.