Abstract:
:The conformational landscapes of p53 peptide variants and phage derived peptide (12/1) variants, all known to bind to MDM2, are studied using hamiltonian replica exchange molecular dynamics simulations. Complementing earlier observations, the current study suggests that the p53 peptides largely follow the 'conformational selection' paradigm in their recognition of and complexation by MDM2 while the 12/1 peptides likely undergo some element of conformational selection but are mostly driven by 'binding induced folding'. This hypothesis is further supported by pulling simulations that pull the peptides away from their bound states with MDM2. This data extends the earlier mechanisms proposed to rationalize the entropically driven binding of the p53 set and the enthalpically driven binding of the 12/1 set. Using our hypothesis, we suggest mutations to the 12/1 peptide that increase its helicity in simulations and may, in turn, shift the binding towards conformational selection. In summary, understanding the conformational landscapes of the MDM2-binding peptides may suggest new peptide designs with bespoke binding mechanisms.
journal_name
Sci Repjournal_title
Scientific reportsauthors
Yadahalli S,Li J,Lane DP,Gosavi S,Verma CSdoi
10.1038/s41598-017-15930-4subject
Has Abstractpub_date
2017-11-15 00:00:00pages
15600issue
1issn
2045-2322pii
10.1038/s41598-017-15930-4journal_volume
7pub_type
杂志文章abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...
journal_title:Scientific reports
pub_type: 已发布勘误
doi:10.1038/s41598-018-23087-x
更新日期:2018-03-19 00:00:00
abstract::The basic leucine zipper (bZIP) is a widely known transcription factors family in eukaryotes. In plants, the role of bZIP proteins are crucial in various biological functions such as plant growth and development, seed maturation, response to light signal and environmental stress. To date, bZIP protein family has been ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-72390-z
更新日期:2020-09-23 00:00:00
abstract::Despite strengthened antimicrobial therapy, biofilm infections of Acinetobacter baumannii are associated with poor prognosis and limited therapeutic options. Assessing antibiotics on planktonic bacteria can result in failure against biofilm infections. Currently, antibiotics to treat biofilm infections are administere...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-42353-0
更新日期:2019-04-19 00:00:00
abstract::The relationship between cumulative exposure to resting heart rate (cumRHR) and mortality remain unclear in the general population. In the Kailuan cohort study, resting heart rate (RHR) was repeatedly measured at baseline and at years 2 and 4 by electrocardiogram among 47,311 adults aged 48.70 ± 11.68. The cumRHR was ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep40212
更新日期:2017-01-09 00:00:00
abstract::Delivering gene constructs into the dorsal root ganglia (DRG) is a powerful but challenging therapeutic strategy for sensory disorders affecting the DRG and their peripheral processes. The current delivery methods of direct intra-DRG injection and intrathecal injection have several disadvantages, including potential i...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep35612
更新日期:2016-10-17 00:00:00
abstract::An unresolved mystery in the field of spinal muscular atrophy (SMA) is why a reduction of the ubiquitously expressed Smn protein causes defects mostly in motoneurons. We addressed the possibility that this restricted vulnerability stems from elevated Smn expression in motoneurons. To explore this, we established an ex...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep27470
更新日期:2016-06-07 00:00:00
abstract::Relative blood volume (RBV) monitoring is frequently used in haemodialysis patients to help guide fluid management and improve cardiovascular stability. RBV changes are typically estimated based on online measurements of certain haemoconcentration markers, such as haematocrit (HCT), haemoglobin (HGB) or total blood pr...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-71830-0
更新日期:2020-09-09 00:00:00
abstract::Oxide heterointerfaces are ideal for investigating strong correlation effects to electron transport, relevant for oxide-electronics. Using hot-electrons, we probe electron transport perpendicular to the La₀.₇Sr₀.₃MnO₃ (LSMO)- Nb-doped SrTiO₃ (Nb:STO) interface and find the characteristic hot-electron attenuation lengt...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep01274
更新日期:2013-01-01 00:00:00
abstract::Raman microspectroscopy provides the means to obtain local orientations on polycrystalline materials at the submicrometer level. The present work demonstrates how orientation-distribution maps composed of Raman intensity distributions can be acquired on large areas of several hundreds of square micrometers. A polycrys...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep18410
更新日期:2015-12-17 00:00:00
abstract::Consecutive eight study phases under the successive presence and absence of UV irradiation, water vapor, and oxygen were conducted to characterize surface changes in the photocatalytic TiO2 powder using near-ambient-pressure X-ray photoelectron spectroscopy (XPS). Both Ti 2p and O 1s spectra show hysteresis through th...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep43298
更新日期:2017-02-27 00:00:00
abstract::The development of electrochemical biosensors for the simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA), tryptophan (Trp), and nitrite ([Formula: see text]) in human serum is reported in this work. Free-standing graphene nanosheets were fabricated on Ta wire using the chemical vapor depositio...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-07646-2
更新日期:2017-08-01 00:00:00
abstract::Arsenic contamination of groundwater is a serious concern worldwide. The research gaps in removing arsenic are selectivity, regeneration and effective removal rate at neutral pH levels. In this study, we discussed the reasons of the high arsenic adsorption from groundwater of our previously developed adsorbent, a cati...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-48233-x
更新日期:2019-08-15 00:00:00
abstract::Predicting function-related amino acids in proteins with unknown function or unknown allosteric binding sites in drug-targeted proteins is a task of paramount importance in molecular biomedicine. In this paper we introduce a simple, light and computationally inexpensive structure-based method to identify catalytic sit...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep14874
更新日期:2015-10-08 00:00:00
abstract::Plant extracts, or phytonutrients, are used in traditional medicine practices as supplements to enhance the immune system and gain resistance to various infectious diseases and are used in animal production as health promoting feed additives. To date, there are no studies that have assessed their mechanism of action a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep09253
更新日期:2015-03-19 00:00:00
abstract::Changes associated with cognitive function in the high-fat high-carbohydrate diet-induced prediabetes animal model and effect of exercise remain unclear. Rats were randomly assigned to the following groups (n = 6): non-diabetic (ND), prediabetic (PD), intermittent exercising PD (PD + IE) and regular exercising PD (PD ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-72098-0
更新日期:2020-09-14 00:00:00
abstract::An initial study of processing bioresorbable polycaprolactone (PCL) through material jetting was conducted using a Fujifilm Dimatix DMP-2830 material printer. The aim of this work was to investigate a potential solvent based method of jetting polycaprolactone. Several solvents were used to prepare a PCL solvent based ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep20852
更新日期:2016-02-12 00:00:00
abstract::Myelopoiesis involves differentiation of hematopoietic stem cells to cellular populations that are restricted in their self-renewal capacity, beginning with the common myeloid progenitor (CMP) and leading to mature cells including monocytes and granulocytes. This complex process is regulated by various extracellular a...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-24203-7
更新日期:2018-05-08 00:00:00
abstract::A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper. ...
journal_title:Scientific reports
pub_type: 已发布勘误
doi:10.1038/s41598-019-42527-w
更新日期:2019-04-12 00:00:00
abstract::In the cricket Gryllus bimaculatus, flying occurs soon after the last imaginal molt and precedes the mating behavior in natural conditions. Here, we tested the hypothesis that flying may improve subsequent behavioral performance in a novel environment in female crickets. We developed a behavioral set-up to test female...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-78969-w
更新日期:2020-12-18 00:00:00
abstract::Graphene's unique physical and chemical properties make it an attractive platform for use in micro- and nanoelectronic devices. However, electrostatically controlling the flow of electrons in graphene can be challenging as a result of Klein tunneling, where electrons normally incident to a one-dimensional potential ba...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep08435
更新日期:2015-02-13 00:00:00
abstract::Magnetic skyrmions are topological quasiparticles of great interest for data storage applications because of their small size, high stability, and ease of manipulation via electric current. However, although models exist for some limiting cases, there is no universal theory capable of accurately describing the structu...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-22242-8
更新日期:2018-03-13 00:00:00
abstract::Fear, anxiety, and preference in fish are generally evaluated by video-based behavioural analyses. We previously proposed a system that can measure bioelectrical signals, called ventilatory signals, using a 126-electrode array placed at the bottom of an aquarium and achieved cameraless real-time analysis of motion and...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-020-80578-6
更新日期:2021-01-08 00:00:00
abstract::The role of topical corticosteroids in management of Acanthamoeba keratitis (AK) remains controversial. Using a rabbit AK model, we investigated whether corticosteroid use is a risk factor of AK. Acanthamoeba (1 × 105/ml) was incubated with two densities of P. aeruginosa (PA; high-PA: 1 × 108/ml, low-PA: 3 × 105/ml) b...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-49128-7
更新日期:2019-09-06 00:00:00
abstract::Black phosphorus (BP) has recently been rediscovered as a new and interesting two-dimensional material due to its unique electronic and optical properties. Here, we study the linear and nonlinear optical properties of BP flakes. We observe that both the linear and nonlinear optical properties are anisotropic and can b...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep15899
更新日期:2015-10-30 00:00:00
abstract::Sand temperatures at nest depths and implications for hatchling sex ratios of hawksbill turtles (Eretmochelys imbricata) and green turtles (Chelonia mydas) nesting in the Chagos Archipelago, Indian Ocean are reported and compared to similar measurements at rookeries in the Atlantic and Caribbean. During 2012-2014, tem...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep20339
更新日期:2016-02-02 00:00:00
abstract::Correlations between fluctuations in resting state BOLD fMRI signals are interpreted as measures of functional connectivity (FC), but the neural basis of their origins and their relationships to specific features of underlying electrophysiologic activity, have not been fully established. In particular, the dependence ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-019-45404-8
更新日期:2019-06-20 00:00:00
abstract::Studies on the phenomenon of magnetoresistance (MR) have produced intriguing and application-oriented outcomes for decades-colossal MR, giant MR and recently discovered extremely large MR of millions of percents in semimetals can be taken as examples. We report here the discovery of novel multiple sign changes versus ...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep42789
更新日期:2017-02-17 00:00:00
abstract::We design an optical scheme to generate hyperentanglement correlated with degrees of freedom (DOFs) via quantum dots (QDs), weak cross-Kerr nonlinearities (XKNLs), and linearly optical apparatuses (including time-bin encoders). For generating hyperentanglement having its own correlations for two DOFs (polarization and...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-018-19970-2
更新日期:2018-02-07 00:00:00
abstract::This study is to investigate the frequencies of T-helper (Th)22, Th17 and Th1 cells and the levels of related cytokines in subchondral bone marrow in patients with rheumatoid arthritis (RA). Bone marrow and peripheral blood samples were collected from RA, osteoarthritis (OA) patients and healthy controls. The frequenc...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/s41598-017-05014-8
更新日期:2017-07-06 00:00:00
abstract::Two-dimensional (2D) cell cultures growing on plastic do not recapitulate the three dimensional (3D) architecture and complexity of human tumors. More representative models are required for drug discovery and validation. Here, 2D culture and 3D mono- and stromal co-culture models of increasing complexity have been est...
journal_title:Scientific reports
pub_type: 杂志文章
doi:10.1038/srep28951
更新日期:2016-07-01 00:00:00