scholarly journals Protein Folding in High-Dimensional Spaces: Hypergutters and the Role of Nonnative Interactions

2005 ◽  
Vol 88 (1) ◽  
pp. 172-183 ◽  
Author(s):  
T.C.B. McLeish
Keyword(s):  
Protein Folding ◽  
High Dimensional

scholarly journals The Role of High-Dimensional Diffusive Search, Stabilization, and Frustration in Protein Folding

2014 ◽  
Vol 106 (8) ◽  
pp. 1729-1740 ◽  
Author(s):  
Supreecha Rimratchada ◽  
Tom C.B. McLeish ◽  
Sheena E. Radford ◽  
Emanuele Paci
Keyword(s):  
Protein Folding ◽  
High Dimensional

scholarly journals The Role of Network Science in Glioblastoma

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1045
Author(s):  
Marta B. Lopes ◽  
Eduarda P. Martins ◽  
Susana Vinga ◽  
Bruno M. Costa
Keyword(s):  
Personalized Medicine ◽  
Drug Development ◽  
Information Flow ◽  
Clinical Studies ◽  
Network Science ◽  
Cancer Genomics ◽  
High Dimensional ◽  
Network Discovery ◽  
Software Implementations

Network science has long been recognized as a well-established discipline across many biological domains. In the particular case of cancer genomics, network discovery is challenged by the multitude of available high-dimensional heterogeneous views of data. Glioblastoma (GBM) is an example of such a complex and heterogeneous disease that can be tackled by network science. Identifying the architecture of molecular GBM networks is essential to understanding the information flow and better informing drug development and pre-clinical studies. Here, we review network-based strategies that have been used in the study of GBM, along with the available software implementations for reproducibility and further testing on newly coming datasets. Promising results have been obtained from both bulk and single-cell GBM data, placing network discovery at the forefront of developing a molecularly-informed-based personalized medicine.

Folding of peptides and proteins: role of disulfide bonds, recent developments

2013 ◽  
Vol 4 (6) ◽  
pp. 597-604 ◽  
Author(s):  
Yuji Hidaka ◽  
Shigeru Shimamoto
Keyword(s):  
Protein Folding ◽  
Disulfide Bonds ◽  
Bond Formation ◽  
Difficult Problem ◽  
Chemical Methods ◽  
Mutant Proteins ◽  
Folding Intermediates ◽  
Peptide Chemistry ◽  
Recent Developments

AbstractDisulfide-containing proteins are ideal models for studies of protein folding as the folding intermediates can be observed, trapped, and separated by HPLC during the folding reaction. However, regulating or analyzing the structures of folding intermediates of peptides and proteins continues to be a difficult problem. Recently, the development of several techniques in peptide chemistry and biotechnology has resulted in the availability of some powerful tools for studying protein folding in the context of the structural analysis of native, mutant proteins, and folding intermediates. In this review, recent developments in the field of disulfide-coupled peptide and protein folding are discussed, from the viewpoint of chemical and biotechnological methods, such as analytical methods for the detection of disulfide pairings, chemical methods for disulfide bond formation between the defined Cys residues, and applications of diselenide bonds for the regulation of disulfide-coupled peptide and protein folding.

scholarly journals Role of mRNA structure in the control of protein folding

2016 ◽  
Vol 44 (22) ◽  
pp. 10898-10911 ◽  
Author(s):  
Guilhem Faure ◽  
Aleksey Y. Ogurtsov ◽  
Svetlana A. Shabalina ◽  
Eugene V. Koonin
Keyword(s):  
Protein Folding ◽  
Mrna Structure

scholarly journals Teasing Apart the Role of the Ribosome and Molecular Chaperones in Cellular Protein Folding

2018 ◽  
Vol 114 (3) ◽  
pp. 414a
Author(s):  
Rayna M. Addabbo ◽  
Matthew D. Dalphin ◽  
Yue Liu ◽  
Miranda F. Mecha ◽  
Silvia Cavagnero
Keyword(s):  
Protein Folding ◽  
Molecular Chaperones ◽  
Cellular Protein

scholarly journals Epitope mapping of human respiratory syncytial virus 22K transcription antitermination factor: role of N-terminal sequences in protein folding

2005 ◽  
Vol 86 (4) ◽  
pp. 1103-1107 ◽  
Author(s):  
Blanca García-Barreno ◽  
John Steel ◽  
Monica Payá ◽  
Luis Martínez-Sobrido ◽  
Teresa Delgado ◽  
...  
Keyword(s):  
Protein Folding ◽  
Respiratory Syncytial Virus ◽  
Western Blotting ◽  
Epitope Mapping ◽  
Human Respiratory Syncytial Virus ◽  
N Terminus ◽  
Transcription Antitermination ◽  
Syncytial Virus ◽  
Antibody Epitopes

The reactivity of a panel of 12 monoclonal antibodies raised against the human respiratory syncytial virus 22 kDa (22K) protein was tested by Western blotting with a set of 22K deletion mutants. The results obtained identified sequences in the C-terminal half of the 22K polypeptide required for integrity of most antibody epitopes, except for epitope 112, which was lost in mutants with short N-terminal deletions. This antibody, in contrast to the others, failed to immunoprecipitate the native 22K protein, indicating that the N terminus of this protein is buried in the native molecule and exposed only under the denaturing conditions of Western blotting. In addition, N-terminal deletions that abolished reactivity with monoclonal antibody 112 also inhibited phosphorylation of the 22K protein previously identified at Ser-58 and Ser-61, suggesting that the N terminus is important in regulating the 22K protein phosphorylation status, most likely as a result of its requirement for protein folding.

scholarly journals Greedy measurement selection for state estimation

2018 ◽  
Author(s):  
J. Nichols ◽  
Albert Cohen ◽  
Peter Binev ◽  
Olga Mula
Keyword(s):  
Hilbert Space ◽  
Differential Operator ◽  
High Dimensional ◽  
Dimensional Vector ◽  
Physical Processes ◽  
Linear Measurements ◽  
Measurement Selection ◽  
Selection For ◽  
Unknown Solution

Parametric PDEs of the general form $$ \mathcal{P}(u,a)=0 $$ are commonly used to describe many physical processes, where $\mathcal{P}$ is a differential operator, a is a high-dimensional vector of parameters and u is the unknown solution belonging to some Hilbert space V. Typically one observes m linear measurements of u(a) of the form $\ell_i(u)=\langle w_i,u \rangle$, $i=1,\dots,m$, where $\ell_i\in V'$ and $w_i$ are the Riesz representers, and we write $W_m = \text{span}\{w_1,\ldots,w_m\}$. The goal is to recover an approximation $u^*$ of u from the measurements. The solutions u(a) lie in a manifold within V which we can approximate by a linear space $V_n$, where n is of moderate dimension. The structure of the PDE ensure that for any a the solution is never too far away from $V_n$, that is, $\text{dist}(u(a),V_n)\le \varepsilon$. In this setting, the observed measurements and $V_n$ can be combined to produce an approximation $u^*$ of u up to accuracy $$ \Vert u -u^*\Vert \leq \beta^{-1}(V_n,W_m) \, \varepsilon $$ where $$ \beta(V_n,W_m) := \inf_{v\in V_n} \frac{\Vert P_{W_m}v\Vert}{\Vert v \Vert} $$ plays the role of a stability constant. For a given $V_n$, one relevant objective is to guarantee that $\beta(V_n,W_m)\geq \gamma >0$ with a number of measurements $m\geq n$ as small as possible. We present results in this direction when the measurement functionals $\ell_i$ belong to a complete dictionary.

scholarly journals 195 The Application of Radiomics in Laryngeal Cancer: The Forgotten Cohort

2021 ◽  
Vol 108 (Supplement_6) ◽  
Author(s):  
A Rajgor ◽  
A McQueen ◽  
T Ali ◽  
E Aboagye ◽  
B Obara ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Head And Neck ◽  
Laryngeal Cancer ◽  
Prognostic Value ◽  
Head And Neck Cancers ◽  
High Dimensional ◽  
Naked Eye ◽  
Online Databases ◽  
Novel Method

Abstract Background Radiomics is a novel method of extracting data from medical images that is difficult to visualise through the naked eye. This technique transforms digital images that hold information on pathology into high-dimensional-data for analysis. Radiomics has the potential to enhance laryngeal cancer care and to date, has shown promise in various other specialties. Aim The aim of this review is to summarise the applications of this technique to laryngeal cancer and potential future benefits. Method A comprehensive systematic review-informed search of the MEDLINE and EMBASE online databases was undertaken. Keywords ‘laryngeal cancer’ OR ‘larynx’ OR ‘larynx cancer’ OR ‘head and neck cancer’ were combined with ‘radiomic’ OR ‘signature’ OR ‘machine learning’ OR ‘artificial intelligence’. Additional articles were obtained from bibliographies using the ‘snowball method’. Results Seventeen articles were identified that evaluated the role of radiomics in laryngeal cancer. Two studies affirmed the value of radiomics in improving the accuracy of staging, whilst fifteen studies highlighted the potential prognostic value of radiomics in laryngeal cancer. Twelve (of thirteen) studies incorporated an array of different head and neck cancers in the analysis and only one study assessed laryngeal cancer exclusively. Conclusions Literature to date has various limitations including, small and heterogeneous cohorts incorporating patients with head and neck cancers of distinct anatomical subsites and stages. The lack of uniform data on solely laryngeal cancer and radiomics means drawing conclusions is difficult, although these studies have affirmed its value. Further large prospective studies exclusively in laryngeal cancer are required to unlock its true potential.

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