A new way to recognize downhill folding based on generalized path length

The protein folding is an important scientific problem and many methods were designed to elucidate the protein folding and obtain insight into the molecular mechanism. A novel means is presented to identify the downhill pathways of protein folding in this paper. This method is based on barrier energy profile projected onto the generalized path length (GPL) with Breadth-first searching (BFS) algorithm. We show the effectiveness of this approach by constructing the barrier energy profile of trpzip2 and comparing with other methods.

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Fast protein folding kinetics

Quarterly Reviews of Biophysics ◽

10.1017/s003358351400002x ◽

2014 ◽

Vol 47 (2) ◽

pp. 95-142 ◽

Cited By ~ 53

Author(s):

Hannah Gelman ◽

Martin Gruebele

Keyword(s):

Experimental Study ◽

Protein Folding ◽

Complex Systems ◽

Experimental Techniques ◽

Computational Power ◽

Folding Kinetics ◽

Major Focus ◽

Native Conformation ◽

Downhill Folding ◽

Insight Into

AbstractFast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well <1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even ‘slow’ folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.

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Spatial localization of unknown proteins in the endoplasmic reticulum predicts functions

Clinical & Investigative Medicine ◽

10.25011/cim.v30i4.2858 ◽

2007 ◽

Vol 30 (4) ◽

pp. 84

Author(s):

Michael D. Jain ◽

Hisao Nagaya ◽

Annalyn Gilchrist ◽

Miroslaw Cygler ◽

John J.M. Bergeron

Keyword(s):

Endoplasmic Reticulum ◽

Protein Folding ◽

Protein Synthesis ◽

Protein Function ◽

Protein Translocation ◽

Spatial Localization ◽

Predict Protein Function ◽

Insight Into ◽

Soluble Fractions ◽

Er Membrane

Protein synthesis, folding and degradation functions are spatially segregated in the endoplasmic reticulum (ER) with respect to the membrane and the ribosome (rough and smooth ER). Interrogation of a proteomics resource characterizing rough and smooth ER membranes subfractionated into cytosolic, membrane, and soluble fractions gives a spatial map of known proteins involved in ER function. The spatial localization of 224 identified unknown proteins in the ER is predicted to give insight into their function. Here we provide evidence that the proteomics resource accurately predicts the function of new proteins involved in protein synthesis (nudilin), protein translocation across the ER membrane (nicalin), co-translational protein folding (stexin), and distal protein folding in the lumen of the ER (erlin-1, TMX2). Proteomics provides the spatial localization of proteins and can be used to accurately predict protein function.

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Molecular Mechanism of Protein Folding in the Cell

Cell ◽

10.1016/j.cell.2011.08.041 ◽

2011 ◽

Vol 146 (6) ◽

pp. 851-854 ◽

Cited By ~ 22

Author(s):

James E. Rothman ◽

Randy Schekman

Keyword(s):

Protein Folding ◽

Molecular Mechanism

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Insight into the molecular mechanism of a herbal injection by integrating network pharmacology and in vitro

Journal of Ethnopharmacology ◽

10.1016/j.jep.2015.07.016 ◽

2015 ◽

Vol 173 ◽

pp. 91-99 ◽

Cited By ~ 10

Author(s):

Yi-min Ma ◽

Xin-zhuang Zhang ◽

Zhen-zhen Su ◽

Na Li ◽

Liang Cao ◽

...

Keyword(s):

Molecular Mechanism ◽

Network Pharmacology ◽

Insight Into

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Quantitative proteomic analysis of global effect of LLL12 on U87 cell's proteome: An insight into the molecular mechanism of LLL12

Journal of Proteomics ◽

10.1016/j.jprot.2014.09.020 ◽

2015 ◽

Vol 113 ◽

pp. 127-142 ◽

Cited By ~ 15

Author(s):

Rekha Jain ◽

Prajakta Kulkarni ◽

Snigdha Dhali ◽

Srikanth Rapole ◽

Sanjeeva Srivastava

Keyword(s):

Molecular Mechanism ◽

Proteomic Analysis ◽

Global Effect ◽

Quantitative Proteomic Analysis ◽

Insight Into

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Insight into the molecular mechanism of the multitasking kinesin-8 motor

The EMBO Journal ◽

10.1038/emboj.2010.220 ◽

2010 ◽

Vol 29 (20) ◽

pp. 3437-3447 ◽

Cited By ~ 44

Author(s):

Carsten Peters ◽

Katjuša Brejc ◽

Lisa Belmont ◽

Andrew J Bodey ◽

Yan Lee ◽

...

Keyword(s):

Molecular Mechanism ◽

Insight Into

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Biophysical Insight into Protein Folding, Aggregate Formation and its Inhibition Strategies

Protein and Peptide Letters ◽

10.2174/0929866528666211125114421 ◽

2021 ◽

Vol 28 ◽

Author(s):

Syed Mohammad Zakariya ◽

Aiman Zehr ◽

Rizwan Hasan Khan

Keyword(s):

Protein Folding ◽

Amyloid Fibrils ◽

Three Dimensional ◽

The Body ◽

Aggregate Formation ◽

Structural Characterisation ◽

Current Scenario ◽

Underlying Mechanisms ◽

Quality Control Mechanism ◽

Insight Into

: The failure of protein to correctly fold into its functional and unique three dimensional form leads to misfolded or partially folded protein. When these rogue proteins and polypeptides escape the quality control mechanism within the body, they result in aberrant aggregation of proteins into characteristic amyloid fibrils. This is the main cause for the number of neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s and Huntington’s diseases. This review aims to summarise the underlying mechanisms of protein folding, misfolding and aggregation. It also highlights the recent technologies for the structural characterisation and detection of amyloid fibrils in addition to the various factors responsible for the aggregate formation and the strategies to combat the aggregation process. Besides, the journey from origin to the current scenario of protein aggregation is also concisely discussed.

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New insight into lignin aggregation guiding efficient synthesis and functionalization of a lignin nanosphere with excellent performance

Green Chemistry ◽

10.1039/d1gc03651c ◽

2021 ◽

Author(s):

Liheng Chen ◽

Si-Man Luo ◽

Cong-Min Huo ◽

Yun-Feng Shi ◽

Jun Feng ◽

...

Keyword(s):

Molecular Mechanism ◽

Efficient Synthesis ◽

Excellent Performance ◽

Biomass Valorization ◽

Insight Into

Understanding the molecular mechanism of lignin nanoparticle (LNP) formation will precisely instruct its functionalization, which is of importance for biomass valorization.

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