Effect of single-site mutations on hydrophobic-polar lattice proteins.

Phys Rev E Stat Nonlin Soft Matter Phys

Center for Simulational Physics, The University of Georgia, Athens, Georgia 30602, USA.

Published: September 2014

We developed a heuristic method for determining the ground-state degeneracy of hydrophobic-polar (HP) lattice proteins, based on Wang-Landau and multicanonical sampling. It is applied during comprehensive studies of single-site mutations in specific HP proteins with different sequences. The effects in which we are interested include structural changes in ground states, changes of ground-state energy, degeneracy, and thermodynamic properties of the system. With respect to mutations, both extremely sensitive and insensitive positions in the HP sequence have been found. That is, ground-state energies and degeneracies, as well as other thermodynamic and structural quantities, may be either largely unaffected or may change significantly due to mutation.

Download full-text PDF

Source
http://dx.doi.org/10.1103/PhysRevE.90.033307DOI Listing

Publication Analysis

Top Keywords

single-site mutations
8
hydrophobic-polar lattice
8
lattice proteins
8
mutations hydrophobic-polar
4
proteins developed
4
developed heuristic
4
heuristic method
4
method determining
4
determining ground-state
4
ground-state degeneracy
4

Similar Publications

Clinical and genetic drivers of oligo-metastatic disease in colon cancer.

Neoplasia

December 2024

AMES, Centro Polidiagnostico Strumentale srl, Via Padre Carmine Fico 24, Casalnuovo Di Napoli 80013, Italy.

Background: Oligo-metastatic disease (OMD) in colon cancer patients exhibits distinct clinical behavior compared to poly-metastatic disease (PMD), with a more responsive and indolent course. This study aims to identify clinical and biological factors uniquely associated with oligo-metastatic behavior.

Methods: Metastatic colon cancer patients from an academic center underwent genetic characterization.

View Article and Find Full Text PDF

Introduction: Large B-cell lymphoma (LBCL) exhibits striking clinical and molecular heterogeneity. New approaches have emerged to explore tumor heterogeneity and classify LBCL into biological categories. Consequently, the informational requirements from diagnostic samples to provide the necessary information have increased, but the adequacy of single-site biopsies to provide such information is largely unknown.

View Article and Find Full Text PDF

A general temperature-guided language model to design proteins of enhanced stability and activity.

Sci Adv

November 2024

School of Physics and Astronomy, & Shanghai National Center for Applied Mathematics (SJTU Center), & Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.

Designing protein mutants with both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants with improved stability and activity without any prior experimental mutagenesis data for the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive ability compared to current state-of-the-art models on the public mutagenesis dataset across 283 protein assays.

View Article and Find Full Text PDF

Evaluation of genotype characteristics and drug resistance mutations in patients with chronic hepatitis B.

Sci Rep

November 2024

Department of Clinical Laboratory, Chongqing Qianjiang Central Hospital, Qianjiang Key Laboratory of Chongqing Qianjiang Central Hospital Laboratory Medicine, Chongqing University Qianjiang Hospital, No. 360 South Section, Zhengzhou Road, Qianjiang District, Chongqing, 409000, China.

Hepatitis B is one of the public health priorities worldwide, especially in the Southwest China. Our study aimed to investigate the relationship between genotypes and drug resistance mutations among HBV patients in Southwest China, with the objective of providing guidance for clinical antiviral treatment. A total of 4266 chronic hepatitis B (CHB) patients treated in the Qianjiang Hospital of Chongqing University were included in our study from 2014 to 2020.

View Article and Find Full Text PDF

Blocking GP130 binding in interleukin-11 through site-specific PEGylation attenuates bleomycin-induced pulmonary fibrosis in mice.

Int J Pharm

December 2024

Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Biopharmaceutics, West China School of Pharmacy, Sichuan University, Chengdu 610041, China. Electronic address:

Recent insights have identified interleukin-11 (IL-11) as a pivotal profibrotic cytokine, with its signaling through IL-11Rα and GP130 receptors emerging as a promising therapeutic target for fibrotic diseases. Herein, we developed receptor-biased IL-11 via site-specific PEGylation at the GP130 binding interface, aiming to explore its therapeutic potential for bleomycin-induced pulmonary fibrosis in mice. By conducting single site-directed cysteine mutagenesis at site II or site III of IL-11, we refined the conjugation site, demonstrating that mutation at site III exhibits heightened sensitivity to GP130 binding and signaling.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!