Conformational Analysis of Charged Homo-Polypeptides

Article Biochemistry & Molecular Biology

Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins

Xi Wang et al.

Summary: This study investigates the mechanism by which D/E repeats in DNA/RNA-binding proteins accelerate the target search process, using experimental and simulation approaches.

NUCLEIC ACIDS RESEARCH (2023)

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Article Biochemistry & Molecular Biology

Negatively Charged Disordered Regions are Prevalent and Functionally Important Across Proteomes

Lavi S. Bigman et al.

Summary: Intrinsically disordered regions (IDRs) of proteins have a high fraction of charged residues, but their overall net charge and organization differ. This study analyzed the charge properties of IDRs in human, mouse, and yeast proteomes to explore the sequence-function relationship. Negatively charged IDRs were found to be longer and have a higher net charge per residue compared to positively charged IDRs. D/E repeats were longer and more prevalent than K/R repeats, especially in nucleic acid-related proteins.

JOURNAL OF MOLECULAR BIOLOGY (2022)

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Article Multidisciplinary Sciences

Affinity of disordered protein complexes is modulated by entropy-energy reinforcement

Milan Kumar Hazra et al.

Summary: This study investigates the formation mechanism of fuzzy complexes between two intrinsically disordered proteins (IDPs) using coarse-grained simulations. The results show that the formation of the high-affinity complex is sensitive to electrostatic interactions and the distribution of charges. Both enthalpy and entropy significantly affect the binding affinity of the fuzzy complexes. Proteins with greater absolute net charges form more stable complexes, indicating a mutually reinforcing effect of enthalpy and entropy.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Biochemistry & Molecular Biology

Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force

Sarah E. Leininger et al.

Summary: The presence of charged residues affects protein synthesis speed by influencing the distance between amino acids at different sites on the ribosome. Positively charged residues move amino acids further apart, while negatively charged residues bring them closer together. These mechanochemical changes impact the transition state barrier height for peptide bond formation.

BIOCHEMISTRY (2021)

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Article Chemistry, Physical

Biophysics of Phase Separation of Disordered Proteins Is Governed by Balance between Short- And Long-Range Interactions

Milan Kumar Hazra et al.

Summary: In this study, the effects of short-range interactions and long-range electrostatic interactions on the stability, structure, and dynamics of liquid-liquid phase separation in protein condensates were investigated using coarse-grained molecular dynamics simulations. It was found that an increase in short-range interactions at the expense of long-range electrostatic interactions led to a decrease in critical temperature of phase separation. Additionally, sequences with a high fraction of short-range interactions exhibited some stabilization, compensating for the loss of long-range interactions. Furthermore, the exchange of long-range electrostatic interactions for short-range interactions impacted the kinetics of breaking intermolecular contacts and intramolecular fluctuations, ultimately affecting the liquid-like behavior of protein condensates.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Chemistry, Physical

Uncovering Differences in Hydration Free Energies and Structures for Model Compound Mimics of Charged Side Chains of Amino Acids

Martin J. Fossat et al.

Summary: This study investigates the hydration free energies and structures of model compounds mimicking ionizable side chains, revealing clear trends in the free energies of hydration for different residues. The analysis shows differences in hydration free energies and heat capacity for ionizable residues, providing a structural explanation for these observations. The results obtained from the AMOEBA model at 298 K are consistent with values obtained from the TCPD approach, indicating the reliability of the estimated hydration free energies.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Chemistry, Physical

What Are the Molecular Requirements for Protein Sliding along DNA?

Lavi S. Bigman et al.

Summary: This study investigates the minimal requirements for protein sliding along DNA, finding that coupling is not universal and some proteins transition from sliding to hopping at higher salt concentrations. Moreover, the sliding mechanism is found to be less dominant for certain DNA-binding proteins, even at low salt concentrations, with the toroidal PCNA protein displaying hopping rather than sliding.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Article Biochemistry & Molecular Biology

Dynamic Autoinhibition of the HMGB1 Protein via Electrostatic Fuzzy Interactions of Intrinsically Disordered Regions

Xi Wang et al.

Summary: This study investigates how D/E repeats cause autoinhibition of HMGB1 and its specific binding to cisplatin-modified DNA. By varying ionic strength, the conformational equilibrium between autoinhibited and uninhibited states can be shifted, revealing fuzzy interactions of D/E repeats with other intrinsically disordered regions. Mutations mimicking post-translational modifications relevant to nuclear export of HMGB1 can moderately modulate DNA-binding affinity, possibly by impacting the autoinhibition.

JOURNAL OF MOLECULAR BIOLOGY (2021)

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Article Chemistry, Physical

Three Reasons Why Aspartic Acid and Glutamic Acid Sequences Have a Surprisingly Different Influence on Mineralization

Tobias Lemke et al.

Summary: Understanding the unique interactions of Asp and Glu peptides with calcium and chloride ions in solution can provide insights into the mineralization processes. The simulations revealed that Asp peptides attract more ions, forming clusters on their surface, while Glu peptides have comparatively fewer ions bound to multiple carboxylate groups. This new understanding of additive-ion interactions sheds light on the precise control over mineralization processes.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

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Review Biochemistry & Molecular Biology