Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity

Riopedre-Fernandez, Miguel; Biriukov, Denys; Dračínský, Martin; Martinez-Seara, Hector

doi:10.1016/j.carbpol.2023.121568

Cited by 5 publications

(1 citation statement)

References 66 publications

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“…Attention should also be paid to various biological subtopics. For instance, while proteins and lipids have received significant focus, carbohydrate research is gaining momentum only now − (including the development of designated databases), partly due to the important role of glycans in the conformational dynamics and shielding of COVID-19 . The adequately distributed efforts across various fields can foster interdisciplinary communication and facilitate unraveling fundamental scientific questions from multiple perspectives.…”

Section: Pathways To 2050mentioning

confidence: 99%

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

Biriukov,

Vácha

2024

ACS Phys. Chem Au

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In the last quarter-century, the field of molecular dynamics (MD) has undergone a remarkable transformation, propelled by substantial enhancements in software, hardware, and underlying methodologies. In this Perspective, we contemplate the future trajectory of MD simulations and their possible look at the year 2050. We spotlight the pivotal role of artificial intelligence (AI) in shaping the future of MD and the broader field of computational physical chemistry. We outline critical strategies and initiatives that are essential for the seamless integration of such technologies. Our discussion delves into topics like multiscale modeling, adept management of ever-increasing data deluge, the establishment of centralized simulation databases, and the autonomous refinement, cross-validation, and self-expansion of these repositories. The successful implementation of these advancements requires scientific transparency, a cautiously optimistic approach to interpreting AI-driven simulations and their analysis, and a mindset that prioritizes knowledge-motivated research alongside AI-enhanced big data exploration. While history reminds us that the trajectory of technological progress can be unpredictable, this Perspective offers guidance on preparedness and proactive measures, aiming to steer future advancements in the most beneficial and successful direction.

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Section: Pathways To 2050mentioning

confidence: 99%

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

Biriukov,

Vácha

2024

ACS Phys. Chem Au

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The spatial separation of basic amino acids is similar in RHAMM and hyaluronan binding peptide P15‐1 despite different sequences and conformations

Erkanli,

Kang,

Kirsch

et al. 2024

Proteoglycan Research

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Peptides that increase pro‐reparative responses to injury and disease by modulating the functional organization of hyaluronan (HA) with its cell surface binding proteins (e.g., soluble receptor for hyaluronan‐mediated motility [RHAMM] and integral membrane CD44) have potential therapeutic value. The binding of RHAMM to HA is an attractive target, since RHAMM is normally absent or expressed at low levels in homeostatic conditions, but its expression is significantly elevated in the extracellular matrix during tissue stress, response‐to‐injury, and in cancers and inflammation‐based diseases. The HA‐binding site in RHAMM contains two closely spaced sequences of clustered basic amino acids, in an alpha‐helical conformation. In the present communication, we test whether an alpha‐helical conformation is required for effective peptide binding to HA, and competitive disruption of HA–RHAMM interaction. The HA‐binding RHAMM‐competitive peptide P15‐1, identified using the unbiased approach of phage display, was examined using circular dichroism spectroscopy and the conformation‐predictive AI‐based AlphaFold2 algorithm. Unlike the HA‐binding site in RHAMM, peptide P15‐1 was found to adopt irregular conformations in solution rather than alpha helices. Instead, our structural analysis suggests that the primary determinant of peptide‐HA binding is associated with a specific clustering and spacing pattern of basic amino acids, allowing favorable electrostatic interaction with carboxylate groups on HA.

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Enzymatically stable unsaturated hyaluronan-derived oligosaccharides with selective cytostatic properties

Klejch,

Buffa,

Šimek

et al. 2024

Carbohydrate Polymers

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Hyaluronan-arginine enhanced and dynamic interaction emerges from distinctive molecular signature due to electrostatics and side-chain specificity

Cited by 5 publications

References 66 publications

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

Pathways to a Shiny Future: Building the Foundation for Computational Physical Chemistry and Biophysics in 2050

The spatial separation of basic amino acids is similar in RHAMM and hyaluronan binding peptide P15‐1 despite different sequences and conformations

Enzymatically stable unsaturated hyaluronan-derived oligosaccharides with selective cytostatic properties

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