Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Atomic Orbitals

Atomic Orbitals

An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.

Atomic Structure

Atomic Structure

What is a Mode?

What is a Mode?

The mode is one of the commonly used measures of a central tendency. It is defined as the most frequent value in a data set.
There can be more than one mode in a data set if multiple values have the same highest frequency. For instance, suppose that the Statistics exam scores of 20 students are: 50; 53; 59; 59; 63; 63; 72; 72; 72; 72; 72; 76; 78; 81; 83; 84; 84; 84; 90; 93. Here, the mode is 72, as it occurs most frequently, five times.
A data set with two modes is called bimodal. For example,...

Hybridization of Atomic Orbitals I

Hybridization of Atomic Orbitals I

The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...

Atomic Mass

Atomic Mass

Atoms — and the protons, neutrons, and electrons that compose them — are extremely small. For example, a carbon atom weighs less than 2 × 10−23 g. When describing the properties of tiny objects such as atoms, we use appropriately small units of measure, such as the atomic mass unit (amu). The amu was originally defined based on hydrogen, the lightest element, then later in terms of oxygen. Since 1961, it has been defined with regard to the most abundant isotope of carbon, atoms of which...

The Energies of Atomic Orbitals

The Energies of Atomic Orbitals

In an atom, the negatively charged electrons are attracted to the positively charged nucleus. In a multielectron atom, electron-electron repulsions are also observed. The attractive and repulsive forces are dependent on the distance between the particles, as well as the sign and magnitude of the charges on the individual particles. When the charges on the particles are opposite, they attract each other. If both particles have the same charge, they repel each other.

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Coarse-Graining Waters: Unveiling The Effective Hydrophilicity/Hydrophobicity of Individual Protein Atoms and The Roles of Waters' Hydrogens.

Journal of chemical theory and computation·2023

Same author

Towards a free energy-based elastic network model and its application to the SARS-COV2 binding to ACE2.

Physical biology·2023

Same author

An efficient algorithm calculating common solvent accessible volume.

PloS one·2022

Same author

The amounts of thermal vibrations and static disorder in protein X-ray crystallographic B-factors.

Proteins·2021

Same author

Bridging between material properties of proteins and the underlying molecular interactions.

PloS one·2021

Same author

Uncovering the release mechanism of nucleotide import by HIV-1 capsid.

Physical biology·2020

Search research articles

Related Experiment Video

Updated: Feb 5, 2026

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Published on: August 9, 2011

All-atom normal mode dynamics of HIV-1 capsid.

Hyuntae Na¹, Guang Song^2,3

¹Department of Computer Science, Penn State Harrisburg, Middletown, Pennsylvania, United States of America.

Plos Computational Biology

|September 19, 2018

Summary

We developed a new model to analyze the dynamics of the HIV-1 capsid. This method reveals how pentamers stabilize the capsid and suggests nucleotide transport occurs near pentamers.

More Related Videos

In vitro Uncoating of HIV-1 Cores

In vitro Uncoating of HIV-1 Cores

Published on: November 8, 2011

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Published on: February 22, 2017

Related Experiment Videos

Last Updated: Feb 5, 2026

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Structure of HIV-1 Capsid Assemblies by Cryo-electron Microscopy and Iterative Helical Real-space Reconstruction

Published on: August 9, 2011

In vitro Uncoating of HIV-1 Cores

In vitro Uncoating of HIV-1 Cores

Published on: November 8, 2011

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Measurement of In Vitro Integration Activity of HIV-1 Preintegration Complexes

Published on: February 22, 2017

Area of Science:

Biophysics
Structural Biology
Computational Biology

Background:

Understanding biomolecular assembly dynamics is crucial for function.
Analyzing large systems like the HIV-1 capsid (5 million atoms) is computationally demanding.

Purpose of the Study:

To perform a full all-atom normal mode analysis of the entire HIV-1 capsid.
To investigate the dynamic role of capsid components in stability and function.

Main Methods:

Developed the BOSE (Block of Selected Elasticity) model based on resonance principles.
Efficiently computed capsid vibrations by projecting capsomere motions into a subspace.
Validated BOSE modes against benchmark calculations using the Hessian matrix.

Main Results:

Revealed the stabilizing role of pentamers in the HIV-1 capsid structure.
Demonstrated agreement with experimental data on pentamer destabilization preceding capsid disassembly.
Identified specific hexamer pores near pentamers as preferential sites for nucleotide transport.

Conclusions:

The BOSE model enables efficient all-atom normal mode analysis of large biomolecular assemblies.
Pentamer dynamics are critical for HIV-1 capsid stability and disassembly.
Nucleotide transport likely occurs at hexamers adjacent to pentamers, particularly at the larger capsid end.