# Towards exome analyses: Surprising outcomes from mutating nonconserved positions

> **NIH NIH R01** · UNIVERSITY OF KANSAS MEDICAL CENTER · 2020 · $307,489

## Abstract

When genomes are sequenced for personalized medicine, each patient can have up to 10,000 varia-
tions in their protein sequences. To identify which amino acid changes are medically relevant, many computer
algorithms have been developed. In thinking about how to improve these algorithms, we considered that,
among their input, many include evolutionary information about the affected proteins. Algorithms also include
“rules” devised from decades of mutation experiments: Similar amino acids allow function (toggle on); other
amino acids abolish function or structure (toggle off); each mutation will have the same outcome in any
homolog. However, experiments have been very heavily biased to conserved positions. In contrast, >50% of
amino acid positions are not conserved during the evolution of most proteins. If nonconserved positions follow
different rules, this may be one source for false positive and negative predictions in genome analyses.
 We are bridging this gap between experimental protein chemistry and computer predictions. In our first
study, we used 10 homologs to assess the outcomes for >1000 mutations at nonconserved positions.
Strikingly, these positions did not follow any of the substitution rules listed above. First, when multiple amino
acids were substituted into one position, they caused a wide range of functional outcomes (“rheostat position”).
Second, chemically similar amino acids did not always have similar outcomes. Third, when a given position
was substituted in multiple homologs, the same amino acid had different outcomes. Thus, rheostatic
nonconserved positions are likely to give false results in current predictions. Preliminary results show that
other proteins have rheostat positions. The central hypothesis of this proposal is that rheostat positions have
general properties that distinguish them from other nonconserved positions. In Aim 1, we will test the hypothe-
sis that rheostat positions can be detected by a particular pattern of evolutionary change, using pyruvate
kinase, aldolase, and an organic anion transmembrane transporter as model systems. If prediction is possible,
amino acid variants at rheostat positions should be – for now – classified as having “unknown significance” to
reduce false predictions. Further, all experimental results can be used by the CAGI community to assess the
development of new algorithms. In Aim 2, we will use molecular dynamics simulations and hydrogen ex-
change experiments to determine how rheostat mutations affect protein motions. In Aim 3, we will use X-ray
crystallography and structural predictions to determine how rheostat mutations affect side-chain packing. The
results from Aims 2-3 (i) can be used to identify regions in other proteins that contain rheostat positions, and (ii)
will provide the groundwork for formulating new rules for predicting the outcomes of rheostat mutations. The
new rules are needed to reach our long-term goals of improving computer predictions and reducing the n...

## Key facts

- **NIH application ID:** 9842546
- **Project number:** 5R01GM118589-04
- **Recipient organization:** UNIVERSITY OF KANSAS MEDICAL CENTER
- **Principal Investigator:** ARON W FENTON
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $307,489
- **Award type:** 5
- **Project period:** 2017-01-01 → 2021-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9842546

## Citation

> US National Institutes of Health, RePORTER application 9842546, Towards exome analyses: Surprising outcomes from mutating nonconserved positions (5R01GM118589-04). Retrieved via AI Analytics 2026-05-22 from https://api.ai-analytics.org/grant/nih/9842546. Licensed CC0.

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